TABLE 1.
Proteins identified from 2-D gels of L. monocytogenes EGDe
| Spota | Protein identification | Mol wt (103)
|
pl
|
Functional classb | TMD predictionc | GRAVY value | ||
|---|---|---|---|---|---|---|---|---|
| Observed | Predicted | Observed | Predicted | |||||
| Spots excised from membrane fraction gels | ||||||||
| 1 | FbaA (lmo2556), similar to fructose-1,6-bisphosphate aldolase | 23 | 30.0 | 5.47 | 5.20 | 2.1.1 | 1/0 | −0.034 |
| 3 | lmo2829, similar to yeast protein Frm2p in fatty acid signaling | 20 | 22.2 | 4.77 | 4.70 | 2.4 | 1/1 | −0.174 |
| 5 | RplJ (lmo0250), ribosomal protein L10 | 16 | 17.7 | 5.60 | 5.36 | 3.7.1 | 1/0 | −0.080 |
| 7 | RplL (lmo0251), ribosomal protein L12 | 10 | 12.5 | 4.54 | 4.54 | 3.7.1 | 1/1 | 0.143 |
| 16 | lmo2149, similar to proteins with no known function | 9.25 | 11.9 | 6.00 | 5.53 | 5.2 | 0/0 | −0.488 |
| 29 | ClpP (lmo2468), ATP-dependent Clp protease proteolytic subunit | 18.5 | 21.6 | 5.06 | 4.94 | 4.1 | 3/2 | −0.072 |
| 36 | TufA (lmo2653), very similar to translation elongation factor EF-Tu | 13.5 | 43.34 | 5.49 | 4.81 | 3.7.4 | 1/0 | −0.272 |
| 37 | lmo1580, similar to proteins with no known function | 14 | 16.9 | 5.05 | 4.98 | 5.2 | 1/0 | −0.192 |
| 38 | MreB (lmo1548), similar to cell shape-determining protein | 35 | 35.5 | 5.66 | 5.16 | 1.1 | 2/1 | 0.061 |
| 41 | lmo1011, similar to tetrahydrodipicolinate succinylase | 24 | 24.8 | 5.14 | 4.95 | 2.2 | 6/2 | 0.193 |
| 55 | LmaA (lmo0118), antigen A | 16.1 | 18.1 | 5.40 | 4.47 | 4.5 | 1/0 | −0.093 |
| 58 | lmo0273, similar to proteins with no known function | 16 | 18.8 | 5.80 | 5.45 | 5.2 | 0/0 | −0.387 |
| Spots excised from cytosolic fraction gels | ||||||||
| 1 | FbaA (lmo2556), similar to fructose-1,6-bisphosphate aldolase | 23 | 30.2 | 5.5 | 5.20 | 2.1.1 | 1/0 | −0.034 |
| 17 | Fri (lmo0943), nonheme iron-binding ferritin | 14.7 | 18.1 | 4.83 | 4.86 | 4.1 | 0/0 | −0.371 |
| 18 | GAPDH (lmo2459), similar to GAPDH | 38 | 36.3 | 5.3 | 5.20 | 2.1.2 | 1/0 | −0.115 |
| 20d | Pfk (lmo1571), similar to 6-phosphofructokinase | 30 | 34.4 | 5.79 | 5.46 | 2.1.1 | 4/1 | −0.104 |
| 21 | Upp (lmo2538), similar to uracil phosphoribosyltransferase | 30 | 22.9 | 5.77 | 5.70 | 2.3 | 1/1 | −0.035 |
| 24 | PykA (lmo1570), similar to pyruvate kinases | 64 | 62.6 | 5.64 | 5.39 | 2.1.1 | 3/1 | −0.034 |
| 28 | PnpA (lmo1331), polynucleotide phosphorylase | 85 | 79.6 | 5.49 | 5.23 | 2.3 | 2/1 | −0.308 |
| 29 | ClpP (lmo2468), ATP-dependent Clp protease proteolytic subunit | 18.5 | 21.6 | 4.96 | 4.94 | 4.1 | 3/0 | −0.072 |
| 30 | Eno (lmo2455), similar to enolase | 43 | 46.5 | 4.71 | 4.70 | 2.1.2 | 1/0 | −0.244 |
| 31 | lmo0796, similar to proteins with no known function | 16 | 19.5 | 4.71 | 4.69 | 5.2 | 0/0 | −0.460 |
