Table 1.
List of proteins from M. extorquens AM1 found to be induced during phyllosphere (P) colonization relative to MM and rhizosphere (R) colonization
| Spot no.* | RMQ no. | Gene product(s)†† | CD search | Mr | pl | Ratio,‡ P/MM | Ratio,‡ P/R |
|---|---|---|---|---|---|---|---|
| Metabolism | |||||||
| 29 | RMQ05966 | MxaF, methanol dehydrogenase, large subunit (M31108) | pfam01011 | 67.2 | 5.8 | + | |
| 48 | RMQ00044 | MxaJ protein (M31108) | pfam00497 | 27.4 | 6.0 | ∞ | |
| 4 | RMQ09682 | Fae, formaldehyde activating enzyme (L43136) | 20.7 | 7.0 | + | ||
| 16 | RMQ08765 | PqqB, PQQ biosynthesis polypeptide (L25889) | 30.6 | 5.4 | ∞ | ||
| 34 n11 | RMQ03830 | PhaA, β-ketothiolase (AF287907) | pfam00108 | 44.1 | 6.7 | + | + |
| 42 | RMQ09548 | Crr, crotonyl-CoA reductase (L48340) | pfam00107 | 47.5 | 6.3 | ∞ | |
| 2 | RMQ01365 | Gap20 (AF442749) | 19.0 | 5.8 | ∞ | ||
| 45 | RMQ05381 | Malyl-CoA lyase-like protein | pfam03328 | 37.9 | 5.8 | ∞ | |
| 24 n10 | RMQ03452 | Aldehyde dehydrogenase | pfam00171 | 62.8 | 6.4 | + | ∞ |
| 28 | RMQ07560 | Xanthine oxidase-related aldehyde oxidoreductase | pfam02738 | 80.6 | 5.3 | + | |
| 44 | RMQ07805 | Putative NADP-dependent oxidoreductase | pfam00107 | 35.9 | 6.0 | + | |
| P12 | RMQ11717 | Putative quinoprotein | 36.0 | 6.9 | + | ||
| 1 | RMQ02894 | GloA, lactoyglutathione lyase | pfam00903 | 16.5 | 5.7 | + | |
| n3 | RMQ09259 | Adenylate kinase | pfam00406 | 21.3 | 5.1 | + | |
| Transport | |||||||
| n4 | RMQ08930 | ABC-type Fe+ transport system, periplasmic component | 36.6 | 6.6 | + | ||
| n6 | RMQ06383 | ABC-type sulfate transport system, periplasmic component | 24.1 | 7.8 | + | ||
| 15 | RMQ02495 | Putative amino acid binding protein | pfam00497 | 28.5 | 5.2 | ∞ | |
| 31 | RMQ05493 | Putative oligopeptide binding protein | pfam00496 | 70.2 | 6.7 | + | |
| Stress proteins | |||||||
| P28 | RMQ01248 | DegP/HrA, Trypsin-like serine proteases | pfam00089 | 50.4 | 6.7 | ∞ | |
| 40 | RMQ04833 | DegP/HrA, Trypsin-like serine proteases | pfam00089 | 51.2 | 8.4 | ∞ | |
| n5 | RMQ08088 | ClpP, ATP-dependent Clp protease proteolytic subunit | pfam00574 | 23.1 | 5.8 | + | |
| 6 | RMQ05519 | Protease I (Serine protease) DJ-1/Pfpl family (GSP18) | pfam01965 | 20.7 | 4.9 | ∞ | |
| P22 | RMQ06501 | Hsp70, heat-shock protein 70 (DnaK) | pfam00012 | 51.9 | 4.9 | + | |
| P35 | RMQ06982 | Hsp70, heat-shock protein 70 (DnaK) | pfam00012 | 68.5 | 5.2 | + | |
| P4 | RMQ02206 | Hsp20, heat-shock protein 20 | pfam00011 | 18.4 | 5.2 | ∞ | |
| P15 | RMQ02531 | SodA, Superoxide dismutase | pfam02777 | 22.5 | 5.8 | + | |
| 37a | RMQ09549 | KatE, catalase (L48340) | pfam00199 | 63.5 | 7.1 | ∞ | |
| 37b | RMQ11789 | KatE, catalase | pfam00199 | 59.9 | 5.8 | ∞ | |
| 9 | RMQ05258 | Dps, DNA protection protein | pfam00210 | 19.9 | 5.0 | + | |
| Proteins of unknown function | |||||||
| 7, 12 | RMQ09016 | NfU-like/thioredoxin-like protein | pfam01106 | 20.3 | 4.8 | ∞ | |
| 43 n7 | RMQ10082 | Major royal jelly protein§ | pfam03022 | 41.4 | 6.3 | ∞ | + |
| P26 | RMQ06718 | Major royal jelly protein§ | pfam03022 | 40.2 | 5.4 | ∞ | |
| n12 | RMQ07439 | Protein of unknown function | 68.3 | 6.4 | + | ||
| 8 | RMQ10020 | Protein of unknown function | pfam05974 | 18.5 | 5.4 | ∞ | |
| 10 | RMQ09099 | Protein of unknown function | 21.1 | 5.9 | ∞ | ||
| 13 | RMQ08861 | Protein of unknown function | 20.3 | 5.3 | ∞ | ||
| 17 | RMQ03063 | Protein of unknown function | 31.7 | 4.9 | ∞ | ||
| 18 | RMQ00428 | Protein of unknown function§ | 31.9 | 5.3 | + | ||
| P30 | RMQ05730 | Protein of unknown function§ | 28.9 | 6.8 | + | ||
| 19 | RMQ01102 | Protein of unknown function | 43.5 | 5.0 | ∞ | ||
| P25 | RMQ00267 | Protein of unknown function | 39.1 | 5.2 | ∞ | ||
| 39 | RMQ03107 | Protein of unknown function | pfam00450 | 55.3 | 6.4 | ∞ | |
| 46 | RMQ03170 | Orf88, dioxygenase (AY034474) | pfam00903 | 36.4 | 6.2 | + | |
| 36 n8 | RMQ09688 | Putative nucleoside binding protein | 54.7 | 9.0 | ∞ | ∞ | |
| Regulator | |||||||
| P16 | RMQ08198 | Response regulator (PhyR, this work) | pfam06182 | 29.1 | 4.8 | ∞ | |
*Spot numbers that are preceded by “P” were identified on gels from independent experiments stained with silver nitrate rather than with SYPRO Ruby. Spot numbers preceded by “n” were detected to be induced in bacteria that were grown in the phyllosphere with respect to the rhizosphere. All other proteins were identified from the proteome of bacteria grown in the phyllosphere with respect to minimal medium supplemented with succinate.
†Accession nos. are in parentheses.
‡Spots indicated as “∞” were only detectable in the proteome from bacteria grown in the phyllosphere and not in the references (mm and rhizosphere, respectively). Spots indicated as “+” were found to be at least 3-fold induced. Proteins were identified from 2D gels stained with SYPRO Ruby and found in two biological repetitions whereby the majority of the spots were in addition also found induced on gels that were stained with silver nitrate.