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. 2013 Dec 13;8(12):e83065. doi: 10.1371/journal.pone.0083065

Table 1. Relative fold-change of normalised protein spot intensities in 2-D DIGE gels corresponding to the cytoplasmic (spots 1-200) and to the membrane-associated (spots 201-281) enriched fractions of B. cenocepacia clonal isolates IST4113 [13] and IST4134 (this work) compared with IST439, and IST4134 compared with IST4113, using a fold-change cut-off of 1.5 (increased content) or 0.67 (decreased content).

 Fold-Change
Spot No. UniProtKB best hit
 J2315 homolog gene Gene Name Protein Function 4113 439 4134 439 4134 * 4113 ANOVAa
Nucleotide metabolism
3 Q1BXD4 BCAL1262 carB Carbamoyl phosphate synthase large subunit 2.2 1.6 0.7 0.008
33 A2VSP0 BCAL3261 purM Phosphoribosylaminoimidazole (AIR) synthetase 2.3 1.5 0.7 <0.001
105 Q39FS0 BCAL1873 purA Adenylosuccinate synthetase 0.7 0.7 1.0 0.010
113 Q0BI80 BCAL3336 purH Bifunctional purine biosynthesis protein PurH 5.2 2.1 0.4 <0.001
115 Q1BHF2 BCAL2061 guaA GMP synthase [glutamine-hydrolyzing] 1.5 1.4 0.9 0.014
121 A4JF47 BCAL2063 guaB Inosine-5‘-monophosphate dehydrogenase 3.2 2.1 0.7 0.007
Protein folding
2 O68191 BCAL3270 dnaK Chaperone protein DnaK 2.0 2.2 1.1 0.011
154 O68191 BCAL3270 dnaK Chaperone protein DnaK 2.1 1.4 0.7 0.012
8 A4JES5 BCAL1919 clpB ClpB heat-shock protein 6.0 2.7 0.4 <0.001
159 A4JES5 BCAL1919 clpB ClpB heat-shock protein 5.4 2.8 0.5 <0.001
29 A9AJR0 BCAL1996 clpP ATP-dependent Clp protease proteolytic subunit 0.7 0.9 1.2 <0.001
130 Q9ZFE0 BCAL3146 groEL 60 kDa chaperonin 1 1.7 1.2 0.7 0.004
176 Q0BEF5 BCAL1997 tig Trigger factor 2.6 1.9 0.7 <0.001
233 Q1BH74 BCAL1985 Putative exported isomerase 1.5 1.5 1.0 0.091
Transcription
258 Q39KI0 BCAL0221 nusG Transcription antitermination protein nusG 0.6 0.6 1.0 0.041
Transcriptional regulation
248 Q0BAX7 BCAL0499 Two-component regulatory system, response regulator protein 0.9 0.7 0.8 0.019
Translation
4 Q1BZ70 BCAL3373 leuS Leucine-tRNA ligase 3.4 2.5 0.7 <0.001
7 A4JDU9 BCAL1486 pheT Phenylalanine-tRNA ligase beta subunit 3.6 1.9 0.5 <0.001
17 B2JF06 BCAL2950 rpsA 30S ribosomal protein S1 2.7 2.2 0.8 <0.001
18 B2JF06 BCAL2950 rpsA 30S ribosomal protein S1 2.3 2.0 0.8 0.003
177 B2JF06 BCAL2950 rpsA 30S ribosomal protein S1 2.4 2.5 1.1 0.032
22 Q123F6 BCAL0232 tuf Elongation factor Tu 2.9 1.8 0.6 <0.001
178 Q1BX19 BCAL1416 alaS Alanine-tRNA ligase 2.9 2.0 0.7 <0.001
181 A2VV06 BCAL0679 argS Arginine-tRNA ligase 2.9 1.7 0.6 <0.001
183 Q1BSL2 BCAL0484 gatA Glutamyl-tRNA (Gln) amidotransferase subunit A 4.1 2.2 0.5 <0.001
186 Q1BRU5 BCAL0231 fusA Elongation factor G1 2.5 1.7 0.7 <0.001
187 A4JH32 BCAL2724 ileS Isoleucine-tRNA ligase 2.5 1.8 0.7 <0.001
190 Q0BE16 BCAL2090 tsf Elongation factor Ts 2.3 1.4 0.6 <0.001
256 Q1BT08 BCAL0630 Putative uncharacterized protein 0.5 0.6 1.4 0.017
Amino acid metabolism
16 Q1BHV4 BCAL2213 Oligopeptidase A 2.5 1.4 0.6 0.009
36 Q39BX5 BCAL0496 argB Acetylglutamate kinase 1.6 1.1 0.7 0.002
37 Q39BX5 BCAL0496 argB Acetylglutamate kinase 2.4 1.3 0.6 <0.001
52 A2VXX6 BCAL1874 hisZ ATP phosphoribosyltransferase regulatory subunit 2.2 1.7 0.8 <0.001
90 Q1BGN7 BCAL1796 Putative saccharopine dehydrogenase 0.7 0.8 1.1 0.001
96 Q1BGN7 BCAL1796 Putative saccharopine dehydrogenase 0.7 0.8 1.1 0.027
