Table I. Most strongly induced proteins during phyllosphere colonization of S. melonis Fr1 and M. extorquens PA1. Only significantly regulated proteins (Benjamini-Hochberg corrected p value ≤ 0.05) are shown.
| Gene | Locus-Tag | Annotation | Log2 FC | p valuea |
|---|---|---|---|---|
| Sphingomonas melonis Fr1 | ||||
| 2517158111 | Sphme2DRAFT_2537 | alanine dehydrogenase | 5.3 | <0.01 |
| 2517158262 | Sphme2DRAFT_2688 | 3-oxoacid CoA-transferase, B subunit | 3.4 | <0.01 |
| 2517158089 | Sphme2DRAFT_2515 | Protease subunit of ATP-dependent Clp proteases | 2.6 | <0.01 |
| 2517158671 | Sphme2DRAFT_3097 | 2-oxoglutarate dehydrogenase complex E2 component | 2.1 | 0.0273 |
| 2517158667 | Sphme2DRAFT_3093 | malate dehydrogenase, NAD-dependent | 2.1 | <0.01 |
| 2517158672 | Sphme2DRAFT_3098 | dihydrolipoamide dehydrogenase | 2.0 | <0.01 |
| 2517159474 | Sphme2DRAFT_3904 | hypothetical protein | 2.0 | <0.01 |
| 2517156663 | Sphme2DRAFT_1089 | d-3-phosphoglycerate dehydrogenase | 1.9 | <0.01 |
| 2517156254 | Sphme2DRAFT_0680 | Predicted outer membrane lipoprotein | 1.9 | <0.01 |
| 2517158622 | Sphme2DRAFT_3048 | hypothetical protein | 1.9 | <0.01 |
| 2517158626 | Sphme2DRAFT_3052 | Predicted sugar kinase | 1.9 | 0.0182 |
| 2517157004 | Sphme2DRAFT_1430 | Sporulation related domain. | 1.8 | <0.01 |
| 2517157264 | Sphme2DRAFT_1690 | N-carbamoylputrescine amidase | 1.7 | 0.0179 |
| 2517157334 | Sphme2DRAFT_1760 | Multidrug resistance efflux pump | 1.6 | <0.01 |
| 2517157234 | Sphme2DRAFT_1660 | Predicted periplasmic/secreted protein | 1.6 | <0.01 |
| 2517158635 | Sphme2DRAFT_3061 | Membrane proteins related to metalloendopeptidases | 1.6 | <0.01 |
| 2517158142 | Sphme2DRAFT_2568 | Deoxyhypusine synthase | 1.6 | <0.01 |
| 2517156139 | Sphme2DRAFT_0565 | pyruvate kinase | 1.6 | <0.01 |
| 2517158432 | Sphme2DRAFT_2858 | NAD-dependent aldehyde dehydrogenases | 1.6 | <0.01 |
| 2517158634 | Sphme2DRAFT_3060 | tyrosyl-tRNA synthetase | 1.6 | <0.01 |
| 2517156628 | Sphme2DRAFT_1054 | methylmalonic acid semialdehyde dehydrogenase | 1.5 | <0.01 |
| 2517157977 | Sphme2DRAFT_2403 | Glutathione S-transferase | 1.5 | <0.01 |
| 2517155766 | Sphme2DRAFT_0192 | ribosomal protein L21 | 1.5 | <0.01 |
| 2517158541 | Sphme2DRAFT_2967 | Peroxiredoxin | 1.5 | <0.01 |
| 2517156538 | Sphme2DRAFT_0964 | Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain | 1.5 | <0.01 |
| 2517158824 | Sphme2DRAFT_3250 | Cysteine synthase | 1.5 | 0.0213 |
| 2517156106 | Sphme2DRAFT_0532 | succinyl-CoA synthetase, beta subunit | 1.4 | <0.01 |
| 2517156919 | Sphme2DRAFT_1345 | Short-chain alcohol dehydrogenase of unknown specificity | 1.4 | 0.0147 |
| 2517158295 | Sphme2DRAFT_2721 | Glucose/sorbosone dehydrogenases | 1.4 | 0.0106 |
| 2517155691 | Sphme2DRAFT_0117 | succinylglutamic semialdehyde dehydrogenase | 1.4 | 0.0115 |
| 2517156060 | Sphme2DRAFT_0486 | Domain of unknown function (DUF3576) | 1.3 | <0.01 |
| 2517158171 | Sphme2DRAFT_2597 | hypothetical protein | 1.3 | <0.01 |
| 2517155822 | Sphme2DRAFT_0248 | RND family efflux transporter, MFP subunit | 1.3 | <0.01 |
| 2517158649 | Sphme2DRAFT_3075 | Long-chain fatty acid transport protein | 1.3 | <0.01 |
| 2517156431 | Sphme2DRAFT_0857 | argininosuccinate lyase | 1.3 | <0.01 |
| 2517156535 | Sphme2DRAFT_0961 | glycine cleavage system T protein | 1.3 | <0.01 |
| 2517156271 | Sphme2DRAFT_0697 | Beta-lactamase class A | 1.3 | <0.01 |
| 2517158162 | Sphme2DRAFT_2588 | Ribosomal protein L10 | 1.3 | <0.01 |
| 2517158942 | Sphme2DRAFT_3368 | ATP-binding cassette protein, ChvD family | 1.2 | <0.01 |
| 2517158985 | Sphme2DRAFT_3411 | Cell shape-determining protein | 1.2 | <0.01 |
| Methylobacterium extorquens PA1 | ||||
