Table 1.
Summary of transcribed genes predicted to be involved in anaerobic and aerobic benzene degradation. First column lists the transcribed genes (based on the order of genes in Fig. 2C) followed by the locus tag of each gene. The third column shows the taxonomy of the locus tag, based on megablast/blastn hits of the whole contig against the NCBI NT database. The fourth column is the relative contribution of this locus tag to this function (e.g. if two genes with equal expression were assigned to one function, both would have 50% contribution to that function). The last four columns show the function of the most similar protein as identified by blastp (based on the locus’ protein sequence) in the Uniprot database, followed by the accession number of the hit, the identity on protein level and the taxonomy of this entry.
| Gene(s) | Locus tag | Taxon of closest match | Contribution to function (%) | Best blast hit a | Accession number of the blast hit | Identity (%) | Taxonomy of the best blast hit |
|---|---|---|---|---|---|---|---|
| ubiD | Contig-100_0_8b | Unclassified Clostridia | 31 | Putative anaerobic benzene carboxylase abcA | D8WWP8 | 98 | BFc |
| ubiD | Contig-100_751_1 | BF | 21 | Putative 3-polyprenyl-4-hydroxybenzoate carboxy-lyase | D8WWN4 | 99 | BF |
| ubiX | Contig-100_0_6 | Unclassified Clostridia | 12 | Putative UbiX-like carboxylase | D8WWQ0 | 96 | |
| bzlA | Contig-100_0_7 | Unclassified Clostridia | 99 | Putative benzoate-CoA ligase BzlA | D8WWP9 | 96 | BF |
| ppsA | Contig-100_29_8 | BF | 69 | Putative phenylphosphate synthase PpsA | D8WWB1 | 78 | BF |
| ppsB | Contig-100_29_7 | BF | 31 | Putative phosphoenolpyruvate synthase/putative phenylphosphate synthase PpsB | D8WWQ5 | 85 | BF |
| ppcC | Contig-100_0_9 | Unclassified Clostridia | 96 | Putative anaerobic benzene carboxylase AbcD | D8WWP7 | 97 | BF |
| hcrL d | — | — | — | — | — | — | — |
| hcrA | Contig-100_79_3 | BF | 100 | Putative 4-hydroxybenzoyl-CoA reductase alpha subunit | D8WWW1 | 95 | BF |
| bcrA/badF/bzdQ | Contig-100_418_1 | Candidatus Kuenenia stuttgartiensis | 18 | Uncharacterized Protein | Q1Q1I6 | 98 | Candidatus Kuenenia stuttgartiensis |
| bcrA/badF/bzdQ | Contig-100_91_3 | Desulfotomaculum gibsoniae | 48 | CoA-substrate-specific enzyme active | K8E0C9 | 73 | Desulfotomaculum hydrothermalte Lam5 |
| bamB | Contig-100_37_6 | BF | 58 | Putative aldehyde ferredoxin oxidoreductase | D8WWJ6 | 85 | BF |
| bamC | Contig-100_37_5 | BF | 18 | Putative benzoate-degrading protein BamC | D8WWR7 | 82 | BF |
| bamD | Contig-100_37_4 | BF | 11 | Putative benzoate-degrading protein BamD | D8WWD0 | 90 | BF |
| bamE | Contig-100_37_2 | BF | 3 | Heterodisulfide reductase subunit A/putative benzoate-degrading protein BamE | A0A101WHV3/D8WWG6 | 78/80 | Desulfosporosinus sp. BRH_c37/BF |
| bamI | Contig-100_37_3 | BF | 7 | Sulfur carrier protein FdhD | A0A0A2U5N3 | 72 | Desulfosporosinus sp. Tol-M |
| bzdW | Contig-100_24_5 | BF | 100 | Uncharacterized Protein | A0A0F2S5R7 | 78 | Peptococcaceae bacterium BRH_c23 |
| bzdX | Contig-100_24_4 | BF | 100 | Alcohol dehydrogenase | A0A0J1I9E0 | 68 | Peptococcaceae bacterium CEB3 |
| bzdY | Contig-100_24_6 | BF | 100 | Putative 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BzdY | D8WWK5 | 93 | BF |
| pimE | Contig-100_24_2 | BF | 70 | Putative carboxyl transferase | D8WWL0 | 91 | BF |
| pimB | Contig-100_24_7 | BF | 67 | 3-ketoacyl-CoA thiolase | A0A0F2JL78 | 78 | Desulfosporosinus sp. I2 |
| acd | Contig-100_40_1 | Desulfosporosinus youngiae | 100 | Putative acyl-CoA dehydrogenase | D8WWL1 | 84 | BF |
| gcdB | Contig-100_40_5 | Desulfosporosinus youngiae | 100 | Sodium ion-translocating decarboxylase, beta subunit | R4KCY5 | 70 | Desulfotomaculum gibsonia DSM7213 |
| gcdC | Contig-100_40_3 | Desulfosporosinus youngiae | 100 | Acetyl/propionyl-CoA carboxylase, alpha subunit | L0HNW4 | 43 | Aciduliprofundum sp. strain MAR08–339 |
| gcdH | Contig-100_24_1 | BF | 63 | Putative acyl-CoA dehydrogenase | D8WWL1 | 89 | BF |
| paaF e | — | — | — | — | — | — | — |
| paaH f | — | — | — | — | — | — | — |
| pcaF | Contig-100_5019_1 | Unclassified bacteria | 100 | Acetyl-CoA acetyltransferase | A0A0M2U9B1 | 64 | Clostridiales bacterium PH28_bin88 |
