Table 2.
Identification of Burkholderia pseudomallei soil isolate, BpMARAN, up-regulated proteins in National Centre for Biotechnology (NCBI) non-redundant sequence using Mascot search engine data from MALDI-TOF mass spectrometry.
| Functional category and Protein namea | Spot | Anova (p-value) | Locus tagb | Fold change | Sequence coverage(%) | Theo/exp MW | Theo/exp pI | SignalPd | TMHMMf | Subcellular locationc |
|---|---|---|---|---|---|---|---|---|---|---|
| Metabolism | ||||||||||
| Energy production and conversion | ||||||||||
| F0F1 ATP synthase subunit alpha (atpA) | 10 | 0.003 | BPSL3398 | 2.0 | 20 | 55891/55781 | 5.48/5.48 | − | − | cytoplamic |
| Betaine aldehyde dehydrogenase (alededh) | 11* | 6.15E-04 | BPSL1550 | 3.2 | 30 | 50453/50353 | 5.67/5.67 | − | − | cytoplamic |
| Isocitrate lyase (aceA) | 12 | 0.042 | BPSL2188 | 2.0 | 12 | 52238/47644 | 7.68/5.73 | − | − | cytoplamic |
| Pyrophosphatase (ppa) | 52* | 0.026 | BPSL1021 | 2.5 | 23 | 19149/19030 | 5.37/5.37 | − | − | cytoplamic |
| Isocitrate dehydrogenase (idhI) | 77 | 0.043 | BPSL0896 | 2.0 | 24 | 46116/46015 | 5.76/5.63 | − | − | unknown |
| F0F1 ATP synthase subunit beta (atpD) | 83 | 0.013 | BPSL3396 | 2.0 | 21 | 50417/50492 | 5.24/5.26 | − | − | cytoplamic |
| F0F1 ATP synthase subunit beta (atpD) | 84 | 0.018 | BPSL3396 | 2.0 | 20 | 50147/50492 | 5.24/5.26 | − | − | cytoplamic |
| Succinate dehydrogenase Iron-sulfur subunit (sdhB) | 85 | 0.007 | BPSS1717 | 2.0 | 21 | 26776/26633 | 6.00/6.00 | − | − | cytoplamic membrane |
| Amino acid transport and metabolism | ||||||||||
| Extracellular ligand binding protein (livK) | 16* | 0.004 | BPSS0802 | 12.2 | 34 | 38875/39791 | 8.75/9.17 | + | − | periplasmic |
| Putrescine-binding periplasmic protein (potF) | 17* | 0.017 | BPSL1555 | 3.9 | 23 | 40171/40035 | 9.03/9.03 | + | − | periplasmic |
| Periplasmic amino acid binding transport protein (livK) | 18 | 0.038 | BPSL3388 | 5.1 | 21 | 39974/39897 | 9.03/9.03 | + | − | periplasmic |
| Argininosuccinate synthase (argG) | 80 | 0.022 | BPSL0298 | 2.0 | 24 | 49666/49566 | 5.375.37 | − | − | cytoplamic |
| Arginine deiminase (arcA) | 81 | 0.002 | BPSL1743 | 2.1 | 32 | 46851/45921 | 5.40/5.57 | − | − | cytoplamic |
| N-acetyl-gamma-glutamyl-Phosphate reductase (argC) | 86* | 0.005 | BPSL3246 | 2.0 | 23 | 33676/33566 | 6.60/6.61 | − | − | cytoplamic |
| Carbohydrate and metabolism | ||||||||||
| Phosphopyruvate hydratase (eno) | 14 | 0.049 | BPSL2270 | 2.0 | 11 | 45656/45552 | 4.78/4.81 | − | − | cytoplamic |
| Glyceraldehyde 3-phosphate dehydrogenase 1 (gapA) | 28 | 0.03 | BPSL2952 | 2.0 | 32 | 36082/35987 | 6.37/6.37 | − | − | cytoplamic |
| Coenzyme metabolism | ||||||||||
| S-adenosylmethionine synthetase (metK) | 82* | 2.31E-04 | BPSL0212 | 3.7 | 16 | 42615/42510 | 5.13/5.13 | − | − | cytoplamic |
| Lipid metabolism | ||||||||||
| Beta-ketoadipyl CoA thiolase (paaJ) | 29* | 3.30E-04 | BPSL3042 | 9.5 | 17 | 42285/42152 | 6.26/6.55 | − | − | cytoplamic |
| Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (scoA) | 58 | 0.039 | BPSL1955 | 2.0 | 20 | 25230/25087 | 5.56/5.55 | − | − | cytoplamic |
| Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (scoB) | 67 | 0.048 | BPSL1954 | 2.0 | 17 | 22273/22156 | 4.70/4.70 | − | − | cytoplamic |
| Inorganic ion transport and metabolism | ||||||||||
| Catalase-peroxidase (katG) | 5* | 0.002 | BPSL2865 | 2.6 | 7 | 79339/81630 | 5.66/5.89 | − | − | cytoplamic |
| Catalase-peroxidase (katG) | 6* | 0.029 | BPSL2865 | 3.8 | 6 | 79339/81630 | 5.66/5.89 | − | − | cytoplamic |
| Phosphate transport system, substrate-binding exported periplasmic protein (pstS) | 20 | 0.031 | BPSL1359 | 2.0 | 26 | 35762/36230 | 8.89/9.01 | + | − | periplasmic |