| NC_010172.1_cdsid_YP_001642205.1 | Mext_4766 | hypothetical protein | 4.5 | <0.01 |
| NC_010172.1_cdsid_YP_001640200.1 | Mext_2738 | photosynthetic reaction center cytochrome c subunit (PufC) | 4.3 | 0.022 |
| NC_010172.1_cdsid_YP_001640859.1 | Mext_3402 | hypothetical protein | 4.2 | <0.01 |
| NC_010172.1_cdsid_YP_001642131.1 | Mext_4692 | protease Do | 3.9 | <0.01 |
| NC_010172.1_cdsid_YP_001641409.1 | Mext_3967 | hypothetical protein | 3.7 | <0.01 |
| NC_010172.1_cdsid_YP_001638811.1 | Mext_1339 | methanol/ethanol family PQQ-dependent dehydrogenase | 3.2 | <0.01 |
| NC_010172.1_cdsid_YP_001640093.1 | Mext_2630 | hypothetical protein | 3.1 | <0.01 |
| NC_010172.1_cdsid_YP_001638682.1 | Mext_1209 | putative oxalyl-CoA decarboxylase | 2.9 | 0.013 |
| NC_010172.1_cdsid_YP_001640767.1 | Mext_3309 | molybdopterin binding oxidoreductase | 2.9 | <0.01 |
| NC_010172.1_cdsid_YP_001641647.1 | Mext_4207 | triple helix repeat-containing collagen | 2.9 | <0.01 |
| NC_010172.1_cdsid_YP_001640025.1 | Mext_2560 | phasin (Gap20) | 2.8 | <0.01 |
| NC_010172.1_cdsid_YP_001642168.1 | Mext_4729 | CsbD family protein | 2.7 | <0.01 |
| NC_010172.1_cdsid_YP_001639679.1 | Mext_2213 | hypothetical protein | 2.7 | <0.01 |
| NC_010172.1_cdsid_YP_001637566.1 | Mext_0067 | hypothetical protein | 2.7 | <0.01 |
| NC_010172.1_cdsid_YP_001639614.1 | Mext_2148 | hypothetical protein | 2.6 | <0.01 |
| NC_010172.1_cdsid_YP_001641262.1 | Mext_3817 | hypothetical protein | 2.6 | <0.01 |
| NC_010172.1_cdsid_YP_001641592.1 | Mext_4152 | hypothetical protein | 2.6 | <0.01 |
| NC_010172.1_cdsid_YP_001638148.1 | Mext_0663 | putative DNA-binding protein | 2.6 | <0.01 |
| NC_010172.1_cdsid_YP_001637886.1 | Mext_0393 | hypothetical protein | 2.6 | <0.01 |
| NC_010172.1_cdsid_YP_001638358.1 | Mext_0882 | PfpI family intracellular peptidase | 2.6 | <0.01 |
| NC_010172.1_cdsid_YP_001639279.1 | Mext_1809 | methanol/ethanol family PQQ-dependent dehydrogenase (XoxF) | 2.5 | <0.01 |
| NC_010172.1_cdsid_YP_001642090.1 | Mext_4651 | aromatic amino acid beta-eliminating lyase/threonine aldolase | 2.5 | <0.01 |
| NC_010172.1_cdsid_YP_001639237.1 | Mext_1767 | hypothetical protein | 2.5 | <0.01 |
| NC_010172.1_cdsid_YP_001638912.1 | Mext_1440 | hypothetical protein | 2.4 | 0.025 |
| NC_010172.1_cdsid_YP_001640238.1 | Mext_2776 | hypothetical protein | 2.4 | <0.01 |
| NC_010172.1_cdsid_YP_001638796.1 | Mext_1324 | hypothetical protein | 2.4 | <0.01 |
| NC_010172.1_cdsid_YP_001637885.1 | Mext_0392 | hypothetical protein | 2.4 | <0.01 |
| NC_010172.1_cdsid_YP_001638850.1 | Mext_1378 | hypothetical protein | 2.4 | <0.01 |
| NC_010172.1_cdsid_YP_001639962.1 | Mext_2496 | hypothetical protein | 2.4 | <0.01 |
| NC_010172.1_cdsid_YP_001640222.1 | Mext_2760 | NAD(P) transhydrogenase subunit PntAB | 2.4 | <0.01 |
| NC_010172.1_cdsid_YP_001640865.1 | Mext_3408 | alkanesulfonate monooxygenase | 2.3 | <0.01 |
| NC_010172.1_cdsid_YP_001642123.1 | Mext_4684 | hypothetical protein | 2.3 | <0.01 |
| NC_010172.1_cdsid_YP_001637681.1 | Mext_0184 | hypothetical protein | 2.3 | <0.01 |
| NC_010172.1_cdsid_YP_001639333.1 | Mext_1863 | hypothetical protein | 2.2 | <0.01 |
| NC_010172.1_cdsid_YP_001640504.1 | Mext_3044 | hypothetical protein | 2.2 | 0.023 |
| NC_010172.1_cdsid_YP_001637884.1 | Mext_0391 | formate dehydrogenase subunit gamma (Fdh3) | 2.2 | <0.01 |
| NC_010172.1_cdsid_YP_001642264.1 | Mext_4825 | gluconate 2-dehydrogenase | 2.2 | 0.021 |
| NC_010172.1_cdsid_YP_001640221.1 | Mext_2759 | NAD(P)(+) transhydrogenase | 2.1 | <0.01 |
| NC_010172.1_cdsid_YP_001640937.1 | Mext_3481 | hypothetical protein | 2.1 | <0.01 |
| NC_010172.1_cdsid_YP_001641211.1 | Mext_3766 | hypothetical protein | 2.1 | <0.01 |
a Benjamini-Hochberg corrected for multiple testing.