Table 4.
Functions of key genes detected by RNA-Seq.
| Gene ID | Description | COG no. | Fold changes (log2 Ratio(T/CK)) | KEGG no. | EC no. | Predicted function |
|---|---|---|---|---|---|---|
| Energy production and conversion | ||||||
| Unigene0002417 | phenol degradation protein | COG4313 | 5.217441542 | N/A | N/A | Protein involved in meta-pathway of phenol degradation |
| Unigene0002240 | bacterial Cytochrome Ubiquinol Oxidase family protein | COG1271 | 4.535288588 | K00425 | [EC:1.10.3.-] | establishment of localization |
| Unigene0001576 | phenol 2-monooxygenase | COG2871 | 6.942107699 | N/A | N/A | oxidoreductase activity |
| Unigene0002249 | ATP F0F1 synthase subunit alpha | COG0056 | 2.197069232 | K02111 | [EC:3.6.3.14] | cation-transporting ATPase activity |
| Secondary metabolites biosynthesis, transport and catabolism | ||||||
| Unigene0001131 | catechol 1,2-dioxygenase | COG3485 | 4.94 | K03381 | [EC:1.13.11.1] | catechol-containing compound metabolic process |
| Unigene0000378 | protocatechuate 3,4-dioxygenase | COG3485 | 5.587102309 | K00448 | [EC:1.13.11.3] | cellular aromatic compound metabolic process |
| Unigene0001606 | coenzyme F390 synthetase | COG1541 | −15.2013869 | K01912 | [EC:6.2.1.30] | aromatic compound catabolic process |
| Unigene0000908 | 3-carboxy-cis,cis-muconate cycloisomerase | COG0015 | 4.01609738 | N/A | N/A | catechol-containing compound catabolic process |
| Unigene0000803 | benzoate 12 dioxygenase alpha subunit | COG4638 | −2.879859554 | K05549 | [EC:1.14.12.10] | cellular aromatic compound metabolic process |
| Unigene0001123 | ligand-gated channel protein | COG4774 | −3.646712089 | K02014 | N/A | iron chelate transport |
| Unigene0000980 | acetyl-CoA acetyltransferase | COG0183 | −1.173807482 | K00632 | [EC:2.3.1.16] | Acetyl-CoA acetyltransferase |
| Unigene0000678 | 3-oxoadipate CoA-transferase | COG1788 | 4.294322399 | K01031 | [EC:2.8.3.6] | Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit |
| Unigene0001528 | ABC transporter ATP-binding protein, partial | COG1127 | 1.998799132 | K02065 | N/A | ABC-type transport system involved in resistance to organic solvents |
| Cell wall/membrane/envelope biogenesis; General function prediction only | ||||||
| Unigene0001341 | muconate cycloisomerase | COG4948 | 2.49 | K01856 | [EC:5.5.1.1] | L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily |
| Unigene0000039 | nitroreductase family protein | COG3560 | 4.047415045 | K07078 | N/A | catalytic activity |
| Unigene0000969 | quercetin 2,3-dioxygenase | COG1741 | 3.101493853 | K06911 | N/A | None predicted |
| Posttranslational modification, protein turnover, chaperones | ||||||
| Unigene0000948 | osmotically inducible protein C | COG1765 | 3.54518103 | K07397 | N/A | response to stress |
| Translation, ribosomal structure and biogenesis; Inorganic ion transport and metabolism | ||||||
| Unigene0002513 | 50 S ribosomal protein L10, partial | COG0244 | 2.634136949 | K02864 | N/A | rRNA binding; structural molecule activity |
| Unigene0001303 | 50 S ribosomal protein L2 | COG0090 | 2.264955891 | K02886 | N/A | RNA binding; structural molecule activity |
| Unigene0000305 | 30 S ribosomal protein S13 | COG0099 | 2.001593462 | K02952 | N/A | RNA binding; structural molecule activity |
| Unigene0000065 | 30 S ribosomal protein S3, partial | COG0092 | 2.392017692 | K02982 | N/A | poly(A) RNA binding; structural molecule activity |
| Unigene0000602 | 50 S ribosomal protein L7/L12 | COG0222 | 2.765846319 | K02935 | N/A | None predicted |
| Unigene0000077 | ATPase, partial | COG2217 | 5.545384277 | K01533 | [EC:3.6.3.4] | transition metal ion binding,copper-transporting ATPase activity |
| Unigene0000176 | E1-E2 ATPase | COG2217 | 3.350705804 | K01533 | [EC:3.6.3.4] | intrinsic component of membrane, copper ion transmembrane transport |
| Coenzyme transport and metabolism; Lipid transport and metabolism | ||||||
| Unigene0001464 | lipoyl synthase | COG0320 | −3.178920684 | K03644 | [EC:2.8.1.8] | cation binding; sulfurtransferase activity; |
| Unigene0001096 | 3-oxoacyl-ACP synthase | COG0332 | 1.099154317 | K00648 | [EC:2.3.1.180] | fatty acid metabolic process |
| Unigene0002287 | fatty acid desaturase family protein | COG3239 | 1.092701954 | K00508 | [EC:1.14.19.3] | none predicted |
| Transcription; Defense mechanism; Signal transduction mechanisms | ||||||
| Unigene0001039 | LysR family transcriptional regulator | COG0583 | 2.992016687 | N/A | N/A | cellular macromolecule biosynthetic process |
| Unigene0000056 | TetR family transcriptional regulator | COG1309 | −0.379311349 | NA | NA | nucleic acid binding |
| Unigene0000663 | Predicted transcriptional regulator,BolA superfamily | COG5007 | 3.489769782 | NA | NA | cellular response to stress |
| Unigene0000886 | AraC family transcriptional regulator | COG2207 | −1.360719141 | NA | NA | DNA binding |
| Unigene0001910 | GntR family transcriptional regulator | COG2186 | −0.97172089 | K05799 | NA | transcriptional repressor for pyruvate dehydrogenase complex |
| Unigene0002400 | CRP/FNR family transcriptional regulator | COG0664 | −0.045371841 | K10914 | NA | nucleic acid binding |
| Unigene0000781 | HTH-type transcriptional regulator | COG0789 | 1.939857402 | N/A | N/A | regulation of transcription, DNA-templated |
| Unigene0000852 | serine hydrolase | COG1680 | 1.512798695 | N/A | N/A | response to toxic substance |
| No related COG | ||||||
| Unigene0000054 | phenol hydroxylase | COG0543 | 15.87929606 | K03380 | [EC:1.14.13.17] | 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases |
| Unigene0002446 | metA-pathway of phenol degradation family protein | N/A | 1.177456264 | N/A | N/A | None predicted |
| Unigene0001290 | biofilm synthesis protein | N/A | 4.094059655 | N/A | N/A | transmembrane transporter activity |
| Unigene0001394 | fimbrial protein | N/A | 15.21820373 | N/A | N/A | cell projection |
| Unigene0000307 | membrane protein | N/A | 4.679820328 | N/A | N/A | intrinsic component of membrane |
| Unigene0002168 | Fis family transcriptional regulator | COG1690 | −6.6691460517 | K14415 | NA | gene expression |
| Unigene0000243 | LuxR family transcriptional regulator | NA | −0.652472163 | NA | NA | nucleic acid binding |
N/A: Not available.