From: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
Gene Group No. | Gene No. | Gene Locus | Gene Name | FP/FN | Pathway | Function/Reaction | Modification to Correct the False Gene Essentiality Prediction | Supporting Literature (References) |
---|---|---|---|---|---|---|---|---|
1 | 1 | Rv1099c | Rv1099c | FN | Glycolysis/gluconeogenesis | Convert fructose-1,6-bisphosphate into fructose-6-phosphate | (1) Blocked the uptake of glucose from environment | |
2 | 2 | Rv2702 | ppgK | FN | Glycolysis/gluconeogenesis | Conversion between glucose-6-phosphate and glucose | (1) Blocked the conversion from maltose to glucose and blocked the uptake of glucose (2) Blocked the conversion between maltose and trehalose and blocked the uptake of glucose | |
3 | 3 4 5 | Rv1350 Rv1483 Rv2947c | fabG2 inhA pks15 | FP FP FP | Fatty acid metabolism | Synthesis of fatty acids | (1) Allowed the uptakes of the following fatty acids: hexadecanoate, octadecanoate, octanoate, dodecanoate, arachidic acid, and hexacosanoate | |
4 | 6 | Rv2503c | scoB | FP | Fatty acid metabolism | Functions as 3-oxoacid CoA-transferase | (1) Let the reaction catalyzed by acetyl-CoA:acetoacetyl-CoA transferase be reversible | Â |
5 | 7 | Rv3229c | desA3 | FN | Fatty acid metabolism | Palmitoyl-CoA desaturation | (1) Blocked the synthesis of hexadecenoate | |
6 | 8 | Rv1185c | fadD21 | FN | Fatty acid metabolism | Synthesis of fatty acid-CoA | (1) Blocked the ability of fadD9 (Rv2590), fadD24 (Rv1529), and fadD23 (Rv3826) to catalyze the synthesis of fatty acid-CoA | Â |
7 | 9 | Rv0098 | Rv0098 | FN | Fatty acid metabolism | Mycolic acid synthesis | (1) Blocked the ability of fabG1 (Rv1483) to catalyze the same reaction | Â |
8 | 10 | Rv2483c | plsC | FN | Fatty acid metabolism | Synthesis of 1,2-diacyl-sn-glycerol 3-phosphate (a phospholipid) | (1) Blocked the ability of Rv2182c to catalyze the same reaction | Â |
9 | 11 | Rv1416 | ribH | FP | Vitamin and cofactor metabolism | Synthesis of riboflavin | (1) Removed riboflavin and flavin mononucleotide (FMN) from the biomass objective function | Â |
10 | 12 | Rv1412 | ribC | FP | Vitamin and cofactor metabolism | Synthesis of riboflavin | (1) Removed riboflavin and FMN from the biomass objective function | Â |
11 | 13 | Rv2671 | ribD | FP | Vitamin and cofactor metabolism | Synthesis of riboflavin precursor | (1) Removed riboflavin and FMN from the biomass objective function | Â |
12 | 14 | Rv2786c | ribF | FP | Vitamin and cofactor metabolism | Synthesis of FMN from riboflavin | (1) Removed FMN from the biomass objective function | Â |
13 | 15 | Rv2421c | Rv2421c | FP | Vitamin and cofactor metabolism | Synthesis of deamino-NAD+ | (1) Removed nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) from the biomass objective function | Â |
14 | 16 | Rv1596 | nadC | FP | Vitamin and cofactor metabolism | Functions as nicotinate-nucleotide diphosphorylase | (1) Removed NAD and NADP from the biomass objective function | Â |
15 | 17 | Rv3215 | entC | FP | Vitamin and cofactor metabolism | Synthesis of isochorismate | (1) Removed menaquinol 8 from the biomass objective fucntion | Â |
16 | 18 | Rv1568 | bioA | FN | Vitamin and cofactor metabolism | Synthesis of a precursor of biotin | (1) Added biotinyl-5'-AMP to the biomass objective function | Â |
17 | 19 | Rv1569 | bioF | FN | Vitamin and cofactor metabolism | Synthesis of a precursor of biotin | (1) Added biotinyl-5'-AMP to the biomass objective function and blocked the ability of bioF2 (Rv0032) to catalyze the same reaction | Â |
