TABLE 5.
Genes associated with PGP traits in E. roggenkampii ED5 genome.
| PGP activities description | Gene name | Gene annotation | E.C. number | Chromosome location |
| Nitrogen metabolism | ||||
| Nitrogen fixation | iscU | Nitrogen fixation protein nifu and related proteins | – | 3496630–3497016 |
| Cyanate hydrolysis | – | Cyanate transport protein CynX | – | 2160759–2161919 |
| Nitrosative stress | norR | Anaerobic nitric oxide reductase transcription regulator NorR | – | 3662018–3663532 |
| norV | Anaerobic nitric oxide reductase flavorubredoxin | – | 3663720–3665162 | |
| Ammonia assimilation | gltB | Glutamate synthase (NADPH/NADH) large chain | 1.4.1.13 1.4.1.14 | 4179778–4184238 |
| gltD | Glutamate synthase (NADPH/NADH) small chain | 1.4.1.13 1.4.1.14 | 4184248–4185666 | |
| ACC deaminase | dcyD | 1-Aminocyclopropane-1-carboxylate deaminase | 4.4.1.15 | 2932253–2933239 |
| Siderophore | ||||
| Siderophore enterobactin | fes | Enterochelin esterase and related enzymes | 4687024–4688199 | |
| entF | Enterobactin synthase subunit F | 6.3.2.14 | 1205182–1209039 | |
| entS | Enterobactin exporter entS | – | 1212020–1213258 | |
| fepA | Ferric enterobactin receptor | – | 1201369–1203618 | |
| – | Iron-enterobactin transporter ATP-binding protein | 3.6.3.34 | 1209127–1209921 | |
| – | Ferric enterobactin transport system permease protein FepD | – | 1210907–1211911 | |
| entD | Enterobactin synthase | 6.3.2.14 2.7.8 | 1200642–1201283 | |
| Plant hormones | ||||
| IAA production | trpCF | Bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase | 4.1.1.48 5.3.1.24 | 2658686–2660044 |
| trpS | Tryptophanyl-trna synthetase | 6.1.1.2 | 555353–556354 | |
| trpE | Anthranilate synthase component | 4.1.3.27 | 2655414–2657087 | |
| trpB | Tryptophan synthase subunit beta | 4.2.1.20 | 2660055–2661248 | |
| – | Tryptophan synthase subunit alpha | – | 2661248–2662057 | |
| trpGD | Bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase | 4.1.3.27 2.4.2.18 | 2657087–2658682 | |
| Auxin biosynthesis | mdcF | Auxin Efflux Carrier | – | 4290745–4291704 |
| Phosphate metabolism | pit | Low-affinity inorganic phosphate transporter | 4407682–4409181 | |
| pstS | Phosphate ABC transporter substrate-binding protein | – | 4682299–4683339 | |
| pstC | Phosphate transporter permease subunit pstC | – | 4683468–4684427 | |
| pstA | Phosphate transporter permease subunit ptsA | – | 4684427–4685317 | |
| pstB | Phosphate ABC transporter ATP-binding protein | 3.6.3.27 | 4685365–4686138 | |
| phoU | Phosphate-specific transport system accessory protein phoU | – | 4686165–4686890 | |
| ugpB | Sn-glycerol-3-phosphate ABC transporter substrate-binding protein | – | 299782–301074 | |
| – | Glycerol-3-phosphate transporter permease | – | 301181–302068 | |
| ugpE | Glycerol-3-phosphate transporter membrane protein | – | 302065–302910 | |
| phoA | Alkaline phosphatase | 3.1.3.1 | 978756–980171 | |
| phoE | Phosphoporin protein E | – | 912190–913242 | |
| phoB | Two-component system, ompr family, phosphate regulon response regulator phoB | – | 991972–992661 | |
| phoR | Two-component system, ompr family, phosphate regulon sensor histidine kinase phoR | 2.7.13.3 | 992683–993978 | |
| phoH | Phosphate starvation-inducible protein phoh and related proteins | – | 1276067–1277113 | |
| Biofilm formation | tomB | Biofilm formation regulator YbaJ | – | 1073128–1073502 |
| luxS | S-ribosylhomocysteinase | 4.4.1.21 | 3643176–3643691 | |
