Table 2.
Growth phenotypes of genes involved in RLV3841 central carbon metabolism.
| VMM INSeq | TY INSeq | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Metabolic step | RLV locus | RLV symbol | Putative product | Growth phenotype | Insertion density | Average read depth | Gene state | Insertion density | Average read depth | Gene state | Riley key | Riley functional information |
| MANNITOL UPTAKE AND CONVERSION TO FRUCTOSE | ||||||||||||
| 1.0 | RL4219 | – | Transcriptional regulator | GN | 0.86 | 16.67 | NE | 0.79 | 25.27 | NE | 6.3.10 | Putative deor family transcriptional regulator (repressor) of sorbitol/mannitol operon |
| 1.0 | RL4215 | – | Mannitol ABC transporter ATP-binding protein | VGI | 0.41 | 1.71 | GD | 0.88 | 12.6 | NE | 1.5.3 | Putative ATP-binding component of ABC transporter CUT1 mannitol transporter (S. Mel SBP homolog smc01496 induced by dulcitol, sorbitol, mannitol) |
| 1.0 | RL4216 | mtlG | Mannitol transmembrane permease component of ABC transporter | VGI | 0.56 | 3.2 | GD | 1 | 34.11 | NE | 1.5.3 | Putative permease component of ABC transporter CUT1 mannitol transporter (S. Mel SBP homolog smc01496 induced by dulcitol, sorbitol, mannitol) |
| 1.0 | RL4217 | mtlF | Mannitol transmembrane permease component of ABC transporter | VGI | 0.53 | 2.78 | GD | 0.94 | 36.06 | NE | 1.5.3 | Putative permease component of ABC transporter CUT1 mannitol transporter (S. Mel SBP homolog smc01496 induced by dulcitol, sorbitol, mannitol) |
| 1.0 | RL4218 | mtlE | Mannitol-binding component of ABC transporter | VGI | 0.48 | 2.3 | GD | 0.9 | 26.11 | NE | 1.5.3 | Putative SBP of ABC transporter CUT1 mannitol transporter (S. Mel SBP homolog smc01496 induced by dulcitol, sorbitol, mannitol) |
| 1.0 | RL4214 | mtlK | Mannitol 2-dehydrogenase | VGI | 0.12 | 7.5 | GD | 0.88 | 24.8 | NE | 3.4.3 | Putative mannitol 2-dehydrogenase |
| 1.0 | RL0098 | – | Mannitol dehydrogenase | GN | 0.93 | 17 | NE | 0.93 | 17.62 | NE | 3.4.3 | Putative mannitol dehydrogenase |
| 1.0 | RL0502 | frk | Fructokinase | VGI | 0.21 | 3 | GD | 1 | 15.71 | NE | 3.5.5 | Fructokinase |
| ENTNER–DOUDOROFF PATHWAY | ||||||||||||
| 1.1 | RL0753 | zwf1 | Putative glucose-6-phosphate 1-dehydrogenase | GI | 0.05 | 1 | ES | 0.09 | 1 | ES | 3.5.6 | Putative glucose-6-phosphate 1-dehydrogenase |
| 1.1 | RL1315 | zwf1 | Glucose-6-phosphate 1-dehydrogenase | GN | 0.93 | 18.72 | NE | 1 | 18.7 | NE | 3.5.6 | Putative glucose-6-phosphate 1-dehydrogenase |
| 1.1 | pRL120561 | – | Glucose-6-phosphate 1-dehydrogenase | PGN | 1 | 19 | NE | 1 | 14.5 | NE | 6.3.0 | Putative XRE family transcriptional regulator |
| 1.2 | RL0752 | pgl | 6-phosphogluconolactonase | GI | 0 | 0 | ES | 0 | 0 | ES | 3.5.6 | Putative 6-phosphogluconolactonase |
| 1.3 | RL0751 | edd | Phosphogluconate dehydratase | VGI | 0 | 0 | ES | 1 | 8.73 | NE | 3.3.3 | Putative phosphogluconate dehydratase |
