Table 3. Differential expression ratios of all known flagellar genes in the HP0906 mutant relative to the wild-type.
Fold-changes and P values were calculated based upon three independent biological replicates, as described in Methods. ORFs and gene annotations are based on the TIGR database (Tomb et al., 1997). The genes were assigned to previously proposed flagellar classes (Niehus et al., 2004). Genes with fold-changes in expression with P ≤0.05 are shown in bold type. Dashes indicate values excluded during array data analysis due to variation or technical problems with array features.
| Proposed class | TIGR ORF no. | Putative gene product (gene) | Δ hp0906 | P value |
|---|---|---|---|---|
| Class I | HP0019 | Chemotaxis protein (cheV) | 1.175 | 0.16 |
| HP0082 | Methyl-accepting chemotaxis transducer (tlpC) | 0.952 | 0.50 | |
| HP0099 | Methyl-accepting chemotaxis protein (tlpA) | 1.051 | 0.77 | |
| HP0103 | Methyl-accepting chemotaxis protein (tlpB) | 1.592 | 0.01 | |
| HP0173 | Flagellar biosynthetic protein (fliR) | 0.978 | 0.79 | |
| HP0244 | Signal-transducing protein, histidine kinase (atoS) | 0.756 | 0.12 | |
| HP0246 | Flagellar basal-body P-ring protein (flgI) | – | – | |
| HP0325 | Flagellar basal-body L-ring protein (flgH) | 1.340 | 0.01 | |
| HP0326 | CMP-N-acetylneuraminic acid synthetase (neuA) | 0.889 | 0.20 | |
| HP0327 | Flagellar protein G (flaG) | 0.684 | 0.16 | |
| HP0351 | Basal-body M-ring protein (fliF) | 1.266 | 0.05 | |
| HP0352 | Flagellar motor switch protein (fliG) | 1.293 | 0.02 | |
| HP0391 | Purine-binding chemotaxis protein (cheW) | 1.780 | 0.02 | |
| HP0392 | Histidine kinase (cheA) | 1.513 | 0.02 | |
| HP0393 | Chemotaxis protein (cheV) | 1.249 | 0.20 | |
| HP0584 | Flagellar motor switch protein (fliN) | 1.451 | 0.05 | |
| HP0599 | Haemolysin secretion protein precursor (hylB) | 1.025 | 0.84 | |
| HP0616 | Chemotaxis protein (cheV) | 1.147 | 0.44 | |
| HP0684 | Flagellar biosynthesis protein (fliP) | 0.432 | 0.00 | |
| HP0685 | Flagellar biosynthesis protein (fliP) | 1.176† | 0.44 | |
| HP0703 | Response regulator | 0.855 | 0.46 | |
| HP0714 | RNA polymerase sigma 54 factor (rpoN) | 0.706* | 0.12 | |
| HP0770 | Flagellar biosynthesis protein (flhB) | 0.649 | 0.19 | |
| HP0815 | Flagellar motor rotation protein (motA) | 1.405 | 0.06 | |
| HP0816 | Flagellar motor rotation protein (motB) | 1.009† | 0.48 | |
| HP0840 | flaA1 protein | 1.211 | 0.26 | |
| HP1041 | Flagellar biosynthesis protein (flhA) | 0.983 | 0.79 | |
| HP1067 | Chemotaxis protein (cheY) | 1.347 | 0.31 | |
| HP1092 | Flagellar basal-body rod protein (flgG) | 1.593 | 0.03 | |
| HP1286 | Conserved hypothetical secreted protein (fliZ) | 1.309 | 0.66 | |
| HP1419 | Flagellar biosynthesis protein (fliQ) | 0.791 | 0.15 | |
| HP1420 | Flagellar export protein ATP synthase (fliI) | 0.774 | 0.12 | |
| HP1462 | Secreted protein involved in flagellar motility | 1.324 | 0.00 | |
| HP1575 | Homologue of FlhB protein (flhB2) | 1.122 | 0.15 | |