| efp | Elongation factor P | – | 412037–412603 | |
| flgN | Flagella synthesis chaperone protein FlgN | – | 1766271–1766666 | |
| flgM | Flagellar biosynthesis protein FlgM | – | 1766701–1766994 | |
| flgA | Flagella basal body P-ring formation protein FlgA | – | 1767088–1767747 | |
| flgB | Flagellar biosynthesis protein FlgB | – | 1767905–1768321 | |
| flgC | Flagellar basal body rod protein FlgC | – | 1768325–1768729 | |
| flgD | Flagellar basal body rod modification protein | – | 1768741–1769451 | |
| flgE | Flagellar hook protein FlgE | – | 1769478–1770686 | |
| flgF | Flagellar basal body rod protein FlgF | – | 1770707–1771462 | |
| flgG | Flagellar basal body rod protein FlgG | – | 1771474–1772256 | |
| flgH | Flagellar basal body L-ring protein | – | 1772305–1773012 | |
| flgI | Flagellar basal body P-ring protein | – | 1773025–1774122 | |
| flgJ | Flagellar rod assembly protein/muramidase FlgJ | – | 1774122–1775075 | |
| flgK | Flagellar hook-associated protein FlgK | – | 1775151–1776791 | |
| flgL | Flagellar hook-associated protein FlgL | – | 1776806–1777759 | |
| motB | Flagellar motor protein MotB | – | 2900550–2901479 | |
| motA | Flagellar motor protein MotA | – | 2901476–2902363 | |
| sacA | Glycosyl hydrolase family 32 | 3.2.1.26 | 2381644–2383050 | |
| hfq | RNA-binding protein Hfq | – | 437637–437948 | |
| Sulfur assimilation | cysZ | Sulfate transporter CysZ | – | 3374729–3375490 |
| cysK | Cysteine synthase A | 2.5.1.47 | 1049190–1050236 | |
| cysM | Cysteine synthase B | 2.5.1.47 | 3380409–3381320 | |
| cysA | Sulfate ABC transporter ATP-binding protein | 3.6.3.25 | 3381439–3382533 | |
| cysW | Sulfate/thiosulfate transporter permease subunit | – | 3382523–3383398 | |
| cysU | Sulfate/thiosulfate transporter subunit | – | 3383398–3384231 | |
| cysP | Sulfate transport system substrate-binding protein | – | 3384231–3385244 | |
| cysC | Adenylylsulfate kinase | 2.7.1.25 | 3708229–3708834 | |
| cysN | Sulfate adenylyltransferase | 2.7.7.4 | 3708834–3710258 | |
| cysD | Sulfate adenylyltransferase small subunit | 2.7.7.4 | 3710268–3711176 | |
| cysH | Phosphoadenosine phosphosulfate reductase | 1.8.4.8 1.8.4.10 | 3713924–3714658 | |
| cysI | Sulfite reductase subunit beta | 1.8.1.2 | 3714674–3716386 | |
| cysJ | Sulfite reductase subunit alpha | 1.8.1.2 | 3716386–3718191 | |
| Sulfur metabolism | cysC | Adenylyl-sulfate kinase | 2.7.1.25 | 3708229–3708834 |
| cysN | Sulfate adenylyltransferase | 2.7.7.4 | 3708834–3710258 | |
| cysD | Sulfate adenylyltransferase small subunit | 2.7.7.4 | 3710268–3711176 | |
| cysG | Siroheme synthase | 2.1.1.107 1.3.1.76 4.99.1.4 | 3711186–3712544 | |
| cysH | Phosphoadenosine phosphosulfate reductase | 1.8.4.8 1.8.4.10 | 3713924–3714658 | |
| cysI | Sulfite reductase subunit beta | 1.8.1.2 | 3714674–3716386 | |
| cysJ | Sulfite reductase subunit alpha | 1.8.1.2 | 3716386–3718191 | |
| cysG | Siroheme synthase | 2.1.1.107 1.3.1.76 4.99.1.4 | 3711186–3712544 | |
| cysE | Serine O-acetyltransferase | 2.3.1.30 | 128779–129600 | |
| cysQ | 3′(2′),5′-bisphosphate nucleotidase CysQ | 3.1.3.7 | 474494–475234 | |
| cysK | Cysteine synthase | 2.5.1.47 | 1049190–1050236 | |
| cysS | Cysteine–tRNA ligase | 6.1.1.16 | 1117790–1119175 | |
| cysZ | Sulfate transporter CysZ | 3374729–3375490 | ||
| cysM | Cysteine synthase B | 2.5.1.47 | 3380409–3381320 | |
| cysA | Sulfate ABC transporter ATP-binding protein | 3.6.3.25 | 3381439–3382533 | |
