Table 1. Differentially expressed proteins associated with PCN production in P. chlororaphis P3.
| Protein description | Gene | IMG locus tag_HT66 | NCBI GI_HT66 | Ratioa |
|---|---|---|---|---|
| Phenazine-1-carboxamide biosynthesis | ||||
| Phenazine biosynthesis protein A/B | phzA | Pchs_06091 | 647490047 | 5.60 |
| Phenazine biosynthesis protein A/B | phzB | Pchs_06092 | 647490048 | 4.48 |
| Isochorismate hydrolase | phzD | Pchs_06094 | 647490052 | 5.52 |
| Anthranilate/para-aminobenzoate synthases component I | phzE | Pchs_06095 | 647490054 | 0.56 |
| Phenazine biosynthesis protein PhzF family | phzF | Pchs_06096 | 647490057 | 1.78 |
| Pyridoxamine 5′-phosphate oxidase | phzG | Pchs_06097 | 647490058 | 2.58 |
| Asparagine synthase | phzH | Pchs_06098 | 647490062 | 3.33 |
| Aromatic amino acid metabolism | ||||
| Tryptophan synthase, alpha chain | trpA | Pchs_00084 | 647491730 | 0.54 |
| Tryptophan synthase, beta chain | trpB | Pchs_00083 | 496337064 | 0.30 |
| Anthranilate synthase, component I | trpE | Pchs_00718 | 647493343 | 0.67 |
| Kynureninase | kynU | Pchs_01436 | 647499417 | 1.88 |
| General amino acid metabolism | ||||
| Phosphoglycerate dehydrogenase and related dehydrogenases | serA | Pchs_00455 | 495208070 | 0.43 |
| Serine hydroxymethyltransferase | glyA_1 | Pchs_06270 | 496341782 | 0.53 |
| Dihydrodipicolinate synthase/N-acetylneuraminate lyase | dapA | Pchs_02172 | 647483598 | 0.40 |
| Methionine synthase (B12-independent) | metE | Pchs_05826 | 647489417 | 0.34 |
| Transcriptional regulator, LysR family | metR | Pchs_05827 | 496341406 | 0.6 |
| Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component | bkdA_2 | Pchs_04155 | 647498492 | 2.27 |
| Branched-chain alpha-keto acid dehydrogenase E2 component | bkdB | Pchs_04156 | 647498496 | 2.21 |
| Dihydrolipoamide dehydrogenase | bkdC | Pchs_04157 | 647498498 | 2.10 |
| Methylmalonate-semialdehyde dehydrogenase | mmsA_2 | Pchs_01422 | 647499383 | 2.34 |
| 3-hydroxyisobutyrate dehydrogenase | mmsB | Pchs_01423 | 647499387 | 1.70 |
| TCA cycles | ||||
| Citrate synthase | gltA | Pchs_02520 | 496338587 | 3.05 |
| Aconitase | acnB | Pchs_04041 | 647498241 | 0.6 |
| Fumarase, class II | fumC_1 | Pchs_01637 | 647490465 | 5.57 |
| Malate:quinone-oxidoreductase | mqoA | Pchs_04769 | 647485851 | 0.52 |
| Fatty acid metabolism | ||||
| Acetyl-CoA carboxylase carboxyltransferase subunit alpha | accA | Pchs_01907 | 495199263 | 0.57 |
| Beta-ketoacyl-acyl-carrier-protein synthase II | fabF_2 | Pchs_02742 | 647484125 | 0.41 |
| 3-oxoacyl-[acyl-carrier-protein] synthase III | fabH_2 | Pchs_02430 | 647487188 | 0.53 |
| 3-ketoacyl-CoA thiolase | fadA | Pchs_02879 | 496338784 | 0.59 |
| Short chain enoyl-CoA hydratase | fadB | Pchs_02880 | 647484600 | 0.62 |
| Acetyl-CoA carboxylase carboxyltransferase subunit alpha | accD | Pchs_02808 | 647484424 | 0.67 |
| Acetate, glutarate, and 3-hydroxybutanoate catabolism | ||||
| Acetoacetyl-CoA synthase | acsA_1 | Pchs_01546 | 647499663 | 2.42 |
| Acyl-CoA dehydrogenases | gcdH | Pchs_00003 | 647491551 | 2.19 |
| 3-hydroxybutyrate dehydrogenase | bdhA | Pchs_01547 | 647499665 | 4.5 |
| Acetyl-coenzyme A synthetase | acsA_2 | Pchs_06191 | 647487629 | 2.32 |
| 3-oxoacid CoA-transferase, A subunit ScoA | scoA | Pchs_03129 | 495195793 | 71.6 |
| 3-oxoacid CoA-transferase, B subunit ScoB | scoB | Pchs_03130 | 495195791 | 7.49 |
| Acetyl-CoA acetyltransferase | atoB | Pchs_03131 | 647487719 | 9.64 |
| Secondary metabolism | ||||