| tmoA | contig-100_165_1 | Unclassified Proteobacteria | 41 | Methane/phenol/toluene hydroxylase:YHS | N6YH50 | 96 | Thauera sp. 27 |
| tmoA | contig-100_78_2 | Pseudomonas aeruginosa | 59 | Toluene monooxygenase | A0A0C5J946 | 87 | Rugosibacter aromaticivorans |
| tmoB | contig-100_165_2 | Unclassified Proteobacteria | 82 | Toluene-4-monooxygenase system B | N6XZS7 | 91 | Thauera sp. 63 |
| tmoB | contig-100_78_3 | Pseudomonas aeruginosa | 18 | Toluene monooxygenase | A0A0F2QUZ5 | 81 | Pseudomonas sp. BRH_c35 |
| tmoC | contig-100_78_7 | Pseudomonas aeruginosa | 100 | Oxidoreductase | A0A0F2QUY4 | 75 | Pseudomonas sp. BRH_c35 |
| tmoD | contig-100_165_4 | Unclassified Proteobacteria | 40 | Toluene 4-monooxygenase protein D | Q479D6 | 66 | Dechloromonas aromatica strain RCB |
| tmoD | contig-100_78_5 | Pseudomonas aeruginosa | 60 | Monooxygenase | A0A0C5J8Z1 | 71 | Rugosibacter aromaticivorans |
| tmoE | contig-100_165_5 | Unclassified Proteobacteria | 21 | Toluene 4-monooxygenase protein E | Q479D7 | 91 | Dechloromonas aromatica strain RCB |
| tmoE | contig-100_78_6 | Pseudomonas aeruginosa | 79 | Toluene monooxygenase | A0A0C5J9A6 | 84 | Rugosibacter aromaticivorans |
| tmoF | contig-100_165_3 | Unclassified Proteobacteria | 65 | Rieske (2Fe-2S) region | N6YA68 | 87 | Thauera sp. 27 |
| tmoF | contig-100_78_4 | Pseudomonas aeruginosa | 35 | Toluene-4-monooxygenase system protein C (Belongs to CMGI-2) | Q1LNS9 | 73 | Cupriavidus metallidurans strain ATCC 43123 |
| dmpK | contig-100_3910_1 | Pseudomonas aeruginosa | 100 | Phenol 2-monooxygenase P0 subunit | Q479F5 | 92 | Dechloromonas aromatica strain RCB |
| dmpL | contig-100_2025_1 | Unclassified Rhodocyclaceae | 51 | Phenol 2-monooxygenase P1 subunit | Q479F6 | 77 | Dechloromonas aromatica strain RCB |
| dmpL | contig-100_3910_2 | Dechloromonas aromatica | 49 | Phenol 2-monooxygenase P1 subunit | Q479F6 | 98 | Dechloromonas aromatica strain RCB |
| dmpM | contig-100_2025_2 | Unclassified Rhodocyclaceae | 100 | Phenol 2-monooxygenase P2 subunit | Q479F7 | 97 | Dechloromonas aromatica strain RCB |
| dmpN | contig-100_1081_2 | Unclassified Rhodocyclaceae | 88 | Phenol 2-monooxygenase P3 subunit | Q479F8 | 84 | Dechloromonas aromatica strain RCB |
| dmpO | contig-100_1081_1 | Unclassified Rhodocyclaceae | 89 | Phenol 2-monooxygenase P4 subunit | Q479F9 | 78 | Dechloromonas aromatica strain RCB |
| dmpP | contig-100_2834_2 | Azoarcus toluclasticus{92003} | 100 | Phenol 2-monooxygenase | N6YI82 | 79 | Thauera sp. 63 |
| dmpB | contig-100_1413_1 | Candidatus Kuenenia stuttgartiensis | 71 | Similar to cysteine dioxygenase type I | Q1PVP4 | 94 | Candidatus Kuenenia stuttgartiensis |
| dmpC | contig-100_1829_1 | Candidatus Kuenenia stuttgartiensis | 73 | Similar to succinate-semialdehyde dehydrogenase [NADP + ] | Q1Q6T5 | 91 | Candidatus Kuenenia stuttgartiensis |
| dmpD | contig-100_761_1 | N/A | 100 | 2-hydroxymuconate semialdehyde hydrolase | Q479G6 | 89 | Dechloromonas aromatica strain RCB |
| dmpE | contig-100_761_2 | N/A | 100 | Hydratase/decarboxylase | Q479G7 | 84 | Dechloromonas aromatica strain RCB |
| dmpF | contig-100_4851_2 | Azoarcus sp. BH72 | 74 | Acetaldehyde dehydrogenase | A0A0K1JCI5 | 92 | Azoarcus sp. CIB |
| dmpG | contig-100_6348_1 | Limnobacter sp. MED105 | 69 | 4-hydroxy-2-oxovalerate aldolase | A0A0K1JC70 | 89 | Azoarcus sp. CIB |
| dmpH | contig-100_1640_1 | Thermincola potens | 39 | 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase | K6T593 | 71 | Methanobacterium sp. Maddingley MBC34 |
| dmpH | contig-100_3980_1 | Unclassified bacteria | 42 | 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase | A0A0P6XMJ4 | 69 | Ornatilinea apprima |
| dmpI | contig-100_834_2 | Desulfosporosinus orientis | 71 | Tautomerase | A0A101WBV1 | 72 | Desulfosporosinus sp. BRH_c37 |
aBased on uniprot May 11, 2016.
bContig-100 is the default IDBA_UD output for a kmer-run of 100, the following number is the contig number and last number is the gene number on that contig.
cClostridia bacterium enrichment culture clone BF.
dAll potential assignments overlap with bzlA.
eAll potential assignments overlap with pimE.