Table 2.
List of proteins found to be positively regulated by PhyR
| Spot no. | RMQ no. | Gene product* | CD search | Mr | pl | Ratio† phy R+ vs. phyR− |
|---|---|---|---|---|---|---|
| Found in phyllosphere proteome (see Table 1) | ||||||
| 20, 21 | RMQ08198 | (PhyR, response regulator) | pfam06182 | 29.1 | 4.8 | ∞ |
| 1, 2 | RMQ09549 | KatE, catalase (L48340) | pfam00199 | 63.5 | 7.1 | + |
| 12 | RMQ02531 | SodA, superoxide dismutase | pfam02777 | 22.5 | 5.8 | + |
| 26, 28 | RMQ02206 | Hsp20, heat-shock protein 20 | pfam00011 | 18.4 | 5.2 | ++ |
| 29 | RMQ05258 | Dps, DNA protection protein | pfam00210 | 19.9 | 5.0 | ∞ |
| 4 | RMQ11717 | Putative quinoprotein (glucose dehydrogenase) | 36.0 | 6.9 | + | |
| 38 | RMQ02894 | Putative lactoylglutathione lyase | pfam00903 | 16.5 | 5.7 | ∞ |
| 8 | RMQ03170 | Orf88, dioxygenase (glyoxalase family protein) (AY034474) | pfam00903 | 36.4 | 6.2 | ∞ |
| 43 | RMQ01365 | Gap20 (AF442748) | 19.0 | 5.8 | + | |
| 25 | RMQ09016 | NifU-like/thioredoxin-like protein | pfam01106 | 20.3 | 4.8 | ∞ |
| 24 | RMQ08861 | Protein of unknown function | 20.3 | 5.3 | ∞ | |
| 15 | RMQ00428 | Protein of unknown function | 31.9 | 5.3 | + | |
| Additional proteins under PhyR control | ||||||
| 3a | RMQ06018 | Glutathione-dependent formaldehyde dehydrogenase | pfam00107 | 42.2 | 5.7 | ∞ |
| 5 | RMQ01240 | ADH, alcohol dehydrogenase | pfam00107 | 39.1 | 6.5 | ∞ |
| 6 | RMQ00842 | ADH, alcohol dehydrogenase | pfam00107 | 35.2 | 6.3 | ∞ |
| 7a | RMQ07799 | Short-chain dehydrogenases/reductases (GSP39) | pfam00106 | 30.8 | 5.9 | ∞ |
| 23 | RMQ00500 | Short-chain dehydrogenases/reductases | pfam00106 | 27.6 | 5.1 | ∞ |
| 51 | RMQ11711 | PccA, propionyl-CoA carboxylase (AY181038) | pfam02786 | 75.6 | 4.9 | + |
| 14 | RMQ06958 | MclA, malyl-CoA lyase (U72662) | 38.0 | 5.6 | + | |
| 18 | RMQ06488 | MDH, malate dehydrogenase (L33465) | pfam02866 | 39.1 | 6.6 | ∞ |
| 30, 31 | RMQ02884 | Phosphoglycerate mutase | pfam00300 | 23.9 | 5.5 | + |
| 48 | RMQ06654 | NAD(P) transhydrogenase α-subunit | pfam01262 | 39.6 | 5.6 | ∞ |
| 19 | RMQ01528 | FixB, Electron transfer flavoprotein, α-subunit | pfam00766 | 32.5 | 4.9 | ∞ |
| 11 | RMQ02643 | WrbA, flavoprotein | pfam00258 | 21.1 | 6.2 | ∞ |
| 32 | RMQ00895 | Carbonic anhydrase | pfam00484 | 28.4 | 9.1 | + |
| 36 | RMQ06760 | Ohr, organic hydroperoxide resistance protein-like protein (GSP17o) | pfam02566 | 15.0 | 5.7 | ∞ |
| 40 | RMQ06032 | AhpC (alkyl hydroperoxide reductase)/TSA (thiol specific antioxidant) family protein | pfam00578 | 18.0 | 5.9 | + |
| 45 | RMQ07144 | Trx, thioredoxin | pfam00085 | 17.4 | 9.7 | + |
| 7b | RMQ06181 | Putative haloacetate dehalogenase/non-heme chloroperoxidase | pfam00561 | 30.6 | 5.8 | ∞ |
| 33 | RMQ07321 | Putative phospholipid-binding proteins | pfam01161 | 19.7 | 5.5 | ∞ |
| 10 | RMQ11238 | Putative 3-hydroxyisobutyrate dehydrogenase | 20.8 | 5.7 | + | |
| 22 | RMQ12169 | CinA-like protein | pfam00994 | 25.0 | 4.8 | + |
| 27 | RMQ09145 | Hbd, d-β-hydroxybutyrate dehydrogenase (AY391854) | pfam00106 | 31.9 | 8.7 | + |
| 42 | RMQ02665 | GreA, transcription elongation factor | pfam01272 | 22.1 | 6.9 | + |
| 13 | RMQ06933 | EF-Ts, elongation factor | pfam00889 | 35.1 | 5.3 | + |
| 50 | RMQ07718 | CzcB, Cobalt-zinc-cadmium resistance protein | pfam00529 | 46.3 | 6.2 | + |
| 3b | RMQ03224 | Hypothetical signaling protein | 42.4 | 8.2 | ∞ | |
| 34 | RMQ04652 | Protein of unknown function (GSP26) | pfam01243 | 19.0 | 5.7 | ∞ |
| 9 | RMQ05442 | Protein of unknown function | pfam01442 | 28.4 | 5.8 | + |
| 41 | RMQ01392 | Protein of unknown function | pfam03928 | 14.8 | 5.0 | + |
| 35 | RMQ12283 | Protein of unknown function | 14.9 | 5.6 | ∞ | |
| 37 | RMQ12368 | Protein of unknown function | 12.7 | 6.6 | ∞ | |
| 44 | RMQ07641 | Protein of unknown function | 16.8 | 5.4 | ∞ | |
*Accession nos. are in parentheses.
†Spots indicated as “∞” were only detectable in the proteome from M. extorquens AM1 ΔphyR pBG11 (phyR overexpression) and not in the strain containing pCM80 (phyR minus). Spots indicated as “+” were found to be at least 3-fold induced.