Table 1 |
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Rhizosphere up-regulated (rup) genes |
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Fold change |
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|
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|
Locus - TIGR annotation |
Log* |
St.† |
Sand‡ |
Combined§ |
|
|
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Cytochrome biosynthesis |
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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 |
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|
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 |
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|
PP3786 - aminotransferase |
5.3 |
4.3 |
2.1 |
- |
|
Chemotaxis and motility |
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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 |
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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 |
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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 |
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|
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 |
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|
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 |
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|
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 |
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|
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 |
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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 |
|
|
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Proteins with predicted general function and hypothetical proteins not mentioned in the text are not included (Additional data file 1). Although the P. putida KT2440 genome is sequenced and annotated [49], the locus functions listed in this table were one by one re-confirmed by comparing the amino acid sequences with those in the databases. The complete list of rup genes (genes with fold induction >2, P value < 0.05, and average signal-to noise A >64) is available in Additional data files 1-3. *Control with LB log cells; †control with LB stationary phase cells; and ‡control with sessile cells from microcosm without plant. §Genes passing the Bonferroni cutoff after a combined analysis of the nine microarrays altogether. A dash is used to mark those rup genes not passing the Bonferroni cutoff, although they did pass the Benjamini and Hochberg adjustment. LS, low signal (below cutoff). |
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Matilla et al. Genome Biology 2007 8:R179 doi:10.1186/gb-2007-8-9-r179 |
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