Table 2.
Genes with increased expression in either the bprR and/or bprS single mutants
| Locus tag | Gene name | Description | bprS mutant Expression (log2) | bprS mutant FDR | bprR mutant Expression (log2) | bprR mutant FDR |
|---|---|---|---|---|---|---|
| BPSL0026 | fliL | flagellar basal body-associated protein FliL | 2.09 | 8.28E-03 | 1.82# | 1.52E-02 |
| BPSL0028 | fliN | flagellar motor switch protein | 2.25 | 5.34E-03 | 1.94 | 9.47E-03 |
| BPSL0031 | fliQ | flagellar biosynthesis protein | 2.15 | 5.34E-03 | 1.93# | 1.08E-02 |
| BPSL0067 | protein of unknown function | 2.54 | 2.16E-05 | 2.30 | 2.20E-05 | |
| BPSL0068 | putative lipoprotein | 2.46 | 2.16E-05 | 2.30 | 2.11E-05 | |
| BPSL0069 | putative anti-sigma factor | 1.02 | 4.78E-03 | 0.89 | 1.09E-02 | |
| BPSL0071 | putative catalase | 1.31 | 4.26E-03 | 1.47 | 2.44E-03 | |
| BPSL0225 | putative flagellar hook-length control protein | 1.76 | 1.24E-03 | 1.24 | 6.62E-03 | |
| BPSL0226 | fliJ | flagellar fliJ protein | 1.87 | 1.75E-03 | 1.34# | 1.09E-02 |
| BPSL0227 | fliI | flagellum-specific ATP synthase | 1.94 | 5.34E-03 | 1.54# | 1.32E-02 |
| BPSL0228 | fliH | flagellar assembly protein H | 2.04 | 8.43E-03 | 1.69# | 1.69E-02 |
| BPSL0230 | fliF | flagellar MS-ring protein | 2.14 | 8.20E-03 | 1.75# | 1.64E-02 |
| BPSL0231 | fliE | flagellar hook-basal body complex protein | 1.81 | 8.84E-03 | 1.39# | 2.52E-02 |
| BPSL0269 | flgA | flagellar basal body P-ring biosynthesis protein FlgA | 2.09 | 2.38E-03 | 1.58# | 1.08E-02 |
| BPSL0271 | flgC | flagellar basal body rod protein FlgC | 2.20 | 6.66E-03 | 1.75# | 1.52E-02 |
| BPSL0272 | flgD | flagellar basal body rod modification protein | 2.12 | 7.33E-03 | 1.76# | 1.43E-02 |
| BPSL0273 | flgE | flagellar hook protein FlgE | 1.88 | 3.02E-03 | 1.39# | 1.22E-02 |
| BPSL0274 | flgF | flagellar basal body rod protein FlgF | 1.79 | 4.69E-03 | 1.29# | 1.66E-02 |
| BPSL0275 | flgG | flagellar basal body rod protein FlgG | 1.92 | 5.66E-03 | 1.43# | 1.64E-02 |
| BPSL0276 | flgH | flagellar basal body L-ring protein | 1.88 | 2.96E-03 | 1.44# | 1.03E-02 |
| BPSL0278 | flgJ | flagellar rod assembly protein/muramidase FlgJ | 1.83 | 4.51E-03 | 1.27# | 1.87E-02 |
| BPSL0403 | mce related protein | 1.19 | 1.26E-03 | 1.22 | 7.78E-04 | |
| BPSL0812 | bpeR | TetR family regulatory protein | 1.09 | 7.33E-03 | 1.08 | 8.20E-03 |
| BPSL0814 | bpeA | RND family acriflavine resistance protein A precursor | 1.65 | 2.23E-03 | 1.56 | 2.22E-03 |
| BPSL0815 | bpeB | RND family acriflavine resistance protein | 1.84 | 7.63E-03 | 1.79 | 7.22E-03 |
| BPSL1053 | putative lipoprotein | 0.48 | 3.05E-01 | 1.50 | 5.74E-03 | |
| BPSL1112 | putative lipoprotein | 1.54 | 1.55E-03 | 1.24 | 6.71E-03 | |
| BPSL1184 | putative sugar-related transport, membrane protein | 1.01 | 6.70E-03 | 0.88 | 1.37E-02 | |
| BPSL1185 | protein of unknown function | 3.95 | 3.83E-05 | 4.04 | 2.11E-05 | |
| BPSL1202 | putative transport-related membrane protein | 0.61 | 8.41E-02 | 1.93 | 2.32E-04 | |
