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− |