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