Table 1.
Knockout mutant genetic backgrounds assayed for D-DIBOA production
| MultiFun Ontology: metabolism, child classes | Superpathways | Knock-out genes | ID (Keio collection) | Protein name | Pathways/reactions/molecular function | Consumed cofactor |
|---|---|---|---|---|---|---|
| Biosynthesis of Macromolecules (cellular constituents)a | Colanic acid (M antigen) | rcsA | JW1935-1 | Rcsa | RcsA + RcsB → RcsAB | |
| Positive DNA-binding transcriptional regulator of capsular polysaccharide synthesis, activates its own expression | ||||||
| wzc | JW2045-1 | Protein-tyrosine kinase Wzc | ATP + a [protein]-l-tyrosine → ADP + a [protein]-l-tyrosine phosphate + H+ | ATP | ||
| Cytoplasmic poysaccharides | dgsA (=mlc) | JW1586-1 | Mlc DNA-binding transcriptional repressor | Controls the expression of a number of genes encoding enzymes of the phosphotransferase (PTS) and phosphoenolpyruvate (PEP) systems. Regulates genes involved in the uptake of glucose | ||
| glgA | JW3392-1 | Glycogen synthase | Glycogen biosynthesis I (from ADP-d-Glucose) | |||
| Enterobacterial common antigen (surface glycolipid) | wzxE | JW3766-1 | Lipid III flippase | Enterobacterial common antigen)-undecaprenyl diphosphate[cytosol] → (enterobacterial common antigen)-undecaprenyl diphosphate[periplasm] | ||
| Flagellum | flgA | JW1059-1 | Flagellar biosynthesis protein FlgA | Assembly of basal-body periplasmic P ring | ATP | |
| flhA | JW1868-1 | Flagellar biosynthesis protein FlhA | Flagellar export apparatus | |||
| fliQ | JW1933-1 | Flagellar biosynthesis protein FliQ | ||||
| Transcriptional level, repressorb | lrhA | JW2284-6 | LrhA DNA-binding transcriptional dual regulator A | LysR homologue A, regulates the transcription of genes involved in the synthesis of type 1 fimbriae. Indirectly, this protein also regulates the transcription of several genes involved in motility, chemotaxis, and flagellum synthesis by directly controlling the expression of the master regulator FlhDC | ||
| Large molecule carriers | ccmA | JW5366-1 | Heme trafficking system ATP-binding protein | Ferroheme b[cytosol] + ATP + H2O → ferroheme b[periplasm] + ADP + phosphate + H+ | ATP | |
| citD | JW0609-1 | Citrate lyase, acyl carrier gamma; subunit |
Citrate → acetate + oxaloacetate citrate + an acetyl-holo [citrate lyase acyl-carrier protein] + H + → a citryl-holo [citrate lyase acyl-carrier protein] + acetate a citryl-holo [citrate lyase acyl-carrier protein] → oxaloacetate + an acetyl-holo [citrate lyase acyl-carrier protein] + H+ |
|||
| Large molecule carriers, Thioredoxin, glutaredoxin | grxA | JW0833-1 | Glutaredoxin 1, redox coenzyme for ribonucleotide reductase |
2 glutathione + an oxidized glutaredoxin → glutathione disulfide + a reduced glutaredoxin an oxidized glutaredoxin + 2 e- = a reduced glutaredoxin S-sulfo-l-cysteine + a reduced glutaredoxin → l-cysteine + sulfite + an oxidized glutaredoxin + H+ + 2 more |
e− | |
| Lipopolysaccharide | lapA (= yciS) | JW1271-1 | Lipopolysaccharide assembly protein LapA | Heat shock protein involved in the assembly of lipopolysaccharides | ||
| Lipopolysaccharide, core region | kdsD | JW3164-1 | d-arabinose 5-phosphate isomerase | Aldehydo-d-arabinose 5-phosphate ↔ d-ribulose 5-phosphate | ||
