TABLE 2.
The 100 most highly upregulated genes in 28-day pea bacteroids compared with succinate-grown free-living cells
| Genea | Fold induction | Distributionc | Gene name | Product description |
|---|---|---|---|---|
| pRL100067b | 18 | B | Putative racemase/decarboxylase | |
| pRL100092 | 5 | PG | Putative transcriptional regulatory protein, pseudogene | |
| pRL100097b | 12 | B | Conserved hypothetical protein | |
| pRL100098 | 14 | B | Conserved hypothetical protein | |
| pRL100099b | 19 | B | Conserved hypothetical protein | |
| pRL100100 | 65 | PG | Putative nitrogenase iron protein, pseudogene (has start of nifH) | |
| pRL100101b | 105 | PG | Putative acetolactate synthase, pseudogene | |
| pRL100103b | 13 | A | Putative alcohol dehydrogenase | |
| pRL100104b | 39 | A | Conserved hypothetical protein | |
| pRL100105b | 10 | A | phaC2 | Putative polyhydroxyalkanoate synthase subunit C (shows 25% identity with residues 252-527 of PhaC (RL2094) of R. leguminosarum bv. viciae 3841) |
| pRL100106b | 21 | A | Hypothetical protein | |
| pRL100117b | 7 | PG | Putative iron-containing alcohol dehydrogenase, pseudogene | |
| pRL100119b | 34 | B | Putative propionate CoA transferase | |
| pRL100120 | 9 | A | Conserved hypothetical protein | |
| pRL100121 | 6 | C | acsA1 | Acetyl-CoA synthetase (shows 64% identity with AcsA1 (SMc04093) of S. meliloti) |
| pRL100137b | 25 | A | metX | Putative homoserine O-acetyltransferase |
| pRL100148b | 19 | PG | thiC | Putative thiamine biosynthesis protein, pseudogene |
| pRL100154 | 5 | A | Hypothetical protein | |
| pRL100156 | 9 | C | fdxB | Putative ferredoxin |
| pRL100157 | 12 | PG | NifX protein, pseudogene | |
| pRL100158 | 23 | C | nifN | Putative nitrogenase iron-molybdenum cofactor biosynthesis protein |
| pRL100159 | 46 | C | nifE | Putative nitrogenase iron-molybdenum cofactor biosynthesis protein |
| pRL100160 | 94 | C | nifK | Nitrogenase molybdenum-iron protein beta chain |
| pRL100161 | 71 | C | nifD | Nitrogenase molybdenum-iron protein alpha chain |
| pRL100162b | 60 | C | nifH | Putative nitrogenase iron protein |
| pRL100169 | 6 | A | rhiA | Rhizosphere-expressed protein |
| pRL100192 | 9 | B | Hypothetical protein | |
| pRL100193 | 9 | B | Conserved hypothetical protein | |
| pRL100194 | 9 | A | Hypothetical protein | |
| pRL100195 | 10 | C | nifB | FeMo cofactor biosynthesis protein |
| pRL100197 | 17 | C | fixX | Ferredoxin-like protein |
| pRL100198 | 24 | C | fixC | Nitrogen fixation protein |
| pRL100199 | 28 | C | fixB | Electron transfer protein |
| pRL100200 | 120 | C | fixA | Electron transfer protein |
| pRL100201b | 26 | A | Conserved hypothetical protein | |
| pRL100205 | 27 | C | fixN | Putative transmembrane cytochrome oxidase subunit |
| pRL100206 | 45 | C | fixO | Putative cytochrome oxidase subunit |
| pRL100206A | 24 | C | fixQ | Putative component of cytochrome oxidase |
| pRL100207 | 38 | C | fixP | Putative cytochrome oxidase subunit |
| pRL100210A | 7 | C | fixS | Putative component of cation pump |
| pRL100444b | 103 | B | Putative oxidoreductase | |
| pRL110199b | 62 | A | Conserved hypothetical protein | |
| pRL120027b | 15 | A | Putative aldolase | |
| pRL120227b | 10 | C | Putative 4-hydroxybutyrate dehydrogenase | |
| pRL120254 | 5 | A | Conserved hypothetical protein | |
| pRL120632b | 31 | C | Putative dehydrogenase | |
| pRL120644 | 7 | A | Conserved hypothetical protein (originally annotated as pRL120645) | |
| pRL90016 | 32 | C | fixP | Putative cytochrome oxidase component cytochrome c protein |
| pRL90016A | 27 | C | fixQ | Putative component of cytochrome oxidase |
| pRL90017 | 21 | C | fixO | Putative transmembrane cytochrome c oxidase protein |
