Table 4.
Genes potentially associated with Plant Growth-Promotion traits in P. agglomerans C1.
| Direct Plant Growth-Promotion | |||
| Gene | EC No. | Annotation | Gene Location, Coding Strand (+/−) |
| IAA production | |||
| ipdC | 4.1.1.74 | Indole-3-pyruvate decarboxylase | Contig1: 2029913-2028261, − |
| amiE | 3.5.1.4 | Aliphatic amidase | Contig1: 254208-254999, + |
| aec | Auxin efflux carrier family protein | Contig1: 1779607-1780566, + | |
| Spermidine biosynthesis | |||
| speA | 3.5.3.11 | Agmatinase | Contig4: 165937-1659017, − |
| speB | 4.1.1.19 | Biosynthetic arginine decarboxylase | Contig4: 168083-1686107, − |
| speD | 4.1.1.50 | S-adenosylmethionine decarboxylase proenzyme | Contig3: 73489-74298, + |
| speE | 2.5.1.16 | prokaryotic class 1A Spermidine synthase | Contig3: 73489-74298, + |
| Phosphate solubilization | |||
| gad | 1.1.99.3 | Gluconate 2-dehydrogenase, membrane-bound, cytochrome c | Contig3: 303092-301830, − |
| gad | 1.1.99.3 | Gluconate 2-dehydrogenase, membrane-bound, flavoprotein | Contig3: 304866-303097, − |
| gad | 1.1.99.3 | Gluconate 2-dehydrogenase, membrane-bound, gamma subunit | Contig3: 305631-304903, − |
| gad | 1.1.99.3 | Gluconate 2-dehydrogenase, membrane-bound, cytochrome c | Contig3: 495485-494175, − |
| gad | 1.1.99.3 | Gluconate 2-dehydrogenase, membrane-bound, flavoprotein | Contig3: 497280-495496, − |
| gad | 1.1.99.3 | Gluconate 2-dehydrogenase, membrane-bound, gamma subunit | Contig3: 498017-497283, − |
| gcd | 1.1.5.2 | Glucose dehydrogenase pyrroloquinoline quinone (PQQ)-dependent | Contig3: 476263-478653, + |
| pqq | Coenzyme PQQ synthesis protein B,C,D,E,F | Contig1: 1076330-1081693, + | |
| phoU | Phosphate transport system regulatory protein | Contig6: 207107-206373, − | |
| pstB | Phosphate transport ATP-binding protein | Contig6: 207898-207125, − | |
| pstA | Phosphate transport system permease protein | Contig6: 208833-207943, − | |
| pstC | Phosphate transport system permease protein | Contig6: 209792-208830, − | |
| pstS | Phosphate ABC transporter, periplasmic phosphate-binding protein | Contig6: 210923-209880, − | |
| Indirect Plant Growth-Promotion | |||
| Gene | EC No. | Annotation | Gene Location, Coding Strand (+/−) |
| Volatile organic compounds (VOCs) | |||
| alsR | Transcriptional regulator of alpha-acetolactate operon | Contig7: 135886-136791, + | |
| alsD | 4.1.1.5 | Alpha-acetolactate decarboxylase | Contig7: 135781-134999, − |
| alsS | 2.2.1.6 | Acetolactate synthase | Contig7: 134984-133305, − |
| bdh | 1.1.1.41.1.1.304 | 2,3-butanediol dehydrogenase, S-alcohol forming, (R)-acetoin-specific/Acetoin (diacetyl) reductase | Contig7: 133283-132510, − |
| GABA production | |||
| gabD | 1.2.1.16 | Succinate-semialdehyde dehydrogenase [NAD(P)+] | Contig4: 449240-447789, − |
| gabT | 2.6.1.19 | Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase | Contig2: 419393-420679, + |
| Siderophores biogenesis | |||
| fes | Enterobactin esterase | Contig3: 384712-385917, + | |
| entA | 1.3.1.28 | 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase | Contig3: 399161-399919, + |
| entB | 3.3.2.1 | Isochorismatase | Contig3: 398310-399164, + |
| entC | 5.4.4.2 | Isochorismate synthase | Contig3: 395486-396664, + |
| entE | 2.7.7.58 | 2,3-dihydroxybenzoate-AMP ligase | Contig3: 396675-398291, + |
| entF | 6.3.2.14 | Enterobactin synthetase component F | Contig3: 386228-390157, + |
| fepA | TonB-dependent receptor; Outer membrane receptor for ferric enterobactin and colicins B, D | Contig3: 384461-382194, − | |
| fepB | Ferric enterobactin-binding periplasmic protein | Contig3: 395308-394340, − | |
| fepC | Ferric enterobactin transport ATP-binding protein | Contig3: 390992-390201, − | |
| fepD | Ferric enterobactin transport system permease protein | Contig3: 392922-391966, − | |
| fepG | Ferric enterobactin transport system permease protein | Contig3: 391969-390989, − | |
| entS | Enterobactin exporter | Contig3: 393083-394345, − | |
| ybdZ | Putative cytoplasmic protein YbdZ in enterobactin biosynthesis operon | Contig3: 386017-386235, + | |
| fhuA | Ferric hydroxamate outer membrane receptor | Contig3: 51852-49651, − | |
| fhuC | Ferric hydroxamate ABC transporter, ATP-binding protein | Contig3: 49611-48817, − | |
| fhuD | Ferric hydroxamate ABC transporter, periplasmic substrate binding protein | Contig3: 48806-47928, − | |
| fhuB | Ferric hydroxamate ABC transporter, permease component | Contig3: 47928-45949, − | |
| Ferrous iron transporter (EfeUOB) | |||
| efeU | Ferrous iron transport permease | Contig1: 1504038-1503214, − | |
| efeO | Ferrous iron transport periplasmic protein contains peptidase-M75 domain and (frequently) cupredoxin-like domain | Contig1: 1504038-1503214, − | |
| efeB | Ferrous iron transport peroxidase | Contig1: 1503155-1502046, − | |