18 | 20 | Rv1589 | bioB | FN | Vitamin and cofactor metabolism | Synthesis of biotin | (1) Added biotinyl-5'-AMP to the biomass objective function | Â |
19 | 21 | Rv2211c | gcvT | FN | Vitamin and cofactor metabolism | Conversion between 5-formyltetrahydrofolate and 5,10-methenyltetrahydrofolate | (1) Added the metabolite 5-formyltetrahydrofolate to the biomass objective function | Â |
20 | 22 | Rv3001c | ilvC | FP | Amino acid metabolism | Synthesis of 2,3-dihydroxy-3-methylbutanoate and 2,3-dihydroxy-3-methylpentanoate | (1) Allowed the uptakes of isoleucine and valine | [61] |
21 | 23 | Rv3002c | ilvN | FP | Amino acid metabolism | Synthesis of acetolactate | (1) Allowed the uptake of valine | [61] |
22 | 24 25 26 27 | Rv2220c Rv1878 Rv2222c Rv2860c | glnA1 glnA3 glnA2 glnA4 | FP FP FP FP | Amino acid metabolism | Synthesis of glutamine | (1) Let the reaction of glutamate synthesis from glutamine to be reversible (2) Let the conversion to CTP and glutamate from UTP and glutamine be reversible | Â |
23 | 28 | Rv3754 | tyrA | FP | Amino acid metabolism | Functions as prephenate dehydrogenase | (1) Allowed the uptake of tyrosine | Â |
24 | 29 | Rv3042c | serB2 | FN | Amino acid metabolism | Remove a phosphate group from phosphoserine to produce serine | (1) Blocked the ability of serB (Rv0505c) to catalyze the same reaction | Â |
25 | 30 | Rv2231c | cobC | FN | Amino acid metabolism | Convert glutamate into histidinol-phosphate | (1) Blocked the ability of hisC2 (Rv3772) and hisC (Rv1600) to catalyze the conversion | Â |
26 | 31 | Rv2945c | lppX | FN | Transport | Transport phthiocerol dimycocerosate A and phenol phthiocerol dimycocerosate out of the cell | (1) Added extracellular phthiocerol dimycocerosate A to the biomass objective function (2) Added extracellular phenol phthiocerol dimycocerosate to the biomass objective function | [62] |
27 | 32 33 34 | Rv1236 Rv1237 Rv1238 | sugA sugB sugC | FN | Transport | Transport of glucose, maltoheptaose, maltose, ribose, trehalose, and xylose into cell | (1) Allowed xylose uptake and added xylose to the biomass objective function | Â |
28 | 35 | Rv3236c | kefB | FN | Transport | Transport of K+ and Na+ into the cell | (1) Blocked the function of potassium ABC transporter (2) Blocked the function of the Na+ antiporter | Â |
29 | 36 | Rv1699 | pyrG | FP | Nucleotide metabolism | Synthesis of CTP from UTP | (1) Allowed the uptake of cytidine | Â |
30 | 37 | Rv1385 | pyrF | FP | Nucleotide metabolism | Functions as orotidine-5'-phosphate decarboxylase | (1) Allowed the uptake of cytidine | Â |
31 | 38 | Rv2139 | pyrD | FP | Nucleotide metabolism | Functions as dihydroorotic acid dehydrogenase | (1) Allowed the uptake of cytidine | Â |
32 | 39 | Rv3393 | iunH | FP | Nucleotide metabolism | Hydrolysis of inosine | (1) Let the reaction catalyzed by ribokinase be reversible | Â |
33 | 40 | Rv2465c | rpi | FP | Pentose phosphate pathway | Functions as ribose-5-phosphate isomerase | (1) Allowed the secretion of D-arabinose | Â |
34 | 41 | Rv3628 | ppa | FP | Multiple pathways | Functions as inorganic diphosphatase | (1) let the reaction catalyzed by nucleoside triphosphate tripolyhydrolase of deoxy-GTP (dGTP) to be reversible | Â |
35 | 42 | Rv3588c | Rv3588c | FN | Multiple pathways | Conversion between carboxylic acid and carbon dioxide | (1) Blocked the ability of Rv3273 to catalyze the same reaction | Â |