| BPSL1203 | putative carbonic anhydrase | 0.63 | 6.17E-02 | 2.03 | 9.28E-05 | |
| BPSL1254 | protein of unknown function | 1.59 | 4.26E-03 | 1.75 | 2.10E-03 | |
| BPSL1289 | osmB | osmotically inducible lipoprotein B precursor | 0.72 | 3.89E-02 | 1.66 | 2.80E-04 |
| BPSL1387 | protein of unknown function | 1.09 | 1.34E-03 | 0.77 | 8.20E-03 | |
| BPSL1563 | putative membrane protein of unknown function | 1.22 | 5.17E-04 | 1.68 | 4.16E-05 | |
| BPSL1564 | putative transcriptional regulatory protein | 0.50 | 1.17E-01 | 1.37 | 9.39E-04 | |
| BPSL1598 | putative transport-related, membrane protein | 0.28 | 3.17E-01 | 1.59 | 1.66E-04 | |
| BPSL1829 | putative methyl-accepting chemotaxis protein | 1.98 | 4.26E-03 | 1.34# | 1.89E-02 | |
| BPSL1872 | putative N-acetylmuramoyl-L-alanine amidase | 1.07# | 3.99E-02 | 1.47 | 9.64E-03 | |
| BPSL1931 | protein of unknown function | 0.83 | 2.35E-02 | 1.01 | 9.10E-03 | |
| BPSL2011 | putative osmosis-related lipoprotein | −0.35 | 2.54E-01 | 1.08 | 2.78E-03 | |
| BPSL2016 | protein of unknown function | 0.78 | 5.21E-02 | 1.30 | 5.35E-03 | |
| BPSL2017 | di-haem cytochrome c peroxidase | 0.67 | 1.09E-01 | 1.38 | 5.35E-03 | |
| BPSL2193 | protein of unknown function | 0.90 | 7.52E-03 | 1.12 | 2.10E-03 | |
| BPSL2282 | protein of unknown function | 0.62 | 6.86E-02 | 1.97 | 1.20E-04 | |
| BPSL2396 | protein of unknown function | 1.27 | 7.30E-03 | 1.30 | 5.74E-03 | |
| BPSL2397 | protein of unknown function | 1.46 | 2.48E-03 | 1.25 | 5.30E-03 | |
| BPSL2398 | protein of unknown function | 1.12# | 1.09E-02 | 1.18 | 7.39E-03 | |
| BPSL2399 | putative glycosyltransferase | 1.36 | 1.55E-03 | 1.19 | 2.72E-03 | |
| BPSL2409 | ABC transporter ATP binding protein | 0.85 | 2.82E-02 | 1.09 | 8.00E-03 | |
| BPSL2466 | protein of unknown function | 0.76 | 1.43E-02 | 2.03 | 2.30E-05 | |
| BPSL2482 | peptidase | 1.25 | 2.38E-03 | 1.32 | 1.27E-03 | |
| BPSL2483 | ribosome-associated GTPase | 0.97 | 5.86E-03 | 1.01 | 4.35E-03 | |
| BPSL3254B | protein of unknown function | 1.63 | 1.22E-03 | 1.94 | 2.75E-04 | |
| BPSL3291 | fliA | flagellar biosynthesis sigma factor | 1.86 | 2.45E-03 | 1.50 | 6.41E-03 |
| BPSL3292 | flhG | flagellar biosynthesis protein FlhG | 2.21 | 3.79E-03 | 1.74# | 1.08E-02 |
| BPSL3293 | flhF | flagellar biosynthesis regulator FlhF | 2.23 | 1.83E-03 | 1.75 | 5.35E-03 |
| BPSL3294 | flhA | flagellar biosynthesis protein FlhA | 2.09 | 7.89E-03 | 1.67# | 1.66E-02 |
| BPSL3323 | putative transferase | 1.55 | 8.43E-03 | 1.13# | 2.51E-02 | |
| BPSL3324 | putative keto/oxo acyl-ACP synthase | 1.51 | 7.17E-03 | 0.98 | 3.22E-02 | |
| BPSL3326 | putative keto/oxo acyl-ACP synthase | 1.78 | 8.43E-03 | 1.39# | 1.99E-02 | |
| BPSL3327 | putative short chain dehydrogenase | 1.74 | 3.62E-03 | 1.26# | 1.52E-02 | |
| BPSL3329 | Rieske (2Fe-2S) domain-containing protein | 1.31 | 7.21E-03 | 0.95 | 2.29E-02 | |
| BPSS0215 | tar | methyl-accepting chemotaxis protein | 1.70 | 6.71E-03 | 1.35# | 1.58E-02 |
| BPSS0216 | putative membrane protein of unknown function | 1.12 | 4.45E-03 | 0.82 | 1.97E-02 | |
