TABLE 5.
Summary of three E. coli expression profiles
| Characteristic (no. of genes summed) | Abundance (100 ppm) in:
|
||
|---|---|---|---|
| Minimal medium
|
LB medium (exponential phase) | ||
| Exponential phase | Transition phase | ||
| Cell processes | |||
| Cell division (26) | 110 | 100 | 100 |
| Chemotaxis and motility (12) | 14 | 7 | 11 |
| Folding and ushering proteins (7) | 32 | 61 | 110 |
| Transport of large molecules: protein, peptide secretion (32) | 82 | 101 | 100 |
| Transport of small molecules | |||
| Amino acids, amines (49) | 91 | 81 | 68 |
| Anions (20) | 29 | 28 | 23 |
| Carbohydrates, organic acids, alcohols (82) | 200 | 160 | 340 |
| Cations (52) | 120 | 98 | 76 |
| Nucleosides, purines, pyrimidines (6) | 10 | 9 | 17 |
| Other (12) | 21 | 27 | 12 |
| Elements of external origin | |||
| Laterally acquired | 240 | 170 | 230 |
| Phage-related functions/prophages (27) | 55 | 42 | 65 |
| Plasmid-related functions (1) | 2 | 6 | 9 |
| Transposon-related functions (34) | 58 | 35 | 38 |
| Global functions | |||
| Energy transfer, ATP proton motive force (9) | 77 | 54 | 150 |
| Global regulatory functions (51) | 176 | 290 | 180 |
| Macromolecule metabolism | |||
| Basic protein synthesis, and modification (6) | 47 | 48 | 74 |
| Degradation of: | |||
| DNA (23) | 38 | 30 | 31 |
| RNA (11) | 29 | 15 | 22 |
| Polysaccharides (3) | 6 | 3 | 4 |
| Proteins and peptides (61) | 84 | 93 | 110 |
| Synthesis and modification of: | |||
| DNA (89) | 230 | 190 | 310 |
| Lipoprotein (11) | 41 | 50 | 37 |
| Phospholipids (11) | 20 | 15 | 21 |
| Polysaccharides (cytoplasmic) (6) | 15 | 16 | 6 |
| Protein translation and modification (34) | 290 | 300 | 430 |
| RNA synthesis (27) | 100 | 100 | 150 |
| Macromolecules | |||
| Glycoprotein | |||
| Lipopolysaccharide (13) | 15 | 12 | 18 |
| tRNA modification and charging (40) | 130 | 130 | 210 |
| Metabolism of small molecules | |||
| Amino acid biosynthesis (110) | 120 | 93 | 33 |
| Biosynthesis of cofactors, carriers (115) | 720 | 690 | 640 |
| Central intermediary metabolism | |||
| 2′-Deoxyribonucleotide metabolism (12) | 34 | 32 | 32 |
| Amino sugars (10) | 12 | 11 | 15 |
| Entner-Douderoff (3) | 4 | 3 | 6 |
| Gluconeogenesis (4) | 9 | 12 | 21 |
| Glyoxylate bypass (5) | 76 | 75 | 12 |
| Other metabolism of glucose (3) | 9 | 5 | 4 |
| Nonoxidative branch, pentose pathway (8) | 26 | 43 | 43 |
| Nucleotide hydrolysis (2) | 1 | 1 | 3 |
| Nucleotide interconversions (13) | 41 | 39 | 20 |
| Phosphorus compounds (17) | 32 | 30 | 22 |
| Polyamine blosynthesis (8) | 16 | 13 | 13 |
| Nucleoside and nucleotide salvage (18) | 37 | 38 | 54 |
| Sugar-nucleotide synthesis, conversion (18) | 42 | 34 | 48 |
| Sulfur metabolism (10) | 39 | 25 | 10 |
| Pool, interconversion (46) | 120 | 190 | 210 |
| Degradation of small molecules | |||
| Amines (9) | 16 | 10 | 25 |
| Amino acids (17) | 22 | 14 | 72 |
| Carbon compounds (90) | 140 | 110 | 250 |
| Fatty acids (10) | 20 | 17 | 30 |
| Others (8) | 15 | 21 | 8 |
| Energy metabolism, carbon | |||
| Aerobic respiration (27) | 77 | 58 | 120 |
| Anaerobic respiration (80) | 75 | 57 | 110 |
| Electron transport (24) | 32 | 24 | 48 |
| Fermentation (21) | 40 | 50 | 44 |
| Glycolysis (18) | 130 | 240 | 150 |
| Oxidative branch, pentose pathway (2) | |||
| Pyruvate dehydrogenase (6) | 46 | 41 | 40 |
| TCA cycle (18) | 89 | 120 | 93 |
| Fatty acid biosynthesis: fatty acid and phosphatidic acid synthesis (23) | 73 | 94 | 150 |
| Nucleotide synthesis | 190 | 130 | 100 |
| Purine ribonucleotide synthesis (22) | 110 | 77 | 83 |
| Pyrimidine ribonucleotide biosynthesis (10) | 79 | 49 | 18 |
| Miscellaneous: not classified (109) | 220 | 230 | 250 |
| ORFs: unknown proteins (1,324) | 3,500 | 3,400 | 2,600 |
| Processes | |||
| Adaptation | |||
| Atypical conditions (16) | 120 | 83 | 74 |
| Osmotic (14) | 38 | 63 | 26 |
| Protection responses | |||
| Cell killing (3) | 5 | 3 | 3 |
| Detoxification (11) | 80 | 83 | 97 |
| Drug or analog sensitivity (32) | 42 | 31 | 38 |
| Structural elements | |||
| Cell envelope | |||
| Murein sacculus, peptidoglycan (34) | 95 | 120 | 130 |
| Outer membrane constituents (17) | 230 | 260 | 200 |
| Cell exterior constituents (16) | 37 | 39 | 62 |
| Surface polysaccharides and antigens: surface structures (57) | 75 | 51 | 52 |
| Ribosome constituents | |||
| Ribosomal and stable RNAs (3) | |||
| Ribosomal proteins (64) | 790 | 860 | 1,500 |
| Ribosomal maturation and modification (6) | 56 | 110 | 7 |
| ORFs not listed (102) | |||