| cysW | Sulfate/thiosulfate transporter permease subunit | – | 3382523–3383398 | |
| cysU | Sulfate/thiosulfate transporter subunit | – | 3383398–3384231 | |
| cysP | Thiosulfate-binding protein | – | 3384231–3385244 | |
| fdx | Ferredoxin, 2Fe-2S type, ISC system | – | 3493495–3493830 | |
| Antimicrobial peptide | pagP | Antimicrobial peptide resistance and lipid A acylation protein PagP | 2.3.1.251 | 1249862–1250437 |
| sapB | Antimicrobial peptide ABC transporter permease SapB | – | 2617964–2618929 | |
| Phenazine | Phenazine biosynthesis-like protein Phenazine biosynthesis-like protein | 2296005–2296793 2296822–2297613 | ||
| Hydrogen peroxide | Robbable hydrogen peroxide-inducible genes activator | 3797368–3798234 | ||
| Synthesis of resistance inducers | ||||
| 2,3-butanediol | alsD | Alpha-acetolactate decarboxylase | 4.1.1.5 | 1173252–1174034 |
| ilvB | Acetolactate synthase catalytic subunit | 2.2.1.6 | 26918–28606 | |
| 2,3-butanediol | ilvH | Acetolactate synthase isozyme 1 small subunit | 2.2.1.6 | 28610–28897 |
| 2,3-butanediol | ilvA | Serine/threonine dehydratase | 4.3.1.19 | 4097837–4098826 |
| ilvC | Ketol-acid reductoisomerase | 1.1.1.86 | 4526147–4527622 | |
| ilvY | Transcriptional regulator IlvY | – | 4527775–4528665 | |
| ilvD | Dihydroxy-acid dehydratase | 4.2.1.9 | 4530258–4532108 | |
| ilvE | Branched chain amino acid aminotransferase | 2.6.1.42 | 4532169–4533098 | |
| ilvM | Acetolactate synthase | 2.2.1.6 | 4533117–4533380 | |
| Methanethiol | metH | Methionine synthase | 2.1.1.13 | 251182–254865 |
| Isoprene | idi | Isopentenyl-diphosphate Delta-isomerase | 5.3.3.2 | 3832468–3833010 |
| gcpE | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase | 1.17.7.1 1.17.7.3 | 3469721–3470839 | |
| ispE | 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 2728216–2729085 | |
| Hydrolase | – | Chitinase | 3.2.1.14 | 1501603–1504335 |
| – | Chitinase II | 3.2.1.14 | 1857320–1858573 | |
| – | Chitinase | – | 1505114–1506868 | |
| – | Cellulase (glycosyl hydrolase family 5) | – | 558158–559246 | |
| sacA | Glycosyl hydrolase family 32 | 3.2.1.26 | 2381644–2383050 | |
| yxeP | Hydrolase | 3. –.–.– | 2474994–2476115 | |
| ycjT | Hypothetical glycosyl hydrolase | 3.2.1. – | 2602137–2604416 | |
| ribA | GTP cyclohydrolase II | 3.5.4.25 | 2641297–2641887 | |
| folE | GTP cyclohydrolase I FolE | 3.5.4.16 | 3154201–3154869 | |
| gdhA | Glutamate dehydrogenase (NADP+) | 1.4.1.4 | 1866296–1867639 | |
| bglA | 6-phospho-beta-glucosidase | 3.2.1.86 | 38745–40121 | |
| bglF | PTS beta-glucoside transporter subunit EIIBCA | 2.7.1. – | 1677933–1679801 | |
| bglX | Beta-glucosidase | 3.2.1.21 | 1927588–1929963 | |
| malZ | Alpha-glycosidase | 3.2.1.20 | 997326–999143 | |
| xynB | xylan 1,4-beta-xylosidase | 3.2.1.37 | 534506–536116 | |
| amyA | Alpha-amylase | 3.2.1.1 | 165374–167404 | |
| Oxidoreductase | – | Superoxide dismutase | 1.15.1.1 | 1974715–1975296 |
| gpx | Glutathione peroxidase | 1.11.1.9 | 2154552–2155034 | |
| osmC | Peroxiredoxin | – | 2398835–2399263 | |
| DOT5 | Peroxiredoxin | 1.11.1.15 | 3413969–3414439 | |
| Symbiosis-related | bacA | Undecaprenyl-diphosphatase | 3.6.1.27 | 4002393–4003214 |
| gcvT | Glycine cleavage system protein T | 2.1.2.10 | 3849289–3850332 | |
| phnC | Phosphonate ABC transporter ATP-binding protein | 3.6.3.28 | 382433–383221 | |
| tatA | Protein translocase tata | – | 4470409–4470663 | |
| pyrC | Dihydroorotase | 3.5.2.3 | 501711–502844 | |
