Table 1 Expression (transcriptomic and proteomic) of P-acquisition and P-stress response loci in F. johnsoniae DSM0264.
Transcriptome | Whole cell proteome | Exoproteome | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Predicted function | Locus_tag | Gene symbol/description | Genomic context | Predicted localisation | Pfam accession | FC | FDR (p-adj) | DE | −Log p value | q value | DE | −Log p value | q value |
Phosphomonoesterase | Fjoh_0023 | PafA | Orphan | Periplasm | pf01663 | 0.26 | 5.52E−01 | 0.82 | 3.61 | 0.00130526 | -2.72 | 2.28 | 0.00 |
Fjoh_1367 | Phytase | Phytase | OM | pf02333 | 5.76 | 2.01E−36 | 6.83 | 0.51 | 9.31E−03 | ND | ND | ND | |
Fjoh_2478 | PhoX_like | PhoX | OM | pf05787 | 12.50 | 2.74E−142 | 11.34 | 0.28 | 0.00E+00 | 8.23 | 4.22 | 0.00E+00 | |
Fjoh_2225 | Putative APase | Orphan | Periplasm | pf01676 | 4.25 | 7.07E−34 | 6.20 | 0.39 | 0.00E+00 | 6.63 | 4.04 | 0.00E+00 | |
Fjoh_3187 | PhoA2 | Orphan | Periplasm | pf00245 | 1.59 | 0.28508 | 3.89 | 3.66 | 1.36E-03 | 0.03 | 0.01 | 9.73E-1 | |
Fjoh_3249 | PhoA1 (putative diesterase activity) | PUSII | Periplasm | pf00245, pf13653 | 7.40 | 4.39E−61 | 4.87 | 0.11 | 0.00E+00 | ND | ND | ND | |
Fjoh_3414 | Hypothetical Lipoprotein - putative phosphatase | Orphan | OM/IM | IPR011044, IPR011048, IPR015943 | 10.32 | 1.41E−90 | 9.09 | 0.08 | 0.00E+00 | 5.00 | 2.53 | 2.71E-03 | |
Phosphodiesterase | Fjoh_0074 | Endo/exonuclease/phosphatase | Orphan | OM | NA; IPR011050 | 1.15 | 4.17E−02 | 1.43 | 2.86 | 6.64E−03 | 0.57 | 0.56 | 0.23 |
Fjoh_3851 | Polyphosphate kinase_like/PlcP D | FI cluster/ PUSIII | Cytoplasm | pf02503, pf13089, pf13090 | 7.80 | 6.37E−75 | ND | ND | ND | ND | ND | ND | |
Fjoh_4172 | Phosphoinositide phospholipase C, Ca2+ -dependent, phosphodiesterases | PUSI | Periplasm | pf00149 | 6.44 | 2.87E−56 | 6.89 | 0.94 | 2.11E−03 | 6.03 | 1.03 | 6.15E-02 | |
Fjoh_4173 | 3′,5′-cyclic AMP phosphodiesterase CpdA | PUSI | Periplasm | pf16670 | 7.17 | 4.47E−69 | 4.48 | 0.37 | 3.79E−03 | 2.18 | 2.03 | 5.44E-03 | |
Fjoh_4721 | Extracellular nuclease, EndA1 | Orphan | OM | pf00041,pf00932, pf04231 | 4.66 | 3.19E−27 | 0.71 | 3.50 | 2.17E−02 | 3.70 | 3.92 | 0.00E+00 | |
Fjoh_4723 | Extracellular nuclease, EndA2 | Orphan | OM | pf00041,pf00932, pf04231 | 4.13 | 1.02E−32 | ND | ND | ND | 2.88 | 4.34 | 0.00E+00 | |
Transporter/Binding | Fjoh_0542 | OprP | PhoBR operon | OM | pf07396 | -1.3 | 0.24533 | ND | ND | ND | ND | ND | ND |
Fjoh_0545 | Tdbt | PhoBR operon | OM | pf07715, pf13715, pf14905 | 8.02 | 8.21E−84 | 6.52 | 0.49 | 7.91E-03 | 5.38 | 5.68 | 0.00E+00 | |
Fjoh_0546 | Hypothetical Lipoprotein - FII | PhoBR operon | OM | NA; IPR011050 | 9.91 | 3.67E−114 | 11.19 | 0.16 | 6.13E−03 | 6.47 | 4.57 | 0.00E+00 | |
Fjoh_0549 | Hypothetical Lipoprotein | PhoBR operon | OM | pf07705 | 7.59 | 1.67E−71 | 5.06 | 1.72 | 3.57E−03 | 7.05 | 3.64 | 0.00E+00 | |