| Long-chain-fatty-acid–CoA ligase | ofaB | Pchs_04408 | 647500074 | 0.36 |
| Chitinase | chiC | Pchs_02788 | 647484393 | 0.12 |
| Chitin-binding protein | cbpD | Pchs_02789 | 647484396 | 0.08 |
| Chitin-binding protein | cbpD | Pchs_03280 | 647496507 | 0.15 |
| Chitinase | chiC | Pchs_03281 | 647496510 | 0.2 |
| Achromobactin biosynthesis | ||||
| TonB-dependent ferric achromobactin receptor protein | – | Pchs_03383 | 647496719 | 4.5 |
| Achromobactin biosynthesis protein AcsF | acsF | Pchs_03384 | 647496722 | 13.41 |
| Achromobactin biosynthesis protein AcsD | acsD | Pchs_03385 | 647496724 | 4.28 |
| Achromobactin biosynthesis protein AcsA | acsA | Pchs_03390 | 647496739 | 7.35 |
| Siderophore achromobactin ABC transporter, ATPase component | fepC | Pchs_03394 | 647496750 | 2.85 |
| Putative achromobactin biosynthesis protein | – | Pchs_03396 | 647496754 | 2.32 |
| Pyoverdine biosynthesis | ||||
| Acyl-homoserine lactone acylase PvdQ (EC 3.5.1.-), quorum-quenching | pvdQ | Pchs_03685 | 647497454 | 3.06 |
| Putative dipeptidase, pyoverdin biosynthesis PvdM | pvdM | Pchs_05058 | 647486584 | 2.96 |
| PvdO, pyoverdine responsive serine/threonine kinase | pvdO | Pchs_05060 | 647486586 | 2.55 |
| Pyoverdine sidechain non-ribosomal peptide synthetase PvdD | pvdD | Pchs_05064 | 647486599 | 1.8 |
| Pyoverdine sidechain non-ribosomal peptide synthetase PvdJ | pvdJ | Pchs_05153 | 647493566 | 4.18 |
| TonB-dependent siderophore receptors | ||||
| TonB-dependent siderophore receptor | fhuA | Pchs_00644 | 647493125 | 15.86 |
| TonB-dependent siderophore receptor | piuA | Pchs_01589 | 647490308 | 8.56 |
| TonB-dependent siderophore receptor | fecA | Pchs_01712 | 647490614 | 1.67 |
| TonB-dependent siderophore receptor | – | Pchs_02718 | 647484077 | 1.65 |
| TonB-dependent siderophore receptor | – | Pchs_03569 | 647497170 | 3.11 |
| TonB-dependent siderophore receptor | – | Pchs_04973 | 647486375 | 1.69 |
| TonB-dependent heme/hemoglobin receptor family protein | phuR | Pchs_05644 | 647488959 | 1.56 |
| Outer membrane transport energization protein ExbB (TC 2.C.1.1.1) | exbB1 | Pchs_00288 | 647492252 | 1.95 |
| Ferric uptake regulation protein FUR | fur | Pchs_01489 | 495196050 | 0.66 |
| Transport systems | ||||
| Carbohydrate ABC transporter substrate-binding protein, CUT1 family (TC 3.A.1.1.-) | glpV | Pchs_04820 | 647485965 | 8.16 |
| Amino acid ABC transporter substrate-binding protein, PAAT family (TC 3.A.1.3.-) | aapJ | Pchs_01762 | 647490729 | 7.84 |
| Amino acid ABC transporter membrane protein 1, PAAT family (TC 3.A.1.3.-) | aapQ | Pchs_01763 | 647490732 | 2.49 |
| Amino acid ABC transporter ATP-binding protein, PAAT family (TC 3.A.1.3.-) | aapP | Pchs_01765 | 496337929 | 4.7 |
| Amino acid/amide ABC transporter ATP-binding protein 2, HAAT family (TC 3.A.1.4.-) | livF | Pchs_00883 | 496337539 | 3.21 |
| Amino acid/amide ABC transporter ATP-binding protein 1, HAAT family (TC 3.A.1.4.-) | livG | Pchs_00884 | 565889081 | 3.35 |
| Amino acid/amide ABC transporter substrate-binding protein, HAAT family (TC 3.A.1.4.-) | livJ | Pchs_00887 | 496337535 | 3.51 |
| Lysine-arginine-ornithine-binding periplasmic protein | aotJ | Pchs_04910 | 647486203 | 3.73 |
| Amino acid ABC transporter substrate-binding protein, PAAT family (TC 3.A.1.3.-) | – | Pchs_00385 | 647492551 | 5.60 |
| ABC-type dipeptide transport system, periplasmic component | dppA_1 | Pchs_01603 | 647490337 | 1.78 |
| Outer membrane porin, OprD family | oprD | Pchs_01604 | 647490339 | 3.1 |
