Table 1.
Overview of the ORFs and their annotations as identified in contigs 1 and 2 (see Fig. 3) and their differential proteomic expressiona
| ORF | Name | Positionb | Possible function | Closest homologous protein (GenBank accession no./% identity) | Organism | Biological replicate 1 |
Biological replicate 2 |
||
|---|---|---|---|---|---|---|---|---|---|
| Score | L/C [SD(geo)] | Score | L/C [SD(geo)] | ||||||
| Contig 1 | |||||||||
| 1 | 3–515 | Cyclase | HMPREF0005_01234 (EFV81793.1/61) | Achromobacter xylosoxidans C54 | |||||
| 2 | 515–1024 | Acyl dehydratase | Rmet_4072 (YP_586209/75) | Cupriavidus metallidurans CH34 | |||||
| 3 | 1021–1944 | Dihydropicolinate synthase | mll1010 (NP_102694.1/52) | Mesorhizobium loti MAFF303099 | |||||
| 4 | 2154–3113 | Extracytoplasmic solute receptor | Reut_A1674 (YP_295884.1/60) | Ralstonia eutropha JMP134 | |||||
| 5 | ccdE | 3151–3873 | Dienelactone hydrolase | Carboxymethylenebutenolidase (YP_001632346.1/68) | Bordetella petrii DSM 12804 | 134 | 2.26 | 216 | 6.37 |
| 6 | ccdD | 3870–5015 | Chloromuconate cycloisomerase | TfdD (AATPP367/53) | Sphingomonas sp. strain tfd44 | ||||
| 7 | ccdF | 5041–6108 | Maleylacetate reductase | TfdF (NP_990894.1/73) | Achromobacter denitrificans | ND | ND | 52 | 3.08 |
| 8 | 6120–6455 | Hypothetical protein | Bpet3729 (YP_001632340.1/85) | Bordetella petrii DSM 12804 | |||||
| 9 | 6601–6837* | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | FAD-dependent pyridine nucleotide-disulfide oxidoreductase (YP_298914.1/56) | Ralstonia eutropha JMP134 | |||||
| 10 | 6825–7124* | Aromatic ring hydroxylating dioxygenase | AndAc (YP_556337.1/79) | Burkholderia xenovorans LB400 | |||||
| 11 | ccdC | 7229–7975 | Chlorocatechol dioxygenase | Chlorocatechol dioxygenase DccAII (CAF32822.1/50) | Sphingobium herbicidovorans | 182 | 3.98 [1.96] | 203 | 3.98 [1.25] |
| 12 | ccdR | 8108–9076 | LysR family transcriptional regulator | LysR family transcriptional regulator Mpe_A3313 (YP_001022501.1/46) | Methylibium petroleiphilum PM1 | ||||
| 13 | 9585–10547 | Extracytoplasmic solute receptor | Extracytoplasmic solute receptor h16_A1254 (YP_725762.1/45) | Ralstonia eutropha H16 | ND | ND | 161 | 2.49 [1.60] | |
| 14 | IS3 orfA | 10659–10925 | Transposase | Putative transposase (NP_395222.1/68) | Yersinia pestis CO92 | ||||
| 15 | IS3 orfB | 10958–11776 | Transposase | Integrase catalytic region AnaeK_1549 (YP_002133907.1/55) | Anaeromyxobacter sp. strain K | ||||
| 16 | 11905–12399 | IclR-type transcriptional protein | Transcriptional regulator Adeg_1855 (YP_003239789.1/31) | Ammonifex degensii KC4 | |||||
| 17 | istB | 12443–13237 | IstB-like ATP-binding protein transposase | IstB protein 22 (YP_195848.1/100) | Achromobacter xylosoxidans A8 | ||||
| 18 | istA | 13227–14783 | IstA transposase | Transposase IstA protein 59 (YP_195883.1/99) | Achromobacter xylosoxidans A8 | ||||
| 19 | dcaR | 14935–15852 | LysR family transcriptional regulator | LysR-type regulator DanR (ABI20712.1/98) | Delftia sp. strain AN3 | 88 | 3.57 | ND | ND |
| 20 | dcaB | 15885–16892 | Aniline dioxygenase reductase | Aniline dioxygenase reductase DanB (ABI20711.1/99) | Delftia sp. strain AN3 | ||||
| 21 | dcaA2 | 16909–17553 | Aniline dioxygenase small subunit | Small subunit of dioxygenase DanA2 (ABI20710.1/100) | Delftia sp. strain AN3 | ND | ND | 128 | 2.5 |
| 22 | dcaA1 | 17550–18896 | Aniline dioxygenase large subunit | Large subunit of dioxygenase TdnA1 (AA038208.1/99) | Delftia acidovorans | 195 | 4.20 [2.23] | 201 | 2.83 [1.44] |
| 23 | dcaT | 18941–19705 | Glutamine amido transferase | Glutamine amido transferase DanT (ABI20709.1/99) | Delftia sp. strain AN3 | ND | ND | 46 | 1.73 |
| 24 | dcaQ | 19725–21230 | Glutamine synthetase | Putative glutamine synthetase DanQ (ABI20708.1/99) | Delftia sp. strain AN3 | 42 | 2.46 | ND | ND |
| 25 | 21515–21658* | Transposase | IS4 family transposase (BAH90225.1/100) | Uncultured bacterium | |||||
| 26 | IS66 orfA | 21742–22083 | Transposase | Transposase IS3/IS911 (YP_003643234/32) | Thiomonas intermedia K12 | ||||
| 27 | IS66 orfB | 22080–22421 | Transposase | Transposase (BAH90226.1/92) | Uncultured bacterium | ||||
| 28 | IS66 orfC | 22501–24084 | Transposase | Transposase ISThsp3 IS66 family (CAZ88005.1/60) | Thiomonas sp. strain sp3As | ||||
| 29 | tnpA | 24388–27300 | Transposase | Transposase TnpA (YP_001967688.1/100) | Comamonas sp. strain CNB-1 | ||||
| 30 | 27378–27842 | Hypothetical protein | MYG1 (XP_002538853.1/56) | Ricinus communis | |||||
| 31 | 28171–28611 | LysR-type transcriptional regulator | LysR-type transcriptional regulator Dtpsy_1784 (YP_002553241/31) | Acidovorax ebreus TPSY | |||||
| 32 | 28717–29250 | No significant match | |||||||
| 33 | 29568–30488* | Transcriptional regulator | Putative transcriptional regulator THI_0620 (CAZ87353.1/57) | Thiomonas sp. strain sp3As | |||||
| Contig 2 | |||||||||
| 41 | 623–1444 | LuxR family transcriptional regulator | Putative transcriptional regulator (YP_789362.1/26) | Pseudomonas aeruginosa UCBPP-PA14 | |||||
| 42 | libA | 1531–2958 | Linuron hydrolase | Putative amidase (YP_002234156.1/52) | Burkholderia cenocepacia J2315 | 2,706 | 13.00 | 3,033 | 8.73 [2.55] |
a
The last four columns show the genes which were upregulated in Variovorax sp. SRS16 cultures when amended with linuron compared to non-linuron-amended cultures as determined by post-digest ICPL analysis of two biological replicates. For each biological replicate the score is a confidence index of the identification of the peptide sequences with a predicted protein of the Variovorax sp. SRS16 genome. L/C represents the average ratio of the quantity of the protein in the crude protein extract of the linuron-amended culture to the quantity of the protein in the non-linuron-amended culture, calculated as the average of the ratios for each peptide detected for this protein. When L/C is significantly different from 1, the value is marked in boldface. SD(geo), geometrical standard deviation; ND, no data.
b
*, truncated ORF.