| 32 | Pgm (lmo2456), similar to phosphoglycerate mutase | 53 | 56.1 | 5.29 | 5.10 | 2.1.2 | 0/0 | −0.342 |
| 33 | CspB (lmo2016), similar to major cold shock protein | 8.5 | 7.29 | 4.24 | 4.44 | 4.1 | 0/0 | −0.398 |
| 34 | ThiD (lmo0662), similar to phosphomethylpyrimidine kinase ThiD | 22 | 28.8 | 5.41 | 5.25 | 2.5 | 2/1 | −0.025 |
| 35 | Tsf (lmo1657), translation elongation factor | 32.5 | 32.6 | 5.20 | 5.11 | 3.5.3 | 0/0 | −0.430 |
| 44 | PtsH (lmo1002), phosphotransferase system phosphocarrier protein (Hpr) | 9 | 9.4 | 4.73 | 4.81 | 1.2 | 1/0 | −0.067 |
| 50 | Adk (lmo2611), similar to adenylate kinases | 22 | 24.2 | 5.23 | 5.08 | 2.3 | 0/0 | −0.586 |
| 51 | SerS (lmo2747), seryl-tRNA synthetase | 22 | 49.2 | 6.26 | 5.26 | 3.7.2 | 1/0 | −0.553 |
| 53 | lmo0355, similar to flavocytochrome c fumarate reductase chain A | 49 | 54.6 | 5.54 | 5.71 | 1.4 | 2/2 | −0.489 |
| 56 | lmo2376, similar to peptidyl-prolyl cis-trans isomerase | 19.5 | 21.5 | 4.57 | 4.59 | 3.9 | 0/0 | −0.327 |
| 57 | DeoD (lmo1856), purine nucleoside phosphorylase | 20 | 25.5 | 4.84 | 4.87 | 2.3 | 2/1 | 0.073 |
| Spots excised from total protein gels | ||||||||
| 6 | GroES (lmo2069), class I heat shock protein | 8.50 | 10.05 | 4.72 | 4.59 | 3.9 | 0/0 | −0.104 |
| 7 | RplL (lmo0251), ribosomal protein L12 | 10.85 | 12.44 | 4.57 | 4.54 | 3.7.1 | 1/1 | 0.143 |
| 8 | Tpi (lmo2457), triosephosphate isomerase | 27.42 | 26.86 | 4.77 | 4.78 | 2.1.2 | 2/1 | 0.096 |
| 9d | MptA (lmo0096), similar to mannose-specific phosphotransferase system enzyme IIAB | 35 | 34.99 | 5.35 | 5.32 | 1.2 | 1/1 | −0.123 |
| 9d | Pfk (lmo1571), similar to 6-phosphofructokinase | 35 | 34.42 | 5.35 | 5.46 | 2.1.1 | 1/1 | −0.104 |
Spots 6, 7, and 8 were identified by N-terminal sequencing, and all other spots were identified by time of flight mass spectrometry.
Functional class codes according to genolist (http://genolist.pasteur.fr/ListiList/help/function-codes.html): 1.1, cell wall; 1.2, transport/binding proteins and lipoproteins; 1.4, membrane bioenergetics; 2.1.1, metabolism of carbohydrate-specific pathways; 2.1.2, main glycolytic pathways; 2.2, metabolism of amino acids and related molecules; 2.3, metabolism of nucleotides and nucleic acids; 2.4, metabolism of lipids; 2.5, metabolism of coenzymes and prosthetic groups; 3.5.3, RNA synthesis—elongation; 3.7.1, protein synthesis—ribosomal proteins; 3.7.2, protein synthesis—aminoacyl-tRNA sysnthetases; 3.7.4., protein synthesis—elongation. 3.9, protein folding; 4.1, adaptation to atypical conditions; 4.5, miscellaneous; 5.2, from other organisms.
Detected TMDs/significant TMDs as calculated at http://www.ch.embnet.org/software/TMPREDform.html.
Spot identified previously (17).