| 1.4 | RL4162 | eda | Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase | VGI | 0.13 | 14 | ES | 0.88 | 3.14 | NE | 3.3.3 | Putative 2-dehydro-3-deoxyphosphogluconate aldolase |
| EMBDEN-MEYERHOF-PARNAS PATHWAY | ||||||||||||
| 2.1 | RL0504 | pgi | Glucose-6-phosphate isomerase | VGI | 0.06 | 30 | ES | 0.76 | 10.69 | NE | 3.5.5 | Putative glucose-6-phosphate isomerase |
| 2.2 | RL3322 | pfp | Pyrophosphate-fructose-6-phosphate 1-phosphotransferase | GN | 1 | 16.8 | NE | 0.95 | 21.79 | NE | 3.5.5 | Putative pyrophosphate–fructose 6-phosphate 1-phosphotransferase |
| 2.3 | RL4012 | Fructose-bisphosphate aldolase | GN | 0.86 | 22.42 | NE | 0.93 | 21.23 | NE | 3.5.5 | Putative fructose-bisphosphate aldolase | |
| 2.3 | pRL120027 | Aldolase | PGN | 0.86 | 23.92 | NE | 0.93 | 21.46 | NE | 3.3.15 | Putative aldolase | |
| 2.3 | pRL120196 | Fructose-1,6-bisphosphate aldolase | PGN | 0.95 | 20.67 | NE | 1 | 22.53 | NE | 3.3.9 | Putative fructose-bisphosphate aldolase | |
| 2.4 | RL2513 | tpiA | Triosephosphate isomerase | GN | 0.9 | 14.56 | NE | 0.9 | 24.22 | NE | 3.6.0 | Putative triosephosphate isomerase |
| 2.4 | pRL120209 | tpiA | Triosephosphate isomerase | PVGI | 0.38 | 2.33 | GD | 0.88 | 8.14 | NE | 3.6.0 | Putative triosephosphate isomerase |
| 2.5 | RL4007 | gap | Glyceraldehyde-3-phosphate dehydrogenase | VGI | 0 | 0 | ES | 1 | 9 | NE | 3.5.1 | Putative glyceraldehyde-3-phosphate dehydrogenase |
| 2.6 | RL4011 | pgk | Phosphoglycerate kinase | VGI | 0.25 | 3.67 | GD | 0.83 | 38.2 | NE | 3.5.1 | Putative phosphoglycerate kinase |
| 2.7 | RL0179 | gpmA | Phosphoglyceromutase | VGI | 0.36 | 1.5 | GD | 0.73 | 9.88 | NE | 3.5.5 | Putative 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (Phosphoglyceromutase) (PGAM) (BPG-dependent PGAM) (dPGM) |
| 2.7 | RL2655 | Hypothetical protein | GN | 0.88 | 10.71 | NE | 1 | 9.38 | NE | 0.0.0 | Hypothetical protein | |
| 2.7 | RL0954 | gpmB | Phosphoglycerate mutase | GN | 1 | 19.22 | NE | 0.89 | 21.38 | NE | 3.5.5 | Putative phosphoglycerate mutase |
| 2.7 | RL1010 | gpmB | Phosphoglycerate mutase | GN | 0.83 | 15.2 | NE | 0.83 | 26.2 | NE | 3.5.5 | Putative phosphoglycerate mutase |
| 2.7 | RL2997 | Phosphoglycerate mutase | GN | 1 | 34.29 | NE | 1 | 39.12 | NE | 3.5.5 | Putative phosphoglycerate mutase | |
| 2.8 | RL2239 | eno | Phosphopyruvate hydratase | VGI | 0.19 | 1 | GD | 0.81 | 4.77 | NE | 3.5.5 | Putative enolase |
| 2.9 | RL4060 | pykA | Pyruvate kinase | GI | 0.23 | 8.67 | ES | 0.92 | 4.83 | GD | 3.5.5 | Putative pyruvate kinase |
| 2.10 | RL1086 | ppdK | Pyruvate phosphate dikinase | GN | 0.84 | 21.26 | NE | 0.91 | 24.69 | NE | 3.5.5 | Pyruvate, phosphate dikinase (pyruvate, orthophosphate dikinase) |
| TRICARBOXYLIC ACID CYCLE | ||||||||||||
