Table 1.
Significantly enriched genes for transporter systems, catabolic enzymes, and carbohydrate-active enzymes in the transcriptome of R. pomeroyi DSS-3 in co-culture with M. commoda.
| Locus Tag | Protein ID | Fold Change | Description |
|---|---|---|---|
| Transporters | |||
| SPO0237 | AAV93562.1 | 36.3 | SN-glycerol-3-phosphate ABC transporter, ATP-binding protein ugpC |
| SPO0238 | AAV93563.1 | 25.4 | SN-glycerol-3-phosphate ABC transporter, permease ugpE |
| SPO0239 | AAV93564.1 | 30.3 | SN-glycerol-3-phosphate ABC transporter, permease ugpA |
| SPO0240 | AAV93565.1 | 23.7 | SN-glycerol-3-phosphate ABC transporter, substrate-binding ugpB |
| SPO0674* | AAV93982.1 | 2.2 | taurine ABC transporter, substrate-binding protein tauA |
| SPO0675 | AAV93983.1 | 3.9 | taurine ABC transporter, ATP-binding protein tauB |
| SPO0676* | AAV93984.1 | 2.2 | taurine ABC transporter, permease tauC |
| SPO0703 | AAV94009.1 | 2.6 | oligopeptide ABC transporter, ATP-binding protein |
| SPO0704 | AAV94010.1 | 2.7 | oligopeptide ABC transporter, permease |
| SPO0705 | AAV94011.1 | 2.8 | oligopeptide ABC transporter, permease |
| SPO0706 | AAV94012.1 | 2.8 | oligopeptide ABC transporter, substrate-binding protein |
| SPO0736 | AAV94041.1 | 2 | TRAP dicarboxylate transporter, large permease |
| SPO0780 | AAV94085.1 | 3.6 | phosphonate ABC transporter, ATP-binding protein phnC |
| SPO0781 | AAV94086.1 | 2.5 | phosphonate ABC transporter, substrate-binding protein phnD |
| SPO0782 | AAV94087.1 | 4.1 | phosphonate ABC transporter, permease phnE-1 |
| SPO0783 | AAV94088.1 | 2.8 | phosphonate ABC transporter, permease phnE-2 |
| SPO1548 | AAV94835.1 | 6.5 | TMAO transporter, substrate-binding protein tmoX |
| SPO1549 | AAV94836.1 | 6.8 | TMAO transporter, ATP-binding protein tmoW |
| SPO1550 | AAV94837.1 | 6.4 | TMAO transporter, permease tmoV |
| SPO2356 | AAV95617.1 | 3.7 | isethionate TRAP transporter, large permease iseM |
| SPO2357* | AAV95618.1 | 3.5 | isethionate TRAP transporter, small permease iseL |
| SPO2358* | AAV95619.1 | 9.3 | isethionate TRAP transporter, substrate-binding protein iseK |
| SPO2370 | AAV95630.1 | 3 | sodium:alanine symporter family protein |
| SPO2699 | AAV95944.1 | 5.4 | opine/polyamine ABC transporter, permease |
| SPO2700 | AAV95945.1 | 3.2 | opine/polyamine ABC transporter, permease |
| SPO2701 | AAV95946.1 | 3.1 | opine/polyamine ABC transporter, substrate binding protein |
| SPO2702 | AAV95947.1 | 3.9 | opine/polyamine ABC transporter, ATP-binding protein |
| SPO3186* | AAV96421.1 | 2.5 | DMSP transporter |
| SPO3472 | AAV96698.1 | 2.6 | polyamine ABC transporter, ATP-binding protein |
| SPO3783 | AAV97003.1 | 4.7 | sugar ABC transporter, ATP-binding protein |
| SPO3784 | AAV97004.1 | 4.6 | sugar ABC transporter, ATP-binding protein |
| SPO3785 | AAV97005.1 | 3.9 | sugar ABC transporter, permease |
| SPO3786 | AAV97006.1 | 5.6 | sugar ABC transporter, permease |