| BPSS0223 | protein of unknown function | 0.82 | 8.44E-03 | 1.44 | 2.34E-04 | |
| BPSS0236 | ltaE | L-allo-threonine aldolase | 0.96 | 2.09E-02 | 1.20 | 6.20E-03 |
| BPSS0264 | protein of unknown function | 1.02# | 2.56E-02 | 1.36 | 6.20E-03 | |
| BPSS0298 | transport related membrane protein | 1.60 | 1.36E-03 | 1.07# | 1.37E-02 | |
| BPSS0299 | malM | fatty-acid CoA ligase | 2.20 | 8.23E-03 | 1.63# | 2.27E-02 |
| BPSS0300 | malL | malonyl CoA-acyl carrier protein | 2.29 | 2.38E-03 | 1.60# | 1.17E-02 |
| BPSS0301 | malK | protein of unknown function | 2.24 | 1.91E-03 | 1.60 | 9.10E-03 |
| BPSS0302 | malJ | fatty acid biosynthesis-related CoA ligase | 2.30 | 2.96E-03 | 1.66# | 1.29E-02 |
| BPSS0303 | malI | diaminopimelate decarboxylase | 2.39 | 8.17E-04 | 1.81 | 2.78E-03 |
| BPSS0304 | malH | protein of unknown function | 2.60 | 3.60E-04 | 1.93 | 1.38E-03 |
| BPSS0305 | malG | ketol-acid reductoisomerase | 2.51 | 3.20E-04 | 1.95 | 9.39E-04 |
| BPSS0306 | malF | multifunctional polyketide-peptide syntase | 2.67 | 5.32E-04 | 2.14 | 1.38E-03 |
| BPSS0307 | malE | gamma-aminobutyraldehyde dehydrogenase | 2.81 | 1.53E-04 | 2.35 | 2.60E-04 |
| BPSS0308 | malD | protein of unknown function | 2.75 | 1.55E-04 | 2.23 | 3.46E-04 |
| BPSS0309 | malC | peptide synthase regulatory protein | 2.89 | 8.78E-05 | 2.33 | 2.10E-04 |
| BPSS0310 | malB | protein of unknown function | 2.98 | 1.53E-04 | 2.62 | 2.20E-04 |
| BPSS0311 | malA | multifunctional polyketide-peptide syntase | 3.10 | 5.17E-04 | 2.87 | 4.96E-04 |
| BPSS0312 | malR | LuxR family transcriptional regulator | 1.47 | 6.27E-04 | 1.12 | 2.72E-03 |
| BPSS0317 | monooxygenase | 1.54 | 1.55E-03 | 2.38 | 6.99E-05 | |
| BPSS0325 | putative membrane protein of unknown function | 0.32 | 2.91E-01 | 1.07 | 3.74E-03 | |
| BPSS0337 | protein of unknown function | 1.38 | 1.24E-03 | 1.91 | 1.20E-04 | |
| BPSS0623 | outer membrane efflux protein | 2.09 | 5.17E-04 | 2.27 | 2.10E-04 | |
| BPSS0624 | macB | macrolide-specific ABC-type efflux carrier | 1.95 | 1.61E-03 | 2.22 | 4.96E-04 |
| BPSS0625 | drug-efflux protein | 1.97 | 6.27E-04 | 2.15 | 2.33E-04 | |
| BPSS0685 | protein of unknown function | 1.21 | 6.63E-04 | 0.89 | 5.35E-03 | |
| BPSS0686a | Predicted 5,10-methylene tetrahydromethanopterin reductase | 3.39 | 1.14E-07 | 0.35 | 1.71E-01 | |
| BPSS0686aa | protein of unknown function | 5.16 | 8.78E-05 | −0.47 | 5.88E-01 | |
| BPSS0687 a | sensor kinase protein | 5.89 | 7.90E-09 | 1.46 | 2.89E-04 | |
| BPSS0688 a | response regulator protein | 4.56 | 9.34E-09 | 4.70 | 7.98E-09 | |
| BPSS0689 | protein of unknown function | 7.12 | 7.90E-09 | 7.78 | 5.57E-09 | |
| BPSS0690 | protein of unknown function | 6.45 | 1.06E-08 | 6.49 | 9.89E-09 | |
| BPSS0692 | fumarylacetoacetate (FAA) hydrolase family protein | 2.26 | 1.55E-04 | 2.16 | 2.10E-04 | |
| BPSS0693 | fumarylacetoacetate (FAA) hydrolase family protein | 2.07 | 1.53E-04 | 1.88 | 2.10E-04 | |
| BPSS0694 | hpcC | 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase | 2.14 | 2.48E-05 | 2.18 | 1.82E-05 |