143 A0AXU0 BCAM0512 Putative aminotransferase 2.5 1.6 0.6 <0.001
153 A2VTH5 BCAL0312 hisD Histidinol dehydrogenase 1.5 1.2 0.8 0.005
243 Q1BHV9 BCAL2221 Putative prolyl oligopeptidase 1.2 2.7 2.3 0.076
255 A2VU73 BCAL0147 metF 5,10-methylenetetrahydrofolate reductase 0.5 0.5 1.0 0.046
270 A2VSL1 BCAL3197 glyA1 Serine hydroxymethyltransferase 0.7 0.9 1.3 0.047
277 A4JGW1 BCAL2641 Putative ornithine decarboxylase 0.4 0.4 1.0 0.016
Cell envelope biogenesis
15 A2W339 BCAM2430 Putative biotin carboxylase 2.0 1.4 0.7 0.025
35 A2VT63 BCAL3460 ddl D-alanine-D-alanine ligase 2.0 1.4 0.7 <0.001
44 A2VT78 BCAL0409 paaF Putative phenylacetic acid degradation enoyl-CoA hydratase PaaF 0.7 0.8 1.1 0.010
149 A2VVY4 BCAL2783 Putative cyclopropane-fatty-acyl-phospholipid synthase 3.1 1.5 0.5 <0.001
156 A2VWW0 BCAL2284 acoE Acetyl-CoA synthetase 1 1.9 1.3 0.7 <0.001
167 A2VT29 BCAL3420 accB Acetyl-CoA carboxylase biotin carboxyl carrier protein subunit 0.6 0.8 1.3 0.008
198 Q13XC7 BCAL2080 fabZ (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase 0.7 0.9 1.3 0.044
201 A2VXD7 BCAL2083 Outer membrane protein assembly factor YaeT 4.7 2.0 0.4 0.018
242 A2VXD7 BCAL2083 Outer membrane protein assembly factor YaeT 1.2 1.7 1.4 0.075
212 A2VQ60 BCAL1829 Putative outer membrane protein 1.6 2.0 1.3 0.084
267 B1JX22 BCAL3113 manB Phosphomannomutase 0.7 0.6 0.9 0.057
269 A4JCW7 BCAL1071 NAD-dependent epimerase/dehydratase 0.6 0.5 0.8 0.017
Energy metabolism
9 Q59097 BCAL2209 aceE Pyruvate dehydrogenase E1 component 3.5 2.0 0.6 <0.001
155 Q59097 BCAL2209 aceE Pyruvate dehydrogenase E1 component 3.4 1.9 0.6 <0.001
160 Q59097 BCAL2209 aceE Pyruvate dehydrogenase E1 component 3.4 1.8 0.5 <0.001
10 Q0BAG3 BCAM0961 acnA Aconitate hydratase 3.0 1.9 0.6 0.008
13 A2W536 BCAL3389 tktA Transketolase 1 1.5 1.3 0.8 0.009
254 A2W536 BCAL3389 tktA Transketolase 1 0.5 0.5 1.0 0.014
38 Q1BY10 BCAL2934 etfA Electron transfer flavoprotein, alpha subunit 1.6 1.3 0.8 0.008
257 Q1BY10 BCAL2934 etfA Electron transfer flavoprotein, alpha subunit 0.5 0.7 1.2 0.002
47 A2VSX6 BCAL3366 eda KHG/KDPG aldolase 1.5 1.4 0.9 0.002
81 Q0B5L9 BCAM0042 Putative aldo/keto reductase 2.3 1.4 0.6 <0.001
87 A2VSZ8 BCAL3388 gapA Glyceraldehyde-3-phosphate dehydrogenase 1 0.7 0.8 1.2 0.094
92 A2VVT0 BCAL2839 cbbA Fructose-bisphosphate aldolase 2.1 1.3 0.6 <0.001
108 A2WDT7 BCAM0972 gltA Citrate synthase 2.3 1.3 0.6 0.001
109 B1YP46 BCAL1517 odhL Dihydrolipoyl dehydrogenase 3.0 2.4 0.8 <0.001
189 B1YP46 BCAL1517 odhL Dihydrolipoyl dehydrogenase 1.7 1.4 0.8 <0.001
112 A2W309 BCAM2468 Putative aldehyde dehydrogenase family protein 3.4 2.1 0.6 <0.001
132 A2VWQ9 BCAL2338 NADH-quinone oxidoreductase 3.6 2.4 0.6 0.002
147 A4JFY5 BCAL2179 eno Enolase 0.7 0.9 1.2 0.017
168 Q1BJZ1 BCAM2821 glcB Malate synthase G 2.6 1.3 0.5 <0.001
170 Q1BNJ4 BCAM1581 pckG Phosphoenolpyruvate carboxykinase 3.8 2.2 0.6 <0.001
171 Q1BNJ4 BCAM1581 pckG Phosphoenolpyruvate carboxykinase 3.9 2.2 0.6 <0.001
204 A2VZR7 BCAM0969 sdhA Succinate dehydrogenase flavoprotein subunit 1.5 1.8 1.2 0.099
205 A2VZR7 BCAM0969 sdhA Succinate dehydrogenase flavoprotein subunit 1.6 1.7 1.1 0.040
238 A2VZR7 BCAM0969 sdhA Succinate dehydrogenase flavoprotein subunit 1.1 0.5 0.5 0.025
