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. Author manuscript; available in PMC: 2010 Dec 13.
Published in final edited form as: Proteomics. 2009 Nov;9(22):5029–5045. doi: 10.1002/pmic.200900196

Table 1.

Differential 2D gel display data for S. dysenteriae serotype 1 proteins comparing in vitro and in vivo spot profiles

Fractiona) Protein name Protein description Mr (kDa)b) pIb) Vs cell cult.c) No. gelsd) CVe) Vs pig #1c) No. gelsd) CVe) Vs pig #2c) No. gelsd) Ratio pig #1/ccf)
Energy metabolism
CL 4.5 – 5.4 YfiD putative formate acetyltransferase 14374 4.96 NA 1.9 2 1.399 1
CL 5.4 – 6.2 AcnB aconitate hydrase B 94038 5.27 2.891 3 27.53% 0.72 4 16.98% 1.393 2 0.249
CL 5.4 – 6.2 Pta phosphotransacetylase 77480 5.52 1.61 3 23.34% 0.959 4 33.35% 0.762 2 0.596
CL 5.4 – 6.2 AspA aspartate ammonia-lyase 54714 5.54 3.279 3 35.45% 6.127 2 5.039 2 1.869
CL 5.4 – 6.2 IcdA isocitrate dehydrogenase 46069 5.28 4.306 3 21.87% 0.607 4 43.48% 0.619 2 0.141
CL 5.4 – 6.2 SucC succinyl-CoA synthetase, beta subunit 41610 5.37 1.999 3 36.57% 0.519 4 37.10% 0.369 2 0.260
CL 5.4 – 6.2 SucB dihydrolipoamide acetyltransferanse 43990 5.58 4.125 3 31.42% 2.31 4 78.41% 1.018 2 0.560
CL 5.4 – 6.2 AnsB periplasmic L-asparaginase II 36942 5.68 0.581 3 6.70% 1.41 4 9.90% 0.862 2 2.427
CL 5.4 – 6.2 LdhA fermentative D-lactate dehydrogenase, NAD-dependent 36869 5.37 0.554 3 33.63% 0.13 4 48.35% NA 0.235
CL 5.4 – 6.2 Mdh malate dehydrogenase 32477 5.61 3.907 3 28.69% 2.174 4 34.52% 1.473 2 0.556
CL 5.4 – 6.2 NuoE NADH dehydrogenase I chain E 18879 5.4 0.24 3 38.36% 0.078 4 30.36% 0.019 2 0.325
CL 6.2 – 7 NuoG NADH dehydrogenase I chain G 101514 5.89 0.757 4 8.11% 0.927 2 NA 1.225
CL 6.2 – 7 PflB formate acetyltransferase 1, pyruvate formate lyase 85581 5.69 1.551 4 17.48% 8.5 2 NA 5.480
CL 6.2 – 7 PykA pyruvate kinase II 51583 6.24 0.679 4 19.62% 0.998 2 NA 1.470
CL 6.2 – 7 GltA citrate synthase 48384 6.06 5.938 4 16.23% 1.328 2 NA 0.224
CL 6.2 – 7 AckA acetate kinase 43593 5.85 0.745 4 33.93% 2.394 2 NA 3.213
CL 6.2 – 7 PflA pyruvate formate lyase activating enzyme 1 28528 6 0.18 4 31.76% 0.689 2 NA 3.828
CL 6.2 – 7 PykF pyruvate kinase I, fructose stimulated 51027 5.77 2.966 4 6.19% 3.89 2 NA 1.312
CL 6.2 – 7 PoxB pyruvate oxidase 62541 5.89 3.722 4 12.92% 2.451 2 NA 0.659
CL 7 – 10 NapA probable nitrate reductase 3, periplasmic 93682 7.85 NA 2.551 2 1.634 1
CL 7 – 10 NuoF NADH dehydrogenase I chain F 49774 6.44 1.404 3 9.86% 0.16 2 NA 0.114
hs-MBR AdhE bifunctional acetaldehyde-CoA/alcohol dehydrogenase 96580 6.32 7.387 2 10.56 2 12.82 1 1.429
hs-MBR SucD succinyl-CoA synthetase, alpha subunit 30128 6.18 12.164 2 0.45 2 0.615 1 0.037
hs-MBR NuoB NADH dehydrogenase I chain B 25339 5.58 1.338 2 0.398 2 0.562 1 0.297
hs-MBR FrdB fumarate reductase, iron-sulfur protein subunit 27735 6.07 1.177 2 0.958 2 0.913 1 0.814
hs-MBR SdhB succinate dehydrogenase, iron sulfur protein 27452 5.97 7.432 2 0.198 2 0.248 1 0.027
hs-MBR NuoI NADH dehydrogenase I chain I 21067 5.4 1.264 2 NA NA
usb-MBR SdhA succinate dehydrogenase, flavoprotein subunit 65024 5.85 8.067 2 0.389 2 0.743 1 0.048
usb-MBR NuoC NADH dehydrogenase I chain C, D 68909 5.98 0.739 4 6.54% 0.293 2 NA 0.396
usb-MBR FumA fumarase A 60744 6.11 3.497 4 3.41% 0.581 2 NA 0.166
usb-MBR LldD L-lactate dehydrogenase 42899 6.33 4.661 4 4.19% 2.402 2 NA 0.515
Acid resistance
CL 4.5 – 5.4 HdeA Hypoth. protein SDY_3543, acid resistance chaperone 11964 5.06 23.858 2 48.96 2 65.16 1 2.052
CL 4.5 – 5.4 HdeB Hypoth. protein SDY_3544, acid resistance chaperone 12610 6.55 2.206 2 5.929 2 2.773 1 2.688
CL 5.4 – 6.2 AdiA biodegradative arginine decarboxylase 85071 5.09 0.128 3 50.89% 9.111 2 NA 71.180
