TABLE 3.

Detection by microarrays of biodegradation genes in genomes of reference microorganisms used in this study

StrainChemical(s)gi no.Gene functionSNRReferences
P. putida PpG7PAH: naphthalene45703Catechol 2,3-dioxygenase13.5 ± 1.5 10, 16, 18, 19, 40
1513791,2-Dihydroxynaphthalene dioxygenase3.2 ± 0.3
151381Salicylate hydroxylase5.4 ± 0.8
151385Naphthalene dioxygenase reductase (Fd)13.4 ± 1.2
151386Naphthalene dioxygenase (Fd)16.5 ± 2.3
151387Naphthalene dioxygenase (large subunit)22.7 ± 2.1
151388Naphthalene dioxygenase (small subunit)6.10 ± 0.5
551908Salicylate hydroxylase5.6 ± 0.6
42354774-Oxalocrotonate decarboxylase19.0 ± 3.1
5070351Dihydroxynaphthalene dehydrogenase7.2 ± 0.9
4837932-Hydroxylchromene2-carboxylate isomerase12.0 ± 2.0
Genes not previously reported in strain PpG7a294344Protocatechuate 3,4-dioxygenase10.9 ± 1.3
294357Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase7.7 ± 0.9
5956754-Oxalocrotonate decarboxylase10.3 ± 1.6
1008926Catechol 1,2-dioxygenase3.9 ± 0.2
1255676Isomerase10.8 ± 1.7
2252625Salicylaldehyde dehydrogenase20.8 ± 1.9
3641341Lactone-specific esterase3.9 ± 0.5
4104766Catechol 2,3-dioxygenase4.9 ± 0.6
42354774-Oxalocrotonate decarboxylase19.0 ± 3.2
11546053Benzoate dioxygenase17.8 ± 2.7
220007122-Hydroxymuconic semialdehyde dehydrogenase5.9 ± 0.5
22000714Acetaldehyde dehydrogenase4.9 ± 0.6
1199116944-Chlorobenzoate CoA ligase5.6 ± 0.4
R. palustris Monoaromatics: benzoate, toluene17302954-Hydroxybenzoyl-CoA reductase HbaB subunit13 ± 1.1 11, 15
17302964-Hydroxybenzoyl-CoA reductase HbaC subunit9.5 ± 0.9
17302974-Hydroxybenzoyl-CoA reductase HbaD subunit14.3 ± 2.0
2190573Cyclohex-1-ene-1-carboxylate CoA ligase24.1 ± 2.1
2190574Cyclohexanecarboxyl-CoA dehydrogenase7.2 ± 0.6
21905762-Hydroxycyclohexanecarboxyl-CoA dehyrogenase15.8 ± 1.8
2190579Benzoyl-CoA reductase subunit18.0 ± 2.2
3165396Benzoyl-CoA reductase subunit9.6 ± 0.9
32430852-Ketocyclohexanecarboxyl-CoA hydrolase8.7 ± 0.9
T. aromatica K172Monoaromatics: benzoate, phenol, toluene3184130Benzylsuccinate synthase gamma subunit11.3 ± 1.0 4, 5, 25, 28, 29
3184131Benzylsuccinate synthase alpha subunit4.0 ± 0.5
3184132Benzylsuccinate synthase beta subunit11.4 ± 1.4
37241666-Oxocyclohex-1-ene-1-carbonyl-CoA hydratase13.4 ± 1.1
3724167Cyclohexa-1,5-diene-1-carbonyl-CoA hydratase10.7 ± 0.8
3724168C subunit of benzoyl-CoA reductase8.9 ± 0.9
3724169B subunit of benzoyl-CoA reductase4.1 ± 0.5
3724170A subunit of benzoyl-CoA reductase9.7 ± 1.3
3724171D subunit of benzoyl-CoA reductase10.3 ± 0.9
3724172Ferredoxin11.3 ± 1.2
9622531BbsA; toluene metabolism3.9 ± 0.5
9622533BbsC; toluene metabolism7.0 ± 0.6
9622534BbsD; toluene metabolism14.4 ± 1.7
9622535BbsE; toluene metabolism9.6 ± 0.8
9622536BbsF; toluene metabolism6.6 ± 0.7
9622538E-phenylitaconyl-CoA hydratase; toluene metabolism15.7 ± 1.3
9622539BbsI; toluene metabolism14.2 ± 1.3
10697118Hypothetical protein; phenol metabolism12.4 ± 1.4
10697119Hypothetical protein; phenol metabolism16.8 ± 1.5
10697121Hypothetical protein; phenol metabolism15.9 ± 1.3
10697123Hypothetical protein; phenol metabolism7.9 ± 0.6
10697124Hypothetical protein; phenol metabolism7.1 ± 0.8
10697125Hypothetical protein; phenol metabolism17.9 ± 1.9
195711782-Oxyglutarate ferredoxin-oxidoreductase beta subunit33.8 ± 2.8
195711792-Oxoglutarate ferredoxin-oxidoreductase alpha subunit7.2 ± 0.6
195711806-Hydroxycylohex-1-ene-1-carbonyl-CoA dehydrogenase4.9 ± 0.4
12667039Putative alcohol dehydrogenase4.2 ± 0.5
12667041Putative alcohol dehydrogenase5.9 ± 0.8
12667042Putative acyl-CoA dehydrogenase15.9 ± 1.4
126670433-Hydroxybenzoate CoA ligase12.9 ± 1.6
12667044Putative hydrolase21.0 ± 2.3
  • a Additional genes not reported but detected in strain PpG7.