Table 1

Rhizosphere up-regulated (rup) genes

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


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).

Matilla et al. Genome Biology 2007 8:R179   doi:10.1186/gb-2007-8-9-r179

Open Data