| SPO3787 | AAV97007.1 | 5.2 | sugar ABC transporter, substrate-binding protein |
| SPOA0278 | AAV97412.1 | 7.5 | TRAP dicarboxylate transporter, large permease dctM |
| SPOA0279 | AAV97413.1 | 7.8 | TRAP dicarboxylate transporter, small permease dctQ |
| SPOA0280 | AAV97414.1 | 13.3 | TRAP dicarboxylate transporter, substrate-binding protein dctP |
| SPOA0296 | AAV97430.1 | 1.9 | branched-chain amino acid ABC transporter, ATP-binding livF-2 |
| SPOA0297 | AAV97431.1 | 2.1 | branched-chain amino acid ABC transporter, ATP-binding livG |
| SPOA0299 | AAV97433.1 | 2 | branched-chain amino acid ABC transporter, permease |
| SPOA0300 | AAV97434.1 | 2.1 | branched-chain amino acid ABC transporter, substrate binding |
| SPOA0374 | AAV97506.1 | 2.2 | TRAP dicarboxylate transporter, substrate-binding protein dctP |
| SPOA0381 | AAV97513.1 | 2.4 | spermidine/putrescine ABC transporter, substrate-binding protein |
| SPOA0384 | AAV97516.1 | 2.8 | spermidine/putrescine ABC transporter, permease |
| SPO1848 | AAV95127.1 | 2.9 | branched-chain amino acid ABC transporter, ATP binding protein |
| SPO1849 | AAV95128.1 | 2 | branched-chain amino acid ABC transporter, ATP binding protein |
| SPO1850 | AAV95129.1 | 2 | branched-chain amino acid ABC transporter, permease |
| SPO2626* | AAV95871.1 | 3.8 | fumarate, succinate, malate TRAP transporter, dctM |
| SPO2627 | AAV95872.1 | 3.2 | fumarate, succinate, malate TRAP transporter, dctQ |
| SPO2628* | AAV95873.1 | 2.3 | fumarate, succinate, malate TRAP transporter, dctP |
| SPO0608* | AAV93923.1 | 7.1 | glycerol ABC transporter, substrate binding protein |
| SPO0609 | AAV93924.1 | 12.2 | glycerol ABC transporter, ATP binding protein |
| SPO0610 | AAV93925.1 | 8.5 | glycerol ABC transporter, ATP binding protein |
| SPO0611 | AAV93926.1 | 12.6 | glycerol ABC transporter, permease |
| SPO0612 | AAV93927.1 | 10.5 | glycerol ABC transporter, permease |
| SPO1017 | AAV94321.1 | 5.7 | lactic acid ABC transporter ATP-binding protein |
| SPO1018 | AAV94322.1 | 6.6 | lactic acid ABC transporter ATP-binding protein |
| SPO1019 | AAV94323.1 | 4.5 | lactic acid ABC transporter, permease |
| SPO1020 | AAV94324.1 | 3.6 | lactic acid ABC transporter, permease |
| SPO1021 | AAV94325.1 | 3.7 | lactic acid ABC transporter, substrate binding protein |
| SPO1485 | AAV94772.1 | 2.4 | sodium:galactoside symporter family protein |
| SPO1707 | AAV94990.1 | 3.4 | urea ABC transporter, ATP binding protein |
| SPO1707a | AAV97140.1 | 4.6 | urea ABC transporter, ATP binding protein |
| SPO1708 | AAV94991.1 | 5.8 | urea ATP transporter, permease |
| SPO1709 | AAV94992.1 | 7.9 | urea ATP transporter, permease |
| SPO1710 | AAV94993.1 | 6.4 | urea ABC transporter, substrate binding protein |
| SPO1810 | AAV95089.1 | 2.9 | sodium/solute symporter family protein (acetate, putative) |
| SPO1848 | AAV95127.1 | 2.9 | branched-chain amino acid ABC transporter, ATP-binding protein |
| SPO1849 | AAV95128.1 | 2 | branched-chain amino acid ABC transporter, ATP-binding protein |