| lpcA | JW0212-1 | d-sedoheptulose 7-phosphate isomerase | d-sedoheptulose 7-phosphate → d-glycero-d-manno-heptose 7-phosphate | |||
| Lipopolysaccharide, Lipid A | arnA | JW2249-1 | Fused UDP-L-Ara4 N formyltransferase and UDP-GlcA dehydrogenase | Polymyxin resistance | ||
| Lipopolysaccharide, O antigen | rfbX | JW2022-2 | O antigen flippase | (O16 antigen)-undecaprenyl diphosphate[cytosol] → (O16 antigen)-undecaprenyl diphosphate[periplasm] | ||
| wbbI | JW2019-1 | β-1,6-galactofuranosyltransferase | Octyl α-d-glucopyranoside + UDP-α-d-galactofuranose → octyl β-1,6-d-galactofuranosyl-α-d-glucopyranoside + UDP + H+ | |||
| Lipoprotein | ybaY | JW0443-1 | Predicted outer membrane lipoprotein | Outer membrane component | ||
| Phospholipid | cdsA | GN80 | CDP-diglyceride synthetase |
CTP + a 1,2-diacyl-sn-glycerol 3-phosphate + H+ → a CDP-diacylglycerol + diphosphate CTP + a 2,3,4-saturated 1,2-diacyl-sn-glycerol 3-phosphate + H+ → a CDP-2,3,4-saturated-diacylglycerol + diphosphate |
CTP/H+ | |
| clsA | JW1241-5 | Cardiolipin synthase 1 | 2 an L-1-phosphatidyl-sn-glycerol → a cardiolipin + glycerol | |||
| pgpA | JW0408-4 | Phosphatidylglycerophosphatase A | 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate + H2O → an L-1-phosphatidyl-sn-glycerol + phosphate | |||
| Carbon utilization | Fatty acids | fadR | JW1176-1 | DNA-binding transcriptional dual regulator FadR | FadR + an acyl-CoA ↔ FadR-acyl-CoA | NADPH |
| Carbon compounds | pfk I | JW3887-1 | 6-phosphofructokinase I | d-sedoheptulose 7-phosphate + ATP → d-sedoheptulose-1,7-bisphosphate + ADP + H+ | NADH/ATP | |
| pfk II | JW5280-1 | 6-phosphofructokinase II | β-d-fructofuranose 6-phosphate + ATP → ADP + β-d-fructose 1,6-bisphosphate + H+ | NADH/ATP | ||
| Central intermediary metabolism | Sugar nucleotide biosynthesis, conversions | sthA (= udhA) | JW5551-1 | Pyridine nucleotide transhydrogenase, soluble | NAD+ + NADPH → NADH + NADP+ | NADPH |
| Energy metabolism, carbon | Anaerobic respiration//electron donors | nuoA | JW2283-1 | NADH:quinone oxidoreductase subunit A | NADH + ubiquinone [inner membrane] + 5 H+ ↔ NAD+ + ubiquinol[inner membrane] + 4 H+ [periplasm] | NADH/H+ |
| nuoB | JW5875-2 | NADH:ubiquinone oxidoreductase, chain B | ||||
| nuoE | JW2280-1 | NADH:ubiquinone oxidoreductase, chain E | ||||
| nuoF | JW2279-3 | NADH:ubiquinone oxidoreductase, chain F | ||||
| nuoG | JW2278-1 | NADH:ubiquinone oxidoreductase, chain G | ||||
| nuoN | JW2271-1 | NADH:ubiquinone oxidoreductase, membrane subunit N | ||||
| Glycolysis | pgi | JW3985-1 | Phosphoglucose isomerase | d-glucopyranose 6-phosphate ↔ β-d-fructofuranose 6-phosphate | ||
| Energy production/transport | Transport → electron acceptors | narG | JW1215-1 | Nitrate reductase A, alpha; subunit | Nitrate + 2H+ + menaquinol – > Nitrite + menaquinone + H2O | H+/e− |
aSelected genes from a random search of biosynthesis of macromolecules as shown in Additional file 2. The other mutant strains have been selected from Table S1B
bTranscriptional protein repressor gene (lrhA) involved in flagellum, motility and chemotaxis related to flagellum protein not included in Metabolism class