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. 2006 Sep;72(9):6183–6193. doi: 10.1128/AEM.00947-06

TABLE 2.

Identity and expression of genes discussed in the textaa

Gene ID Gene name Gene product Expression ratiob
Signal intensityc
BEN BPH ETB PYR BEN BPH ETB
ro00423 Cytochrome P450 CYP254 0.96 3.3 4.4 390 270 1,300 2,200
ro00477d Type I extradiol dioxygenase 0.71 0.70 0.63 260 160 230 150
ro00515d Probable 4-hydroxy-2-oxovalerate aldolase 1.3 2.1 3.4 70 72 210 220
ro00516d Acetaldehyde dehydrogenase 1.2 1.0 1.4 86 100 90 130
ro00517d Probable 2-oxopent-4-enoate hydratase 0.87 1.6 1.3 180 12 350 240
ro00519d ohpC 2-Hydroxy-6-ketonona-2,4-dienedoic acid hydrolase 0.84 0.95 0.87 1,000 590 1,100 970
ro00536d Type I extradiol dioxygenase 1.1 1.2 2.4 16 23 20 33
ro01333d pcaJ1 3-Oxoacid CoA-transferase 5.8 3.2 1.1 71 400 270 75
ro01334d pcaI Probable 3-oxoacid CoA-transferase alpha subunit 4.1 3.5 4.5 110 360 440 510
ro01336 pcaG Protocatechuate dioxygenase alpha subunit 2.9 1.3 0.38 440 1,100 610 180
ro01338d pcaL 3-Oxoadipate enol-lactone hydrolase/ 4-carboxymuconolactone decarboxylase 3.2 2.4 1.3 140 410 380 160
ro01509 Possible NADPH: quinone reductase 0.67 11 10 1,400 470 13,000 20,000
ro02371 catC Muconolactone delta-isomerase 38 43 2.2 27 960 1,300 81
ro02372 catB Muconate cycloisomerase 40 23 1.7 62 2,200 1,800 90
ro02373 catA1 Catechol 1,2-dioxygenase 17 12 1.5 330 5,100 4,600 420
ro02374d catR Transcriptional regulator, IclR family 0.96 0.62 0.51 12,000 7,400 6,500 7,800
ro02381d benR Transcriptional regulator, AraC family 2.1 1.5 0.19 82 140 150 39
ro02383 Cytochrome P450, reductase 2.0 5.2 5.5 61 99 350 380
ro02384 benA Benzoate 1,2-dioxygenase alpha subunit 33 14 1.1 270 9,100 5,000 190
ro02385d benB Benzoate 1,2-dioxygenase beta subunit 3.3 1.2 0.52 3,800 8,200 5,100 2,300
ro02386 benC Benzoate 1,2-dioxygenase reductase subunit 32 10 0.70 470 13,000 6,600 260
ro02387 benD cis-1,6-Dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase 8.1 4.7 0.68 250 2,100 1,400 140
ro02388d benK Benzoate transporter, MFS superfamily 6.9 5.0 2.2 440 2,700 2,400 990
ro02488d Type I extradiol dioxygenase 1.1 1.2 2.4 32 32 40 84
ro02511 Cytochrome P450 CYP147 1.1 2.2 4.1 110 110 280 470
ro03865d Type I extradiol dioxygenase 1.0 1.0 1.4 120 110 140 160
ro03866d Acetaldehyde dehydrogenase 0.82 1.4 1.2 210 150 310 250
ro03867d Possible 4-hydroxy-2-oxovalerate aldolase 0.91 0.72 0.63 3,300 2,100 2,300 2,800
ro03881d 2-Oxopent-4-enoate hydratase 1.2 1.0 1.1 46 48 47 50
ro03975d Type I extradiol dioxygenase 1.3 0.85 1.3 450 520 400 650
ro04533d Hydratase 0.79 0.94 0.97 920 580 880 1,100
ro04534d Acetaldehyde dehydrogenase 1.1 2.2 2.7 66 63 150 200
ro04535d 4-Hydroxy-2-oxovalerate aldolase 0.95 0.86 0.84 41 29 37 36
ro04540d Alpha/beta-fold C-C bond hydrolase 1.2 2.7 2.8 58 66 170 170
ro04541 Type I extradiol dioxygenase 0.92 17 16 52 33 850 1,100
ro04667 or ro02355e Cytochrome P450 CYP125 0.79 3.5 4.9 290 170 1,200 1,700
ro04905d Type I extradiol dioxygenase 0.79 1.1 1.0 2,200 1,200 3,000 2,800
ro05797d Alpha/beta-fold C-C bond hydrolase 1.2 1.0 1.1 350 340 390 480
ro05799d 2-Keto-4-pentenoate hydratase 1.1 0.88 0.91 830 660 910 820
ro05800 Acetaldehyde dehydrogenase (acetylating) 2.1 1.6 1.0 660 1,100 1,000 810
ro05803d Type I extradiol dioxygenase 1.1 0.70 0.71 6,200 4,600 4,600 6,900