Fjoh_1368 | Tbdt | Phytase | OM | pf07715; pf13715 | 9.22 | 1.84E−30 | 8.94 | 0.65 | 0.00E+00 | 3.72 | 2.41 | 5.29E-03 | |
Fjoh_3250 | PusD2 | PUSII | OM | pf07980, pf14322 | 8.94 | 1.49E−79 | 5.47 | 3.11 | 0.00E+00 | 8.85 | 4.43 | 0.00E+00 | |
Fjoh_3251 | PusC2 | PUSII | OM | pf00593, pf07715, pf13715, pf16344 | 9.03 | 7.60E−87 | 4.53 | 0.24 | 0.00E+00 | ND | ND | ND | |
Fjoh_3841 | Tbdt | Orphan | OM | pf13620 | 7.69 | 2.64E−81 | 8.44 | 0.11 | 0.00E+00 | 8.34 | 4.60 | 0.00E+00 | |
Fjoh_3856 | Hypothetical Lipoprotein - FI | FI cluster/ PUSIII | OM | NA, lipoprotein | 14.47 | 5.36E−31 | 6.33 | 0.01 | 1.48E−3 | 5.39 | 3.07 | 0.00E+00 | |
Fjoh_3857 | Tbdt | FI cluster/ PUSIII | OM | pf07715, pf13715 | 12.50 | 7.00E−100 | 5.18 | 4.08 | 1.41E-03 | 3.73 | 2.48 | 3.38E-03 | |
Fjoh_4168 | PusD1 | PUSI | OM | pf07980, pf14322 | 10.17 | 7.54E−94 | 6.23 | 1.84 | 0.00E+00 | 8.55 | 4.99 | 0.00E+00 | |
Fjoh_4169 | PusC1 | PUSI | OM | pf00593, pf07715, pf13715 | 10.66 | 8.26E−101 | 3.17 | 0.01 | 1.33E−01 | ND | ND | ND | |
Fjoh_4889 | Hypothetical Lipoprotein - FIII | Orphan | OM | NA | 11.56 | 4.44E−118 | 9.13 | 1.42 | 0.00E+00 | 9.56 | 4.13 | 0.00E+00 | |
Lipid remodelling | Fjoh_0541 | Glycosyl transferase | PhoBR operon | Cytoplasm | pf04101 | 5.42 | 2.94E−49 | 7.04 | 5.08 | 0.00E+00 | ND | ND | ND |
Fjoh_4577 | PlcP | Orphan | Cytoplasm | pf12850 | 8.59 | 2.12E−77 | ND | ND | ND | ND | ND | ND | |
Accessory | Fjoh_0543 | PhoR | PhoBR operon | Cytoplasm | pf00512, pf02518 | 0.76 | 0.056401 | ND | ND | ND | ND | ND | ND |
Fjoh_0544 | PhoB | PhoBR operon | Cytoplasm | pf00072, pf00486 | 3.06 | 9.42E−20 | 3.23 | 4.49 | 0.00E+00 | ND | ND | ND | |
Fjoh_2477 | MauG_like | PhoX | Cytoplasm | pf03150 | 9.58 | 3.54E−95 | 7.33 | 0.64 | 8.36E−03 | ND | ND | ND | |
Fjoh_3252 | FecR_like regulator | PUSII | Cytoplasm | pf04773, pf16344 | 9.88 | 7.70E−61 | ND | ND | ND | ND | ND | ND | |
Fjoh_3853 | C-terminal peptidase S41 | FI cluster/ PUSIII | Periplasm | pf03572 | 9.08 | 9.92E−74 | ND | ND | ND | 4.44 | 2.79 | 0.00E+00 | |
Fjoh_3854 | T9SS-secretion domain, lipoprotein | FI cluster/ PUSIII | OM | NA, | 9.64 | 1.90E−66 | 3.30 | 0.65 | 6.04E−03 | 5.75 | 4.29 | 0.00E+00 | |
Fjoh_3855 | T9SS-secretion domain, | FI cluster/ PUSIII | OM | NA | 10.04 | 7.54E−94 | ND | ND | ND | 8.61 | 3.90 | 0.00E+00 | |
Fjoh_3858 | FecR_like regulator | FI cluster/ PUSIII | Cytoplasm | pf04773, pf16344 | 9.79 | 9.56E−90 | 1.53 | 1.75 | 7.02E−02 | ND | ND | ND | |
Fjoh_3859 | Sigma factor - regulator | FI cluster/ PUSIII | Cytoplasm | pf04542, pf08281 | 7.94 | 2.29E−70 | ND | ND | ND | ND | ND | ND | |
Fjoh_4171 | ECF Sigma factor | PUSI | Cytoplasm | pf04542, pf08281 | 8.88 | 1.19E−70 | 0.05 | 3.82 | 9.50E−01 | ND | ND | ND | |