215 A2W2F4 BCAM2710 Putative acetyl-CoA synthetase 4.7 1.5 0.3 0.048
216 B1K5B2 BCAM1537 Putative dehydrogenase, zinc-binding subunit 1.4 1.5 1.1 0.081
227 A2VTZ2 BCAL0034 atpA ATP synthase subunit alpha 1.8 1.8 1.0 0.014
229 Q1BNJ5 BCAM1588 Isocitrate lyase 1.5 1.4 0.9 0.023
236 A2WG89 BCAM2323 Putative N-methylproline demethylase 1.3 2.2 1.7 0.086
253 Q1BRR9 BCAL0205 NADP-dependent malic enzyme 0.3 0.5 1.7 0.065
261 A2WBM9 BCAL2908 fumC Fumarate hydratase class II 0.6 0.5 0.8 0.012
262 Q1BNF8 BCAM1542 Putative aldehyde dehydrogenase 0.6 0.6 1.0 0.052
272 Q1BJI6 BCAM2702 prpC 2-methylcitrate synthase 1.3 1.7 1.7 0.055
276 A9AIN1 BCAL2074 ppsA Phosphoenolpyruvate synthase 0.5 0.5 0.5 0.016
Iron transport
68 B1YXQ3 BCAM0026 Putative siderophore-interacting protein 3.2 1.9 0.6 0.033
202 A2W3M3 BCAM2224 Putative pyochelin receptor protein FptA 1.8 1.6 0.9 0.016
203 Q1BM21 BCAM0948 TonB-dependent receptor 1.8 1.5 0.8 0.017
240 Q1BWE3 BCAL1691 orbC Putative iron transport-related ATP-binding protein 1.0 1.5 1.5 0.010
Intracellular trafficking and secretion
232 A2VW75 BCAL2669 Hypothetical protein 1.7 1.7 1.0 0.011
Secondary metabolites biosynthesis
34 A2W219 BCAM0023 adc Probable acetoacetate decarboxylase 2.3 1.4 0.6 <0.001
Coenzyme metabolism
20 A4JIQ4 BCAL0509 metK S-adenosylmethionine synthetase 0.7 0.9 1.3 0.001
69 A0K8R4 BCAL2212 folD Bifunctional protein FolD 1.6 1.4 0.9 0.026
64 A4JKF8 BCAM0022 Putative D-beta-hydroxybutyrate dehydrogenase 2.1 1.4 0.7 <0.001
Replication
220 Q1BLY0 BCAM0904 polA DNA polymerase I 1.1 1.8 1.6 0.078
Adaptation to atypical conditions
75 A2VVV1 BCAL2816 S-formylglutathione hydrolase 1.6 1.4 0.8 0.038
25 A2VT33 BCAL2013 AhpC/TSA family protein 0.7 1.0 1.4 0.002
252 A2VXR9 BCAL1937 Putative phosphorous metabolism-related protein 0.5 0.5 1.0 0.015
Transport of small molecules
213 Q1BGR3 BCAL1823 potG Putrescine ABC transporter ATP-binding protein 1.2 1.8 1.5 0.077
231 A2W3K2 BCAM2247 livF Putative amino acid ABC transporter ATP-binding protein 1.5 1.4 0.9 0.019
235 A9AH88 ABC transporter related (Polar amino acid transport) 1.6 2.5 1.6 0.046
263 Q1BIT4 BCAS0242 Hypothetical protein 0.6 0.6 1.0 0.041
Adhesion
266 Q1BKJ6 BCAM0184 bclB Lectin (Fucose-binding lectin II) 0.6 0.6 1.0 0.056
Unknown
128 Q1BJ23 BCAS0293 aidA Nematocidal protein AidA 3.0 3.2 1.1 <0.001
131 B1KBA2 BCAS0292 Hypothetical protein 0.7 0.8 1.1 0.017
207 B1KBA2 BCAS0292 Hypothetical protein 0.8 0.7 0.9 0.043
250 A2VS76 BCAL3052 Hypothetical protein 0.8 0.7 0.9 0.015

For each protein, the Genebank accession number of the best-hit protein identified by MS and the respective J2315 homolog gene are indicated.

a Values were calculated as the average data from two independent experiments (six replicates of each sample) and data were filtered to retain spots with ANOVA P-value lower than 0.05. In some specific cases, results with ANOVA P-value up to 0.05 are shown.

vs. IST439 and IST4134 vs. IST439. * Indirect determination based on the analysis of IST4113

The 30S ribosomal protein S2 (BCAL2091, spot 219) was used as a reference spot control, since its quantity remained constant across all replicates and strains. Individual spot volumes were automatically normalised against the total volume for a given gel using Progenesis Samespots software.