| Secondary metabolites biosynthesis, transport and catabolism | ||||||||||
| Non-ribosomally encoded peptide/polyketide synthase (phyH) | 75 | 0.004 | BPSS1183 | 2.0 | 24 | 39771/35275 | 7.73/5.77 | − | − | cytoplamic |
| Cellular Processes | ||||||||||
| Cell wall/membrane/envelope biogenesis | ||||||||||
| Cell division protein (FtsZ) | 15 | 0.008 | BPSL3020 | 2.0 | 22 | 41574/41469 | 4.87/4.86 | − | − | cytoplamic |
| Outer membrane protein (ompW) | 31* | 0.003 | BPSL1552 | 3.1 | 17 | 22749/22632 | 8.60/8.60 | + | − | outer membrane |
| Post-translation modification and chaperones | ||||||||||
| Molecular chaperone (DnaK) | 1 | 0.013 | BPSL2827 | 2.9 | 15 | 69700/69571 | 4.66/4.93 | − | − | cytoplamic |
| Chaperonin (GroEL) | 2 | 0.009 | BPSL2697 | 2.1 | 38 | 57080/56985 | 5.13/5.13 | − | − | cytoplamic |
| ClpB heat-shock protein | 4* | 0.005 | BPSL1484 | 2.2 | 9 | 95991/97147 | 5.66/5.66 | − | − | cytoplamic |
| Chaperonin (GroEL) | 27 | 0.021 | BPSL2697 | 4.3 | 23 | 57486/56985 | 5.13/5.13 | − | − | cytoplamic |
| Chaperonin (GroEL) | 68 | 0.041 | BPSL2697 | 2.2 | 19 | 57080/56985 | 5.13/5.13 | − | − | cytoplamic |
| Chaperonin (GroEL) | 72* | 0.042 | BPSL2697 | 2.0 | 18 | 57486/56985 | 5.13/5.13 | − | − | cytoplamic |
| Information Storage And Processing | ||||||||||
| Translation, ribosomal structure and biogenesis | ||||||||||
| Ribosome recycling factor (frr) | 22 | 0.039 | BPSL2156 | 2.0 | 14 | 20886/20990 | 7.88/7.88 | − | − | cytoplamic |
| 50 S ribosomal protein L9 (rplI) | 30 | 0.041 | BPSL1461 | 2.1 | 50 | 16235/16114 | 6.85/6.85 | − | − | cytoplamic |
| Elongation factor Tu (tuf) | 79 | 0.037 | BPSL3215 | 2.0 | 25 | 42964/42860 | 5.36/5.34 | − | − | cytoplamic |
| Transcription | ||||||||||
| DNA-directed RNA polymerase subunit alpha (rpoA) | 76 | 0.048 | BPSL3187 | 2.0 | 24 | 35663/35554 | 5.76/5.76 | − | − | cytoplamic |
| Poorly Characterised | ||||||||||
| Function unknown | ||||||||||
| Hypothetical protein BPSS0837 (usp) | 25 | 0.019 | BPSS0837 | 2.8 | 16 | 29814/29832 | 8.04/8.05 | − | − | unknown |
| Chitin-binding protein (cpbD) | 26 | 0.048 | BPSS0493 | 3.0 | 8 | 39260/39153 | 8.59/8.59 | + | − | extracellular |
| BPSL0348 (pixA) | 66* | 0.042 | BPSL0348 | 2.3 | 43 | 20170/27756 | 4.55/6.59 | − | − | unknown |
| Moonlighting proteins | ||||||||||
| Amino acid transport and metabolism/Signal transduction mechanisms | ||||||||||
| Glutamate/aspartate periplasmic binding protein (gltI) | 19 | 0.038 | BPSL2924 | 2.9 | 33 | 32699/31300 | 9.17/9.17 | + | − | periplasmic |
| Lysine-arginine-ornithine transport system, binding exported protein (argT) | 24 | 0.044 | BPSS0269 | 2.0 | 16 | 27833/28350 | 7.64/8.61 | + | − | periplasmic |
| Secondary metabolites biosynthesis, transport and catabolism/General function prediction | ||||||||||
| Acetyacetyl-CoA reductase (phbB) | 32 | 0.036 | BPSL1536 | 2.5 | 22 | 26722/26377 | 6.84/6.84 | − | − | cytoplamic |
| Acetoacetyl-CoA reductase (phbB) | 33 | 0.042 | BPSS1916 | 2.1 | 26 | 26408/26298 | 6.60/6.30 | − | − | cytoplamic |
| Carbohydrate and metabolism/Cell wall/membrane/envelope biogenesis | ||||||||||
| Chain A, crystal structure of putative exported protein (wcaG) | 23 | 0.039 | − | 2.0 | 27 | 25261/25582 | 8.41/8.12 | − | − | unknown |
*Missing proteins in Bpmouse-adapted.
aFunctional category based on Clusters of Orthologous Groups (COG) of protein.
bLocus tag obtained from Burkholderia Database.
cSubcellular location predicted using the PSORT analysis.
dPresence of signal peptide predicted by SignalP server v. 3.0.
eNumber of predicted transmembrane helices in protein using TMHMM server v. 2.0.