| pyrC | Dihydroorotase | 3.5.2.3 | 1759073–1760119 | |
| zur | Transcriptional repressor | – | 318300–318812 | |
| Root colonization | ||||
| Chemotaxis | cheZ | Protein phosphatase CheZ | 2884011–2884655 | |
| cheY | Two-component system response regulator | – | 2884666–2885055 | |
| cheB | Chemotaxis response regulator protein-glutamate methylesterase | 3.1.1.61 | 2885073–2886122 | |
| cheR | Chemotaxis protein-glutamate O-methyltransferase | 2.1.1.80 | 2886119–2886985 | |
| cheW | Chemotaxis protein CheW | – | 2897986–2898489 | |
| cheA | Chemotaxis protein CheA | 2.7.13.3 | 2898509–2900539 | |
| cheV | Chemotaxis protein CheV | – | 3237160–3238164 | |
| tsr | Methyl-accepting chemotaxis protein I | – | 609842–611506 | |
| trg | Chemotaxis protein | – | 2243792–2245465 | |
| aer | Chemotaxis protein | – | 478104–2479639 | |
| tar | Methyl-accepting chemotaxis protein II | – | 2888651–2890318 | |
| mcp | Methyl-accepting chemotaxis protein | – | 3943578–3945125 | |
| Motility | flhE | Flagellar protein flhE | – | 2880251–2880643 |
| flhA | Flagellar biosynthesis protein FlhA | – | 2880643–2882721 | |
| flhB | Flagellar biosynthesis protein FlhB | – | 2882714–2883769 | |
| flhC | Transcriptional activator FlhC | – | 2902487–2903065 | |
| flhD | Transcriptional regulator | – | 2903068–2903418 | |
| fliY | Cystine ABC transporter substrate-binding protein | – | 2933346–2934146 | |
| fliZ | Flagellar regulatory protein FliZ | – | 2934233–2934784 | |
| fliA | RNA polymerase sigma factor FliA | – | 2934839–2935558 | |
| fliB | Hypothetical protein | – | 2935687–2936892 | |
| fliC | Flagellin | – | 2936955–2937779 | |
| fliD | Flagellar filament capping protein FliD | – | 2938181–2939605 | |
| fliS | Flagellar protein FliS | – | 2939627–2940031 | |
| fliT | Flagellar biosynthesis protein FliT | – | 2940037–2940411 | |
| fliE | Flagellar hook-basal body complex protein FliE | – | 2942532–2942846 | |
| fliF | Flagellar M-ring protein FliF | – | 2943123–2944754 | |
| fliG | Flagellar motor switch protein FliG | – | 2944747–2945745 | |
| fliH | Flagellar assembly protein H | – | 2945738–2946445 | |
| fliI | Flagellum-specific ATP synthase FliI | 3.6.3.14 | 2946445–2947815 | |
| fliJ | Flagellar protein FliJ | – | 947837–2948280 | |
| fliK | Flagellar hook-length control protein | – | 2948277–2949509 | |
| fliL | Flagellar basal body-associated protein FliL | – | 2949616–2950086 | |
| fliM | Flagellar motor switch protein FliM | – | 2950091–2951095 | |
| fliNY | Flagellar motor switch protein FliN | – | 2951092–2951505 | |
| fliOZ | Flagellar biosynthesis protein FliO | – | 2951508–2951882 | |
| fliP | Flagellar biosynthetic protein FliP | – | 2951882–2952619 | |
| fliQ | Flagellar export apparatus protein FliQ | – | 2952629–2952898 | |
| fliR | Flagellar biosynthesis protein FliR | – | 2952906–2953691 | |
| Adhesive structure | pilT | Type IV pili twitching motility protein PilT | – | 3897208–3898050 |
| pilD | Prepilin peptidase | 3.4.23.43 2.1.1. | 1500548–1501345 | |
| hofC | Type IV pilin biogenesis protein | – | 771182–772183 | |
| Adhesin production | pgaA | Poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA | – | 3922273–3924732 |
| pgaB | Outer membrane N-deacetylase | 3.5.1. – | 3924744–3926678 | |
| pgaC | Poly-beta-1,6 N-acetyl-D-glucosamine synthase | 2.4.1. – | 3926671–3927999 | |
| pgaD | Poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD | – | 3927999–3928430 | |