| SPO1850 | AAV95129.1 | 2 | branched-chain amino acid ABC transporter, permease |
| SPO2658 | AAV95903.1 | 2.3 | possible sulfonate ABC transporter, substrate binding protein |
| SPO2660 | AAV95905.1 | 2.6 | possible sulfonate ABC transporter, permease |
| SPO2661 | AAV95906.1 | 2.1 | possible sulfonate ABC transporter, ATP binding protein |
| SPO2802 | AAV96043.1 | 2.3 | nucleoside ABC transporter, substrate binding protein |
| SPO2803 | AAV96044.1 | 4.1 | nucleoside ABC transporter, ATP binding protein |
| SPO2804 | AAV96045.1 | 3.1 | nucleoside ABC transporter, permease |
| SPO2805 | AAV96046.1 | 3.1 | nucleoside ABC transporter, permease |
| SPO3290 | AAV96517.1 | 2.2 | branched-chain amino acid ABC transporter, ATP-binding protein |
| CAZymes | |||
| SPO1205 | AAV94501.1 | 3.1 | UDP-3-0-acyl N-acetylglucosamine deacetylase (CE11) |
| SPO3555 | AAV96780.1 | 2.1 | transglycosylase (GH23) |
| SPO2587 | AAV95835.1 | 2.4 | penicillin-binding protein 1 A (GT51) |
| SPO0898 | AAV94203.1 | 2.4 | hypothetical protein (GT0) |
| SPO3258 | AAV96493.1 | 2.9 | glycosyl hydrolase (GH25) |
| SPO0190 | AAV93516.1 | 2.1 | choline oxidoreductase (AA3) |
| Organic Sulfur Utilization | |||
| SPO1913 | AAV95190.1 | 2 | dimethylsulfoniopropionate demethylase (dmdA) |
| SPO2045 | AAV95316.1 | 1.9 | 3-methylmercaptopropionyl-CoA ligase (dmdB2) |
| SPO3804 | AAV97018.1 | 12.4 | 3-methylmercaptopropionyl-CoA dehydrogenase (dmdC) |
| SPO3805 | AAV97019.1 | 11.3 | methylthioacryloyl-CoA hydratase (dmdD) |
| SPOA0318 | AAV97450.1 | 28.9 | methionine gamma-lyase (megL) |
| SPO0673 | AAV93981.1 | 2.7 | taurine-pyruvate aminotransferase (tpa) |
| SPO0658 | AAV93966.1 | 2.9 | N-acetyltaurine amidohydrolase (naaS) |
| SPO2359 | AAV95620.1 | 10.3 | isethionate dehydrogenase (iseJ) |
| SPO3560 | AAV96785.1 | 19.3 | phosphate acetyltransferase (pta) |
| SPO3561 | AAV96786.1 | 27.2 | sulfoacetaldehyde acetyltransferase (xsc) |
| SPO2657 | AAV95902.1 | 3.1 | sulfolyase (cuyA2) |
| Organic Nitrogen Utilization | |||
| SPO1562 | AAV94849.2 | 1.5 | trimethylamine-oxide aldolase (tdm) |
| SPO1579 | AAV94866.1 | 6.3 | dimethylamine monooxygenases submit (dmmD) |
| SPO1580 | AAV94867.1 | 5.5 | dimethylamine monooxygenases submit (dmmA) |
| SPO1581 | AAV94868.1 | 5.8 | dimethylamine monooxygenase subunit (dmmB) |
| SPO1582 | AAV94869.1 | 4.9 | dimethylamine monooxygenase subunit (dmmC) |
| SPO0222 | AAV93547.1 | 14.6 | alanine dehydrogenase (ald) |
| SPO1711 | AAV94994.1 | 2.9 | urease accessory protein (ureD) |
| SPO1712 | AAV94995.1 | 3.3 | urease gamma subunit (ureA) |
| SPO1713 | AAV97135.1 | 3.1 | urease beta subunit (ureB) |
| Organic Phosphate Utilization | |||
| SPO0732 | AAV94037.1 | 6.3 | aerobic glycerol-3-phosphate dehydrogenase (glpD) |
All genes have an adjusted p-value ≤ 0.01.
GH glycoside hydrolase, AA auxiliary activity, GT glycosyl transferase, CE carbohydrate esterase.
*Function confirmed with mutant strain.