Table 1 Rhizosphere up-regulated (rup) genes
From: Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere
Fold change | ||||
|---|---|---|---|---|
Locus - TIGR annotation | Log* | St.† | Sand‡ | Combined§ |
Cytochrome biosynthesis | ||||
PP0109 - membrane protein putative | P > 0.05 | 10.3 | 7.9 | 7.7 |
PP0110 - cyoE-1-protoheme IX farnesyltransferase | 13.2 | 51.5 | 10.2 | - |
PP3183 - SCO1/SenC family protein/cytochrome c | 2.9 | 5 | 3 | - |
Metabolism | ||||
PP0326 - soxG-sarcosine oxidase gamma subunit | 4.8 | 7.9 | 5.8 | 6 |
PP1403 - bglX-periplasmic beta-glucosidase | 2.5 | 2.9 | 2.5 | 2.6 |
PP2694 - aldehyde dehydrogenase family protein | 9 | 8.3 | LS | 10.2 |
PP2847 - ureJ-urease accessory protein UreJ | 22.9 | 29.6 | 21.9 | 24.6 |
PP3281 - phenylacetic acid degradation protein PaaI putative | 6.2 | 8.1 | 8.6 | 7.5 |
PP3352 - arylsulfatase putative | 36.5 | 17.6 | 49.4 | 31.5 |
PP3746 - glcE-glycolate oxidase subunit GlcE | 3.6 | 3.4 | 3.6 | 3.5 |
PP3923 - phosphoglycerate mutase family protein | 4.5 | 4.3 | 2.8 | 3.8 |
PP4588 - nitroreductase family protein | 2.6 | 2.3 | 3.3 | 2.7 |
PP4782 - thiD-phosphomethylpyrimidine kinase | 8.5 | 5.8 | 5.5 | 6.5 |
PP5076 - gltB-glutamate synthase large subunit | 3.4 | 5.5 | 2.1 | - |
PP5197 - ubiF-2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase | 6.9 | 3.5 | 5.8 | 5.2 |
Secondary metabolism | ||||
PP3786 - aminotransferase | 5.3 | 4.3 | 2.1 | - |
Chemotaxis and motility | ||||
PP4331 - conserved hypothetical protein | 4.9 | 5.6 | 4.5 | 5 |
PP4359 - fliL-flagellar protein FliL | 4 | 4.6 | 2.8 | 3.7 |
PP4391 - flgB-flagellar basal-body rod protein FlgB | 3 | 5.2 | 5.2 | 4.3 |
PP4987 - chemotaxis protein putative | 6.4 | 7.3 | 4.4 | 5.9 |
Regulators and sensor proteins | ||||
PP1066 - sigma-54 dependent response regulator | 13 | 41.9 | 10.1 | 17.6 |
PP3640 - transcriptional regulator AraC family | 19.7 | 28.9 | 10.3 | - |
PP4295 - transcriptional regulator TetR family | 8.9 | 8.7 | 6 | 7.7 |
PP4508 - transcriptional regulator AraC family | 3.2 | 2.7 | 3.2 | 3 |
PP0700 - transmembrane sensor putative | 21.9 | 50.4 | 26.2 | 30.7 |
PP2127 - sensor histidine kinase | 31.8 | 14.1 | 17.3 | 19.8 |
PP4959 - sensory box protein/response regulator | 14.7 | 5.1 | 9.4 | 8.9 |
PP5321 - phoR-sensory box histidine kinase PhoR | 10.5 | 9.1 | 9.7 | 9.8 |
Stress adaptation and detoxification | ||||
PP0373 - Pmp3 family protein | 8.1 | 8.4 | 8 | 8.1 |
PP1874 - glutathione peroxidase (GSH_peroxidase) | 4.3 | 7.9 | 5.4 | 5.7 |
PP2376 - cti-esterified fatty acid cis/trans isomerase | 2.4 | 3.6 | 2.3 | - |
PP3535 - ggt-1-gamma-glutamyltransferase | 2.2 | 2.2 | 2.1 | 2.2 |
ABC transporters | ||||
PP0196 - ABC transporter ATP-binding protein putative | 2.4 | 6.7 | 3.7 | - |
PP2669 - outer membrane protein putative | 9.5 | 11.6 | 4.7 | 8 |
PP3210 - ABC transporter pernease protein | 3.4 | 4.3 | 3.9 | 3.8 |
PP3223 - ABC transporter periplasmic binding protein (dipeptide) | 36.9 | 25.4 | 66.4 | 39.5 |
PP3802 - cation ABC transporter ATP-binding protein putative | 13.8 | 20.1 | 5.2 | - |
PP4305 - periplasmic thiosulfate-binding protein | 3.2 | 3.8 | 2.7 | 3.2 |
PP4483 - basic amino acid ABC transporter ATP-binding protein | 3.5 | 4.6 | 2.6 | 3.5 |
Efflux pumps | ||||
PP0670 - transporter bile acid/Na+ symporter family | 5.7 | 11.1 | 3.7 | - |
PP0906 - multidrug efflux RND transporter putative | 3.5 | 8.5 | 2.6 | - |
PP1271 - multidrug efflux MFS transporter putative | 11.3 | 25.6 | 18.1 | 17.4 |
PP2817 - mexC-multidrug efflux RND membrane fusion protein MexC | 3.8 | 6 | 2.2 | - |
PP3583 - RND efflux transporter permease protein | 2.7 | 4.2 | 3 | - |
Other transporters | ||||
PP2385 - azlC-branched-chain amino acid transport protein AzlC | 4 | 4.1 | 3.2 | 3.8 |
PP3132 - polysaccharide transporter putative | 3.1 | 3.9 | 2.6 | 3.2 |
PP5297 - amino acid transporter putative (polyamines) | 6.6 | 8.8 | 6.7 | 7.3 |
DNA replication, recombination and repair | ||||
PP1476 - conserved hypothetical protein | 17.3 | 76.2 | 29 | 33.7 |
PP2565 - helicase putative | 5.5 | 12.6 | 5.1 | - |
PP3966 - ISPpu14 transposase Orf1 | 17.3 | 11.4 | 8.1 | 11.7 |
Others | ||||
PP2076 - hypothetical protein | 4.4 | P > 0.05 | 7.5 | 5.2 |
PP2155 - lolD-lipoprotein releasing system ATP-binding protein | 4 | 2.4 | 5.2 | - |
PP2560 - transport protein HasD putative | 23.3 | 60 | 9 | - |
PP3184 - hypothetical protein | 6.6 | 3.9 | 3.9 | 4.6 |