| 3.1 | RL2241 | pdhA | Pyruvate dehydrogenase subunit | GI | 0 | 0 | ES | 0.18 | 1 | GD | 3.5.5 | Putative pyruvate dehydrogenase subunit A |
| 3.1 | RL2242 | pdhB | Pyruvate dehydrogenase subunit beta | GI | 0 | 0 | ES | 0.22 | 1.25 | GD | 3.5.5 | Putative pyruvate dehydrogenase subunit B |
| 3.1 | RL2243 | pdhC | Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex | GI | 0 | 0 | ES | 0 | 0 | GD | 3.5.5 | Putative dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (PDC) |
| 3.1 | pRL80081 | – | Hydrolase | PGN | 0.86 | 9.33 | NE | 0.86 | 9.33 | NE | 3.3.15 | Putative hydrolase |
| 3.2 | RL2234 | gltA | Type II citrate synthase | VGI | 0.7 | 4.32 | GD | 0.85 | 14.09 | NE | 3.5.8 | Putative citrate synthase |
| 3.2 | RL2508 | gltA | Citrate synthase II | GN | 0.85 | 14.82 | NE | 1 | 13.54 | NE | 3.5.8 | Putative citrate synthase II |
| 3.2 | RL2509 | citA | Citrate synthase 2 | GN | 0.8 | 19 | NE | 0.8 | 19.17 | NE | 3.5.8 | Putative citrate synthase I |
| 3.3 | RL4536 | acnA | Aconitate hydratase | GI | 0.05 | 1 | ES | 0.05 | 1 | ES | 3.5.8 | Putative aconitate hydratase |
| 3.4 | RL2631 | icd | Isocitrate dehydrogenase | GI | 0.12 | 10.5 | ES | 0.12 | 8 | ES | 3.5.8 | Putative isocitrate dehydrogenase [NADP] |
| 3.5 | RL4435 | sucA | 2-oxoglutarate dehydrogenase E1 component | GI | 0.05 | 1.5 | ES | 0.23 | 1.5 | GD | 3.5.8 | Putative 2-oxoglutarate dehydrogenase E1 component |
| 3.5 | RL4433 | citM | Dihydrolipoamide succinyltransferase | GI | 0.2 | 9 | ES | 0.3 | 4.33 | GD | 3.5.8 | Putative dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase |
| 3.6 | RL4436 | sucD | Succinyl-CoA synthetase subunit alpha | GI | 0.15 | 1 | GD | 0.23 | 1.33 | GD | 3.5.8 | Putative succinyl-coa synthetase alpha chain |
| 3.6 | RL4438 | sucC | Succinyl-CoA synthetase subunit beta | GI | 0.09 | 1 | GD | 0.36 | 1 | GD | 3.5.8 | Putative succinyl-coa synthetase beta chain |
| 3.7 | RL4443 | sdhB | Succinate dehydrogenase iron-sulfur subunit | GI | 0.13 | 3 | GD | 0.73 | 2.82 | GD | 3.5.8 | Putative succinate dehydrogenase iron-sulfur protein |
| 3.7 | RL4444 | sdhA | Succinate dehydrogenase flavoprotein subunit | GI | 0.53 | 1.5 | GD | 0.76 | 3.77 | GD | 3.5.8 | Putative succinate dehydrogenase flavoprotein subunit |
| 3.7 | RL4445 | sdhD | Succinate dehydrogenase hydrophobic membrane anchor protein | GI | 0.67 | 1.25 | GD | 0.67 | 4 | GD | 3.5.8 | Putative succinate dehydrogenase hydrophobic membrane anchor protein |
| 3.7 | RL4446 | sdhC | Succinate dehydrogenase cytochrome b556 subunit | GI | 0.46 | 1.83 | GD | 0.77 | 4.6 | GD | 3.5.8 | Putative succinate dehydrogenase cytochrome b556 subunit |
| 3.8 | RL2701 | fumC | Fumarate hydratase class II | GN | 0.94 | 18.56 | NE | 0.88 | 19.8 | NE | 3.5.8 | Putative fumarate hydratase class II |