| ABC-type dipeptide transport system, periplasmic component | dppA_2 | Pchs_01605 | 647490341 | 2.02 |
| Amino acid ABC transporter ATP-binding protein, PAAT family (TC 3.A.1.3.-) | hisP | Pchs_02011 | 647491334 | 1.58 |
| Amino acid ABC transporter substrate-binding protein, PAAT family (TC 3.A.1.3.-) | hisJ | Pchs_02015 | 496338179 | 1.65 |
| Phosphate transport | ||||
| Phosphate ABC transporter substrate-binding protein, PhoT family (TC 3.A.1.7.1) | pstS | Pchs_00239 | 495203739 | 0.37 |
| Phosphate transport system permease protein PstC (TC 3.A.1.7.1) | pstC | Pchs_00240 | 647492140 | 0.54 |
| Phosphate transport system permease protein PstA (TC 3.A.1.7.1) | pstA | Pchs_00241 | 496342427 | 0.58 |
| Phosphate transport ATP-binding protein PstB (TC 3.A.1.7.1) | pstB | Pchs_00242 | 496342426 | 0.54 |
| Phosphate transport system regulatory protein PhoU | phoU | Pchs_00243 | 495203747 | 0.65 |
| Phosphate regulon transcriptional regulatory protein PhoB | phoB | Pchs_00249 | 495171678 | 0.65 |
| Uncharacterized protein conserved in bacteria | – | Pchs_00250 | 647492159 | 0.59 |
| Nitrate uptake and metabolism (Nitrogen metabolism) | ||||
| Nitrate ABC transporter, nitrate-binding protein | nrtA | Pchs_02944 | 647484724 | 2.81 |
| Assimilatory nitrite reductase (NAD(P)H) large subunit precursor (EC 1.7.1.4) | nasR | Pchs_02949 | 647484728 | 3.23 |
| L-glutamine synthetase (EC 6.3.1.2) | glnA | Pchs_01089 | 647495467 | 3.05 |
| Nitrogen regulatory protein P-II family | glnK | Pchs_00342 | 488618959 | 2.25 |
| Nitrogen regulation protein NR(I) | ntrC | Pchs_01102 | 647495504 | 4.04 |
| Urea ABC transporter, ATP-binding protein UrtD | urtD | Pchs_00853 | 647494818 | 2.48 |
| Urease subunit alpha [EC:3.5.1.5] | ureC | Pchs_00860 | 647494842 | 1.83 |
| Urease accessory protein UreE | ureE | Pchs_00876 | 647494888 | 2.64 |
| Urease accessory protein UreG | ureG | Pchs_00878 | 496337543 | 2.79 |
| Secretion systems | ||||
| Type I secretion C-terminal target domain (VC_A0849 subclass) | lapA | Pchs_01388 | 647496163 | 1.71 |
| Type I secretion membrane fusion protein, HlyD family | hlyD | Pchs_02366 | 647487032 | 2.19 |
| Type I secretion system ATPase, LssB family | lapB | Pchs_02367 | 647487034 | 2.33 |
| Type I secretion outer membrane protein, TolC family | tolC | Pchs_02368 | 647487037 | 2.90 |
| VCBS repeat/type I secretion C-terminal target domain (VC_A0849 subclass) | lapA | Pchs_02369 | 647487039 | 2.66 |
| Type VI secretion protein, VC_A0107 family | impB | Pchs_00257 | 495205505 | 2.09 |
| Type VI secretion protein, EvpB/VC_A0108 family | impC | Pchs_00258 | 495205504 | 2.22 |
| Type VI secretion protein, VC_A0110 family | impG | Pchs_00265 | 647492201 | 2.50 |
| Type VI secretion ATPase, ClpV1 family | clpV | Pchs_00267 | 647492206 | 1.77 |
| Type VI secretion protein, VC_A0114 family | impJ | Pchs_00272 | 495205486 | 1.74 |
| Type IV/VI secretion system protein, DotU family | dotU | Pchs_00273 | 647492220 | 1.65 |
| Type VI secretion protein IcmF | icmF | Pchs_00274 | 647492224 | 1.99 |
| Type VI secretion system effector, Hcp1 family | hcp | Pchs_04376 | 496335162 | 2.11 |
| Type VI secretion protein, VC_A0114 family | impJ | Pchs_04382 | 647500000 | 1.53 |
| Type VI secretion system effector, Hcp1 family | hcp_1 | Pchs_01292 | 495200970 | 1.59 |
aFold change between two strains (mutant P3/control HT66), ratio >1.5 represented upregulation, ratio <0.7 represented downregulation.