CL 5.4 – 6.2 ClpB protein disaggregation chaperone 95725 5.37 1.686 3 25.34% 7.259 4 25.31% 5.716 2 4.305
CL 5.4 – 6.2 GadB glutamate decarboxylase isozyme 53220 5.28 9.42 3 28.92% 14.74 4 5.14% 17.01 2 1.564
hs-MBR AdiA biodegradative arginine decarboxylase 85071 5.09 NA 2 3.618 2 0.575 1
hs-MBR ClpB protein disaggregation chaperone 95725 5.37 0.992 2 6.245 2 4.791 1 6.295
hs-MBR GadB glutamate decarboxylase isozyme 53220 5.28 0.254 2 5.082 2 7.561 1 20.008
usb-MBR AdiA biodegradative arginine decarboxylase 85071 5.09 NA 4 11.85% 11.48 2 NA
usb-MBR ClpB protein disaggregation chaperone 95725 5.37 0.165 4 29.63% 8.74 2 NA 52.970
usb-MBR GadB glutamate decarboxylase isozyme 53220 5.28 0.641 4 21.81% 10.29 2 NA 16.055
Host cell invasion and subversion of host immune response
CL 4.5 – 5.4 IpgC cytoplasmic chaperone for IpaB and IpaC 17916 4.58 NA 1.324 2 4.156 1
CL 5.4 – 6.2 IpaD invasion plasmid antigen IpaD 36738 5.69 0.08 2 0.199 4 19.49% 0.012 1 2.488
CL 5.4 – 6.2 PhoN2 periplasmic ATP diphosphohydrolase PhoN2/Apy 27728 5.46 0.377 3 36.02% NA NA
CL 5.4 – 6.2 StxB Shiga toxin subunit B precursor 9851 7.77 0.267 3 6.74% NA NA
CL 6.2 – 7 IpaD invasion plasmid antigen IpaD 36738 5.69 NA 0.634 2 NA
CL 6.2 – 7 PhoN1 periplasmic non-specific acid phosphatase PhoN1 27266 6.43 2.28 4 20.56% 0.948 2 NA 0.416
CL 7 – 10 OspC2 outer Shigella protein family protein OspC2 55775 6.58 0.467 4 28.58% 2.262 2 NA 4.844
CL 7 – 10 IpaC invasion plasmid antigen IpaC 38731 7.85 1.252 3 39.25% 18.38 2 3.453 2 14.681
CL 7 – 10 IcsB invasive protein IcsB 56540 9.34 NA 2.951 2 NA
CL 7 – 10 OspF mouse killing factor, phosphothreonine lyase 28167 8.2 NA 1.493 2 NA
CL 7 – 10 IpgB1 membrane ruffles-inducing protein IpgB1 23731 9.45 3.906 2 5.383 2 3.143 2 1.378
CL 7 – 10 StxA Shiga toxin subunit A precursor 34906 9.63 1.454 2 NA NA
usb-MBR IpaA invasion plasmid antigen IpaA 70223 6.27 NA 0.932 2 NA
Oxidative stress response, iron storage, quorum sensing
CL 4.5 – 5.4 Ftn cytoplasmic ferritin 19468 4.77 9.182 2 1.733 2 2.389 1 0.189
CL 4.5 – 5.4 Bfr iron storage and detoxification protein, bacterioferrin 18326 4.64 12.636 2 1.713 2 1.155 1 0.136
CL 5.4 – 6.2 YgaG S-ribosylhomocysteinase, LuxS ortholog 19575 5.18 1.491 3 16.03% 0.209 4 77.25% 0.117 2 0.140
CL 5.4 – 6.2 SodB superoxide dismutase, iron 21310 5.58 3.337 3 32.21% 6.554 4 13.95% 5.134 2 1.964
CL 5.4 – 6.2 WrbA putative NAD(P)H:quinone oxidoreductase 20862 5.59 1.682 3 14.05% 3.675 4 4.96% 3.394 2 2.185
CL 5.4 – 6.2 SodC superoxide dismutase (Cu-Zn) 17764 6.04 1.697 3 1.11% 0.181 4 36.38% 0.125 2 0.107
CL 6.2 – 7 SodA superoxide dismutase, manganese 23079 6.45 3.279 4 9.47% 0.401 2 NA 0.122
CL 7 – 10 SitA iron transport protein, periplasmic-binding protein 33565 8.34 2.108 3 10.84% NA NA
hs-MBR Dps stationary phase protection protein Dps 18684 5.72 26.394 2 6.843 2 12.9 1 0.259
a)

subcellular fraction in which the protein spot was identified; CL, cell lysate listed with the pI range for protein detection; hs-MBR, high salt-extracted membrane fraction; usb-MBR, urea/thiourea/amidosulfobetaine-14-extracted membrane fraction;

b)

predicted molecular weight (Mr) and pI values;

c)

normalized relative spot intensity volume (or sum of spot volumes) for a S. dysenteriae protein measured using the software Proteomweaver v.4.0; cell cult. (in vitro cell culture, stationary phase); pig #1, cells isolated from the gut of piglet #1; pig# 2, cells isolated from the gut of piglet #2;

d)

number of gels in which the protein was quantitated;

e)

CV, if at least 3 spot intensity measurements per group were available;

f)

ratio of protein spot quantities: in vivo piglet #1 vs. in vitro cell culture; NA: protein was not detected in 2D gels.