| HP1585 | Flagellar basal-body rod protein (flgG) | 0.748 | 0.09 | |
| Class II | HP0114 | Hypothetical protein | 1.199 | 0.43 |
| HP0115 | Flagellin B (flaB) | 2.432* | 0.01 | |
| HP0295 | Flagellin B homologue (fla) | 1.459 | 0.02 | |
| HP0869 | Hydrogenase expression/formation protein (hypA) | 1.808 | 0.00 | |
| HP0870 | Flagellar hook (flgE) | 2.407* | 0.01 | |
| HP0906 | Hook-length-control regulator (fliK) | Not valid | Not valid | |
| HP1076 | Hypothetical protein | 3.374 | 0.01 | |
| HP1119 | Flagellar hook-associated protein 1 (HAP1) (flgK) | 1.442 | 0.04 | |
| HP1120 | Hypothetical protein | 1.772 | 0.03 | |
| HP1154 | Hypothetical protein (operon with murG) | 1.614 | 0.09 | |
| HP1155 | Transferase, peptidoglycan synthesis (murG) | 1.668 | 0.06 | |
| HP1233 | Putative flagellar muraminidase (flgJ) | 1.396 | 0.00 | |
| Class III | HP0472 | Outer-membrane protein (omp11) | 1.142 | 0.47 |
| HP0601 | Flagellin A (flaA) | 1.204 | 0.47 | |
| HP1051 | Hypothetical protein | 1.083 | 0.59 | |
| HP1052 | UDP-3-O-acyl N-acetylglucosamine deacetylase (envA) | 1.013 | 0.94 | |
| Intermediate | HP0165 | Hypothetical protein | 1.422 | 0.44 |
| HP0166 | Response regulator (ompR) | 1.923* | 0.06 | |
| HP0366 | Spore coat polysaccharide biosynthesis protein C | 0.941 | 0.77 | |
| HP0367 | Hypothetical protein | 1.790 | 0.02 | |
| HP0488 | Hypothetical protein | 0.789 | 0.06 | |
| HP0907 | Hook-assembly protein, flagella (flgD) | 0.909 | 0.40 | |
| HP0908 | Flagellar hook (flgE) | 0.802 | 0.06 | |
| HP1028 | Hypothetical protein | 1.271 | 0.17 | |
| HP1029 | Hypothetical protein | 1.035 | 0.57 | |
| HP1030 | FliY protein (fliY) | 1.094 | 0.54 | |
| HP1031 | Flagellar motor switch protein (fliM) | 1.018 | 0.82 | |
| HP1032 | Alternative transcription initiation factor, sigma 28 (fliA) | 1.120 | 0.18 | |
| HP1033 | Hypothetical protein | 0.921 | 0.44 | |
| HP1034 | ATP-binding protein (ylxH) | 0.921 | 0.55 | |
| HP1035 | Flagellar biosynthesis protein (flhF) | 0.999 | 0.96 | |
| HP1122 | Anti-sigma 28 factor (flgM) | 1.392 | 0.03 | |
| HP1440 | Hypothetical protein | 0.323 | 0.00 | |
| HP1557 | Flagellar basal-body protein (fliE) | 1.254 | 0.08 | |
| HP1558 | Flagellar basal-body rod protein (flgC) (proximal rod protein) | 1.055 | 0.71 | |
| HP1559 | Flagellar basal-body rod protein (flgB) (proximal rod protein) | 1.716 | 0.01 | |
| HP0751 | Polar flagellin (flaG2) | 1.130 | 0.27 | |
| HP0752 | Flagellar cap protein (fliD) | 0.831 | 0.19 | |
| HP0753 | Flagellar chaperone (fliS) | 1.118 | 0.39 | |
| HP0754 | Flagellar chaperone (fliT) | – | – | |
| Not assigned | HP0410 | Flagellar sheath-associated protein (hpaA2) | 0.944 | 0.52 |
| HP0492 | Flagellar sheath-associated protein (hpaA3) | 1.161 | 0.18 | |
| HP0797 | Flagellar sheath-associated protein (hpaA) | 1.420 | 0.11 |
*
Confirmatory analysis by qRT-PCR was performed for these genes.
†
The values for these genes were missing in the microarray analysis and were then investigated by qRT-PCR.