Table 2. The components of Spo0A phosphorelay differently expressed in B. subtilis WT and RM cells.
| Gene | Sigma factor/ regulon |
mRNA ratioa RM/WT |
Qvalue | Transcription profile modificationb | PAIc | PAI ratio RM/WT |
Function | |
|---|---|---|---|---|---|---|---|---|
| WT | RM | |||||||
| Kinases | ||||||||
| kinA | SigH/Spo0A | 1.22 | 1.00E-03 | nm | nd | 0.05 | - | sensor kinase |
| kinB | SigA/CodY | 4.06 | 3.55E-07 | no termination | nd | 0.21 | - | sensor kinase |
| kinC | SigA | 0.80 | 2.00E-03 | nm | 0.43 | 0.26 | 0.61 | sensor kinase |
| kinD | SigA | 0.92 | 6.30E-02 | nm | 0.19 | 0.13 | 0.68 | sensor kinase |
| kinE | SigH | 1.38 | 1.37E-04 | nm | nd | 0.15 | - | sensor kinase |
| Proteins controlling kinase activity | ||||||||
| sivB | SigA/AbrB; LutR ; DegU | 0.51 | 5.39E-07 | low activation | nd | nd | - | Inhibitor of KinA |
| sivA | SigA/AbrB | 0.43 | 1.17E-06 | low activation | nd | nd | - | Inhibitor of KinA |
| kbaA | SigA/AbrB | 4.10 | 4.47E-07 | 3’-extention of upstream RNA | nd | nd | - | positive KinB effector |
| Phosphotransferases | ||||||||
| spo0B | SigA | 2.27 | 1.89E-06 | 3’-extention of upstream RNA | 0.17 | 0.50 | 2.94 | phospho- transferase |
| spo0F | SigH/Spo0A | 1.86 | 4.24E-06 | nm | 0.22 | 0.33 | 1.50 | phospho-transferase |
| Ultimate target | ||||||||
| spo0A | SigA;SigH/Spo0A | 0.71 | 2.00E-03 | nm | 0.62 | 0.89 | 1.44 | response regulator |
| Phosphatases and their modulators | ||||||||
| yisI | SigA | 5.46 | 2.43E-06 | high activation | nd | nd | - | Spo0A~P phosphatase |
| rapA | SigA/CodY; ComA;Spo0A | 4.44 | 4.82E-06 | no termination | nd | 0.54 | - | Spo0F~P phosphatase |
| phrA | SigA/CodY; ComA;Spo0A | 5.73 | 1.20E-06 | no termination | nd | nd | - | RapA inhibitor |
| rapB | SigA;SigD | 0.60 | 1.45E-05 | low activation | 0.45 | 0.33 | 0.73 | Spo0F~P phosphatase |
(a)mRNA levels were computed on the normalized-aggregated data for the sense strand (S1 Table, Materials and methods)
(b)modifications of expression profiles can be visualized on http://genome.jouy.inra.fr/cgi-bin/seb/index.py; (nm) no visible modifications
(c)The PAI is the ratio between the total number of spectra obtained during the protein identification process on the theoretical number of peptides ranging between 800 to 2,500 Da and detectable by mass spectrometry for a given protein [66] (S3 Table);
(nd) not detected.