| 3.8 | RL2703 | fumA | Fumarate hydratase class I | GN | 0.93 | 23.36 | NE | 0.96 | 20.81 | NE | 3.5.8 | Putative fumarate hydratase class I, aerobic |
| 3.9 | RL4439 | mdh | Malate dehydrogenase | GI | 0.25 | 1.33 | GD | 0.17 | 1 | GD | 3.5.8 | Putative malate dehydrogenase |
| 3.10 | RL0761 | - | Isocitrate lyase | GN | 0.91 | 17.29 | NE | 0.83 | 25.79 | NE | 3.3.5 | Putative isocitrate lyase |
| 3.11 | RL0054 | glcB | Malate synthase G | GN | 0.88 | 20 | NE | 1 | 24.06 | NE | 3.3.5 | Putative malate synthase |
| 3.12 | RL0407 | maeB | Malic enzyme | GN | 0.86 | 18.97 | NE | 0.89 | 24.74 | NE | 3.5.8 | Putative NADP-dependent malate dehydrogenase |
| 3.12 | RL2671 | maeB | Malic enzyme | GN | 0.83 | 31.47 | NE | 0.96 | 26.41 | NE | 3.5.8 | Putative NADP-dependent malic enzyme |
| 3.13 | RL0037 | pckA | Phosphoenolpyruvate carboxykinase | GN | 1 | 16.09 | NE | 0.91 | 21.55 | NE | 3.3.4 | Putative phosphoenolpyruvate carboxykinase |
| 3.14 | RL4638 | – | Pyruvate carboxylase | VGI | 0 | 0 | ES | 0.94 | 29.35 | NE | 3.5.8 | Putative pyruvate carboxylase |
| PENTOSE PHOSPHATE PATHWAY | ||||||||||||
| 4.1 | RL2807 | gnd | 6-phosphogluconate dehydrogenase | GN | 0.92 | 10.27 | NE | 0.92 | 12.27 | NE | 3.5.6 | Putative phosphogluconate dehydrogenase |
| 4.1 | RL3998 | gntZ | 6-phosphogluconate dehydrogenase | GN | 0.89 | 20.68 | NE | 1 | 21.89 | NE | 3.5.6 | Putative 6-phosphogluconate dehydrogenase,decarboxylating |
| 4.2 | RL2547 | rpiB | Ribose-5-phosphate isomerase B | GN | 0.57 | 25.75 | NE | 0.71 | 16 | NE | 3.3.9 | Putative ribose-5-phosphate isomerase B |
| 4.2 | RL2698 | rpiA | Ribose-5-phosphate isomerase A | GI | 0 | 0 | ES | 0.33 | 7 | ES | 3.3.9 | Putative ribose-5-phosphate isomerase A |
| 4.2 | pRL120210 | – | Ribose-5-phosphate isomerase B | PVGI | 0.83 | 5.2 | GD | 0.83 | 21.8 | NE | 3.3.9 | Putative ribose-5-phosphate isomerase B |
| 4.3 | RL2598 | rpe | Ribulose-phosphate 3-epimerase | VGI | 0.38 | 2.33 | GD | 0.63 | 9.2 | NE | 3.3.9 | Putative ribulose phosphate 3-epimerase |
| 4.3 | pRL120033 | – | D-allulose-6-phosphate 3-epimerase | PGN | 1 | 20.6 | NE | 1 | 21 | NE | 3.3.9 | Putative D-allulose-6-phosphate 3-epimerase |
| 4.4, 4.6 | RL2718 | – | Transketolase | GN | 1 | 16.23 | NE | 0.92 | 14.83 | NE | 3.3.15 | Putative transketolase, alpha subunit, terpenoid biosynth? |
| 4.4, 4.6 | RL2719 | – | Transketolase | GN | 0.93 | 17.31 | NE | 0.93 | 24.38 | NE | 3.3.15 | Putative transketolase, beta subunit, terpenoid biosynth? |
| 4.4, 4.6 | RL4006 | cbbT | Transketolase | GN | 0.67 | 8.38 | NE | 0.92 | 18.95 | NE | 3.5.1 | Putative transketolase |
| 4.4, 4.6 | pRL100453 | – | Transketolase | PGN | 0.86 | 17.16 | NE | 0.9 | 22.46 | NE | 3.5.6 | Putative transketolase |
| 4.5 | RL4203 | talB | Transaldolase B | GN | 0.56 | 4.2 | NE | 0.89 | 32.13 | NE | 3.3.9 | Putative transaldolase B |