| pRL90018 | 11 | C | fixN | Putative cytochrome oxidase transmembrane component |
| pRL90021b | 14 | C | azuP | Putative pseudoazurin protein |
| pRL90031 | 10 | B | Conserved hypothetical protein | |
| pRL90039 | 6 | B | Conserved hypothetical protein | |
| pRL90046 | 5 | A | Hypothetical protein | |
| pRL90047b | 14 | B | Putative universal stress protein | |
| pRL90194 | 5 | C | Putative UPF0261 domain protein | |
| pRL90322 | 18 | PG | Hypothetical protein, pseudogene | |
| RL0018b | 11 | C | Putative transmembrane protein | |
| RL0054b | 9 | C | glcB | Putative malate synthase |
| RL0102 | 7 | C | gabT | Putative 4-aminobutyrate aminotransferase |
| RL0540 | 7 | C | Putative two-component sensor histidine kinase transcriptional regulatory protein | |
| RL0680b | 35 | B | secDF2 | Putative transmembrane export SecD/F family protein |
| RL0702 | 7 | C | fliM | Putative flagellum motor switch protein |
| RL0913b | 11 | C | Putative PRC family protein | |
| RL1145 | 12 | A | Putative conjugated bile salt hydrolase | |
| RL1148b | 33 | A | Hypothetical protein | |
| RL1149 | 6 | B | Putative exported arylsulfatase | |
| RL1150 | 7 | A | Hypothetical protein | |
| RL1151 | 7 | B | Conserved hypothetical protein | |
| RL1173 | 10 | C | Putative transmembrane protein | |
| RL1249 | 5 | A | Hypothetical protein | |
| RL1259 | 6 | B | Conserved hypothetical protein | |
| RL1423 | 6 | C | Putative transmembrane protein | |
| RL1606 | 5 | A | Putative esterase (beta-lactamase family) | |
| RL1694b | 22 | B | Putative aldo-keto reductase | |
| RL1860 | 6 | B | phhA | Putative phenylalanine-4-hydroxylase |
| RL1868 | 9 | B | Putative universal stress-related protein | |
| RL1870 | 7 | A | dksA | Putative DNAK suppressor protein |
| RL1871 | 5 | B | Putative transmembrane cation ATPase transporter | |
| RL1873 | 5 | B | Putative pyridoxine oxidase protein | |
| RL1876b | 5 | B | adh | Putative alcohol dehydrogenase |
| RL1877 | 5 | B | Putative protease | |
| RL1878b | 13 | B | Putative peptidoglycan binding protein | |
| RL1883b | 56 | A | hspF | Putative small heat shock protein |
| RL2271b | 30 | A | Conserved hypothetical protein | |
| RL2272b | 19 | B | Conserved hypothetical protein | |
| RL2323b | 6 | C | Putative GFO/IDH/MocA dehydrogenase | |
| RL2561 | 7 | C | Putative transmembrane efflux/MDR protein | |
| RL3016b | 137 | B | pcaH | Protocatechuate 3,4-dioxygenase beta chain (3,4-pcd) |
| RL3130b | 14 | A | Putative phosphatase protein | |
| RL3274 | 5 | C | prkA | Putative PrkA protein kinase |
| RL3366b | 14 | B | Putative flavoprotein | |
| RL3495 | 5 | B | Conserved hypothetical protein | |
| RL3533 | 5 | C | gbcX | Putative solute-binding component of ABC transporter, QAT family |
| RL3682b | 9 | C | Putative transmembrane component of ABC exporter | |
| RL4089b | 21 | C | hspA | Putative heat shock protein A |
| RL4244 | 7 | A | Putative transmembrane component of ABC transporter, CUT1 family | |
| RL4279 | 5 | C | clpB | Putative chaperone ClpB (heat shock protein) |
| RL4530 | 6 | C | Putative orphan ATP-binding component of ABC transporter, family unclassified |
a
Genes are listed in order; the first gene in a putative operon is in boldface.
b
A strain with this gene mutated was isolated and tested on peas for nitrogen fixation.
c
Found (≥50% amino acid identity) as follows: A, unique to R. leguminosarum bv. viciae 3841; B, in one other species; C, in three or more species. PG, pseudogene (excluded from search). The species investigated were R. etli CFN42, S. meliloti 1021, B. japonicum USDA 110, A. tumefaciens C58, M. loti MAFF303099, and S. medicae WSM419.