Table 1.
Expression of sulfur metabolism genes by Ruegeria pomeroyi in the three-member model system
| Module | Locus tag | Gene name | Function | Reference | Differential expression results | |
|---|---|---|---|---|---|---|
| Fold difference | Adjusted p value | |||||
| DMSP utilization | ||||||
| Regulation | SPO1912 | dmdR | Transcriptional regulator | [52] | 6.2 | < 0.001 |
| Demethylation pathway | SPO1913 | dmdA | Dimethylsulfoniopropionate demethylase | [62] | 7.8 | < 0.001 |
| SPO2045 | dmdB-1 | 3-Methylmercaptopropionyl-CoA ligase | [63] | 0.7 | 0.025 | |
| SPO0677 | dmdB-2 | 3-Methylmercaptopropionyl-CoA ligase | [64] | −1.2 | 0.404 | |
| SPO3804 | dmdC | 3-Methylmercaptopropionyl-CoA dehydrogenase | [63] | −1.2 | 0.747 | |
| SPO3805 | dmdD | Methylthioacryloyl-CoA hydratase | [63] | −1.2 | 0.715 | |
| Methanethiol to methionine | SPOA0318 | megL | Methionine gamma-lyase | [65] | 1.3 | 0.178 |
| Methanethiol oxidation | SPOA0269 | mtoX | Methanethiol oxidase | [45] | 15.7 | < 0.001 |
| Cleavage pathway | SPO0453 | dddW | DMSP lyase | [66] | 25.7 | < 0.001 |
| SPO1703 | dddD | DMSP lyase | [67] | −1.6 | 0.091 | |
| SPO2299 | dddP | DMSP lyase | [68] | 1.7 | 0.312 | |
| SPO1596 | dddQ | DMSP lyase | [69] | 1.1 | 0.724 | |
| SPO2934 | prpE | Acrylate-CoA ligase | [63] | 2.1 | 0.225 | |
| SPO1914 | acuI | Acryloyl-CoA reductase | [47] | 15.0 | < 0.001 | |
| N-acetyltaurine, taurine and isethionate utilization | ||||||
| Regulation | SPO0659 | naaR | Transcriptional regulator | [70] | 3.0 | 0.008 |
| N-acetyltaurine transport | SPO0660 | naaA | N-acetyltaurine ABC transporter, periplasmic | [30] | 1.8 | 0.118 |
| SPO0661 | naaB | N-acetyltaurine ABC transporter, permease | [30] | 1.0 | 0.920 | |
| SPO0662 | naaB' | N-acetyltaurine ABC transporter, permease | [30] | 1.2 | 0.700 | |
| SPO0663 | naaC | N-acetyltaurine ABC transporter, ATP-binding | [30] | 1.5 | 0.371 | |
| SPO0664 | naaC' | N-acetyltaurine ABC transporter, ATP-binding | [30] | 1.9 | 0.108 | |
| N-acetyltaurine metabolism | SPO0657 | naaT | Metallochaperone, putative | [30] | −1.1 | 0.878 |
| SPO0658 | naaS | N-acetyltaurine amidohydrolase | [30] | 1.6 | 0.239 | |
| Taurine transport | SPO0674 | tauA | Taurine ABC transporter, periplasmic | [31] | 1.4 | 0.423 |
| SPO0675 | tauB | Taurine ABC transporter, ATP-binding | [31] | 1.8 | 0.172 | |
| SPO0676 | tauC | Taurine ABC transporter, permease | [31] | 1.3 | 0.554 | |
| Regulation | SPO2355 | iseR | Transcriptional regulator | [32] | 1.8 | 0.056 |
| Isethionate transport | SPO2356 | iseM | Isethionate TRAP transporter, DctM | [32] | 12.5 | < 0.001 |
| SPO2357 | iseL | Isethionate TRAP transporter, small permease | [32] | 6.2 | < 0.001 | |
| SPO2358 | iseK | Isethionate TRAP transporter, periplasmic | [32] | 18.4 | < 0.001 | |
| Isethionate metabolism | SPO2359 | iseJ | Isethionate dehydrogenase | [32] | 20.8 | < 0.001 |
| Regulation | SPO3562 | tauR | Transcriptional regulator | [31] | 5.7 | < 0.001 |
| Taurine/N-acetyltaurine metabolism | SPO0673 | tpa | Taurine-pyruvate aminotransferase | [31] | 4.6 | < 0.001 |
| Taurine/N-acetylaurine/isethionate metabolism | SPO3561 | xsc | Sulfoacetaldehyde acetyltransferase | [31] | 11.7 | < 0.001 |
| SPO3560 | pta | Phosphate acetyltransferase | [31] | 12.0 | < 0.001 | |
| DHPS utilization | ||||||
| Regulation | SPO0590 | hpsR | Transcriptional regulator | [28] | −6.3 | < 0.001 |
| DHPS transport | SPO0591 | hpsK | Dihydroxypropanesulfonate (DHPS) transporter | [28] | −67.7 | < 0.001 |
| SPO0592 | hpsL | Dihydroxypropanesulfonate (DHPS) transporter | [28] | −28.5 | < 0.001 | |
| SPO0593 | hpsM | Dihydroxypropanesulfonate (DHPS) transporter | [28] | −17.5 | < 0.001 | |
| DHPS metabolism | SPO0594 | hpsN | Dihydroxypropanesulfonate-3-dehydrogenase | [28] | −28.7 | < 0.001 |
| SPO0595 | hpsO | R- or S-DHPS-2-dehydrogenase | [28] | −28.9 | < 0.001 | |
| SPO0596 | hpsP | S- or R-DHPS-2-dehydrogenase | [28] | −40.2 | < 0.001 | |
| SPO0598 | slcD | Sulfolactate dehydrogenase | [28] | −21.4 | < 0.001 | |
| Regulation | SPOA0159 | cuyR | Transcriptional regulator | [28] | 1.2 | 0.70 |
| DHPS metabolism | SPOA0158 | cuyA | L-cysteate sulfolyase | [28] | −3.0 | 0.010 |
| Cysteate utilization | ||||||
| Cysteate metabolism | SPO2657 | cuyA-2 | l-Cysteate sulfolyase | This study | −27.8 | < 0.001 |
| Cysteate transport | SPO2658 | ABC transporter, periplasmic | This study | −8.6 | < 0.001 | |
| SPO2659 | ABC transporter, permease | This study | −6.3 | < 0.001 | ||
| SPO2660 | ABC transporter, permease | This study | −3.1 | 0.003 | ||
| SPO2661 | ABC transporter, ATP-binding | This study | −5.0 | < 0.001 | ||
| Choline-O-sulfate utilization | ||||||
| Choline-O-sulfate metabolism | SPO1083 | betC | Choline sulfatase | [35] | 2.6 | 0.015 |
| Choline metabolism | SPO1088 | betA | Choline dehydrogenase | [35] | −2.7 | 0.039 |
| SPO0084 | betB | Betaine-aldehyde dehydrogenase | [35] | −1.9 | 0.065 | |
| SPO3398 | Glycine betaine:homocysteine methyltransferase | [35] | 4.4 | < 0.001 | ||
| SPO3400 | Dimethylglycine dehydrogenase | [35] | 6.0 | < 0.001 | ||
| SPO3396 | Sarcosine dehydrogenase | [35] | 1.7 | 0.008 | ||
Positive fold differences indicate genes with higher relative expression during the dinoflagellate-dominated phase; negative fold differences represent genes with higher relative expression during the diatom-dominated phase. Numbers in bold indicate statistical significance. Experimental verification of gene function in R. pomeroyi is indicated in the Reference column.