| BPSS0695 | hpcB | 3,4-dihydroxyphenylacetate 2,3-dioxygenase | 1.81 | 8.07E-05 | 1.84 | 4.84E-05 |
| BPSS0696 | hpcD | 5-carboxymethyl-2-hydroxymuconate delta-isomerase | 2.19 | 1.53E-04 | 1.98 | 2.44E-04 |
| BPSS0697 | hpcG | 2-oxo-hepta-3-ene-1,7-dioic acid hydratase | 1.85 | 2.01E-04 | 1.89 | 1.69E-04 |
| BPSS0698 | hpcH | 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase | 2.01 | 1.55E-04 | 1.99 | 1.67E-04 |
| BPSS0724 | protein of unknown function | 0.83 | 7.33E-03 | 1.09 | 1.38E-03 | |
| BPSS0755 | LysR family regulatory protein | 0.57 | 3.11E-02 | 1.03 | 1.23E-03 | |
| BPSS0796A | H-NS-like protein | 1.71 | 2.38E-03 | 4.39 | 1.27E-06 | |
| BPSS0797 | IclR family regulatory protein | 1.03 | 6.40E-02 | 3.95 | 1.96E-05 | |
| BPSS0798 | protein of unknown function | 0.68 | 1.60E-01 | 3.35 | 2.11E-05 | |
| BPSS0799 | diguanylate phosphodiesterase | 1.04 | 9.65E-03 | 4.48 | 1.31E-07 | |
| BPSS0828 | protein of unknown function | 0.82 | 3.54E-02 | 1.21 | 5.35E-03 | |
| BPSS0852 | inosine-uridine preferring nucleoside hydrolase | 1.60 | 6.57E-03 | 1.74 | 3.49E-03 | |
| BPSS0941 | protein of unknown function | 1.07 | 8.73E-03 | 1.33 | 2.78E-03 | |
| BPSS0946 | penA | beta-lactamase precursor | 1.94 | 2.38E-03 | 2.65 | 2.44E-04 |
| BPSS1038 | protein of unknown function | 0.04 | 9.47E-01 | 1.66 | 5.01E-03 | |
| BPSS1239 | peptidase | 0.33 | 6.92E-01 | 2.76 | 2.53E-03 | |
| BPSS1250 | acetylpolyamine aminohydrolase | 0.95 | 2.14E-02 | 1.10 | 9.81E-03 | |
| BPSS1275 | RNA polymerase sigma factor | 1.25 | 7.92E-03 | 1.51 | 2.99E-03 | |
| BPSS1296 | O-methyltransferase-like protein | 0.88 | 1.11E-02 | 1.05 | 4.84E-03 | |
| BPSS1553 | bprP | Transcriptional regulator | 1.57 | 2.04E-03 | 1.19 | 8.84E-03 |
| BPSS1554 | bprQ | Protein associated with bprP | 1.43 | 1.28E-03 | 1.31 | 2.27E-03 |
| BPSS1862 | ABC transport system, ATP-binding protein | 1.70 | 8.43E-03 | 1.71 | 7.39E-03 | |
| BPSS1866 | lipoprotein | 0.21 | 5.80E-01 | 1.44 | 2.10E-03 | |
| BPSS1867 | protein of unknown function | 1.42# | 1.21E-02 | 2.20 | 9.10E-04 | |
| BPSS1980 | protein of unknown function | 0.66 | 1.61E-02 | 1.31 | 2.44E-04 | |
| BPSS1996 | protein of unknown function | 1.13 | 8.44E-02 | 2.84 | 8.95E-04 | |
| BPSS2162 | protein of unknown function | 0.42 | 5.50E-01 | 2.13 | 6.14E-03 | |
| BPSS2307 | amidase | 0.61 | 1.05E-01 | 1.47 | 1.92E-03 | |
| BPSS2308 | protein of unknown function | 1.01 | 1.26E-03 | 1.97 | 1.14E-05 |
Genes were identified as differentially expressed if they showed >2-fold expression change (log2 > 1.0) compared to the wild-type strain with a False Discovery Rate (FDR) of <0.01. All significant gene expression changes are shown in bold and the locus tag, gene name and description are shown in bold when significant expression changes were observed for both mutants
aIncreased RNA expression also observed in the bprRS double mutant (Table 1)
#Genes showing increased expression of >2-fold with a FDR of >0.01 and <0.05