ro08044 or ro10146e etbD1/etbD2 2-Hydroxy-6-oxohepta-2,4-dienoate hydrolase 0.54 42 36 130 36 6,200 6,200
ro08051 or ro10121e bphT1/bphT2 Response regulator, two-component system 0.68 1.4 1.4 1,200 570 1,600 2,200
ro08052 bphS1 Sensor kinase, two-component system 0.85 25 24 720 280 16,000 22,000
ro08054 bphB1 cis-2,3-Dihydrobiphenyl-2,3-diol dehydrogenase 0.16 29 14 2100 54 32,000 32,000
ro08055 bphC1 2,3-Dihydroxybiphenyl 1,2-dioxygenase 0.15 21 8.7 2700 51 29,000 29,000
ro08057 bphAd Biphenyl 2,3-dioxygenase, reductase 0.34 33 21 750 51 18,000 21,000
ro08058 bphAc Biphenyl 2,3-dioxygenase, ferredoxin component 0.16 37 21 1400 49 37,000 39,000
ro08059 bphAb Biphenyl 2,3-dioxygenase beta subunit 0.17 22 14 2,100 70 39,000 35,000
ro08060 bphAa Biphenyl 2,3-dioxygenase alpha subunit 0.36 43 43 1,200 300 41,000 39,000
ro08079d Type I extradiol dioxygenase 0.90 0.88 0.76 980 780 870 980
ro08081d Alpha/beta-fold C-C bond hydrolase 1.0 1.3 1.6 110 99 180 160
ro08083 bphF3 4-Hydroxy-2-oxovalerate aldolase 0.72 13 16 180 76 2,400 3,900
ro08084 bphG3 Acetaldehyde dehydrogenase 1.3 12 11 180 37 2,500 3,100
ro08085d bphE3 2-Oxopent-4-enoate hydratase 0.98 3.8 3.7 340 260 1,500 1,400
ro09005d Type I extradiol dioxygenase 0.91 0.64 1.1 90 71 76 82
ro09014d Alpha/beta-fold C-C bond hydrolase 0.79 1.3 1.7 310 190 430 600
ro09018d bphG1 Acetaldehyde dehydrogenase 1.1 1.2 2.0 37 41 70 33
ro09019d bphF1 4-Hydroxy-2-oxovalerate aldolase 0.88 0.59 0.49 1,600 1,000 1,100 860
ro09021d bphE1 2-Hydroxypenta-2,4-dienoate hydratase 0.84 1.1 1.3 460 310 610 570
ro10112d bphF4 4-Hydroxy-2-oxovalerate aldolase 0.81 1.5 1.8 590 320 870 1,400
ro10116 bphG4 Acetaldehyde dehydrogenase 0.79 25 22 170 61 4,800 5,100
ro10117d bphE4 2-Hydroxypenta-2,4-dienoate hydratase 1.2 1.3 1.1 3,300 2,900 3,500 4,900
ro10121 or ro08051e bphT2/bphT1 Response regulator, two-component system 0.79 1.6 1.7 990 600 1,600 1,900
ro10122 or ro08052e bphS2/bphS1 Sensor kinase, two-component system 0.96 18 19 630 370 12,000 15,000
ro10125 etbAd Ferredoxin reductase 1.1 15 12 1,500 490 21,000 29,000
ro10126 bphB2 cis-3-Phenylcyclohexa-3,5-diene-1,2-diol dehydrogenase 0.47 13 6.4 2,700 100 30,000 31,000
ro10135d etbC 2,3-Dihydroxybiphenyl 1,2-dioxygenase 0.20 79 40 1,500 100 47,000 35,000
ro10136 bphD1 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase 0.71 44 24 980 110 37,000 32,000
ro10137 bphE2 2-Oxopent-4-enoate hydratase 0.89 38 19 1,400 240 35,000 33,000
ro10138 bphF2 4-Hydroxy-2-oxovalerate aldolase 1.1 41 28 260 70 12,000 10,000
ro10143 or ro10133e etbAa2/etbAa1 Ethylbenzene dioxygenase alpha subunit 0.31 68 79 2,000 210 45,000 46,000
ro10144 or ro10134e etbAb2/etbAa1 Ethylbenzene dioxygenase beta subunit 0.29 140 75 670 57 52,000 41,000
ro10145 etbAc Ethylbenzene dioxygenase, ferredoxin component 0.27 58 39 890 99 26,000 32,000
ro10303 Probable ferredoxin FdxD 0.88 5.3 8.5 84 54 520 780
ro10315d Type I extradiol dioxygenase 0.92 1.1 1.6 560 410 590 1,100
a

Expression of all genes differed significantly for the four substrates tested, unless otherwise noted.

b

Average normalized expression ratio (treatment/control; n = 3).

c

Uncorrected average probe signal intensity (n = 3).

d

Expression did not differ significantly among substrates (P ≥ 0.05 for ANOVA).

e

Probe lacks specificity due to high similarity of genes.