Table II Ubiquitous proteins identified by iTRAQ in the GC cell envelope
AccessionNameGeneAverage ratio ± S.D.aSbTc
F62:FA1090MS11:FA10901291:FA1090
Extracellular
    Q5F7V4LipoproteinNGO10631.31 ± 0.261.45 ± 0.171.18 ± 0.1YN
Outer membrane
    Q5F5F6Adhesin mafA 1/4mafA1/NGO1067 mafA4/NGO19720.63 ± 0.031.1 ± 0.011.47 ± 0.32NN
    Q5F9W0Competence lipoproteinbamD, comL/NGO02771.07 ± 0.091.25 ± 0.391.06 ± 0.02YN
    Q5F679Efflux pump protein, fatty acid resistanceemrA/NGO16831.33 ± 0.220.98 ± 0.31.42 ± 0.11NY
    Q5F651LPS-assembly protein LptDlptD, imp, ostA/NGO17151.14 ± 0.191.34 ± 0.291.23 ± 0.1YN
    Q5F6J5OmpA/MotB domain-containing proteinNGO15591.33 ± 0.21.64 ± 0.311.1 ± 0.16YN
    Q5F5W8Outer membrane protein assembly factor BamAbamA/NGO18011.27 ± 0.211.15 ± 0.391.16 ± 0.03YN
    Q5F6I1Outer membrane protein PIIIrmp/NGO15771.22 ± 0.271.22 ± 0.170.73 ± 0.02YN
    Q5F7A4Nitrite reductasedaniA/NGO12761.46 ± 0.261.15 ± 0.241.13 ± 0.31YY
    Q5F8E4Periplasmic proteinNGO08341.49 ± 0.141.16 ± 0.090.8 ± 0.07YN
    Q5F7F3Peptidyl-prolyl cis-trans isomerase Ng-MIPemip/NGO12251.15 ± 00.94 ± 0.091.17 ± 0.07YY
    Q5F6Q7PhospholipasepldA/NGO14921.42 ± 0.141.37 ± 0.011.15 ± 0NN
    Q5FAG7Pilus-associated proteinpilC/NGO00551.13 ± 0.041.14 ± 0.11.21 ± 0.14NY
    Q5FAC9Putative pilus assembly proteinpilN/NGO00971.01 ± 0.051.13 ± 0.061.31 ± 0.03NN
    Q5F7H3Putative TonB-dependent receptor proteinNGO12050.88 ± 0.041.11 ± 0.030.67 ± 0.13YN
    Q5F518Putative uncharacterized proteinNGO21210.69 ± 0.051.14 ± 0.090.83 ± 0.06YN
    Q5F526Putative uncharacterized proteinNGO21111.08 ± 0.180.82 ± 0.040.81 ± 0.01NY
    Q5F5E4Putative uncharacterized proteinNGO19850.88 ± 0.061.17 ± 0.010.83 ± 0.04NN
    Q5F5H0Putative uncharacterized proteinNGO19561.18 ± 0.081.4 ± 0.171.41 ± 0.02NN
    Q5F5H1Putative uncharacterized proteinNGO19551.2 ± 0.11.15 ± 0.241.15 ± 0.1NN
    Q5F743Putative uncharacterized proteinNGO13441.01 ± 0.051.05 ± 0.140.9 ± 0.11NN
    Q5FAD2Type IV pilus biogenesis and competence protein pilQpilQ, omc/NGO00941.12 ± 0.191.15 ± 0.090.89 ± 0.13YN
Periplasmic
    Q5F601CatalasekatA/NGO17670.92 ± 0.051.09 ± 0.390.97 ± 0.05NN
    Q5F544Ferric enterobactin periplasmic binding proteinfetB/NGO20921.06 ± 0.060.99 ± 0.331.27 ± 0.09NN
    Q5F581Genome-derived Neisserial antigen 33NGO20481.38 ± 0.211.24 ± 0.011.28 ± 0.04YN
    Q5F809Lipid modified azurin proteinazu/NGO09941.09 ± 0.241.07 ± 0.041.15 ± 0.01YY
    Q5F765LipoproteinNGO13211.14 ± 0.251 ± 0.321.1 ± 0.08NN
    Q5F848LipoproteinNGO09481.47 ± 0.211.34 ± 01.05 ± 0.02NN
    Q5F8T2LipoproteinNGO06781.08 ± 0.220.99 ± 0.050.78 ± 0.09YN
    Q5F8W2Membrane lipoproteinNGO06481.47 ± 0.121.02 ± 01.43 ± 0.21NN
    Q5FAC7Penicillin-binding protein 1AmrcA/NGO00991.46 ± 0.140.7 ± 00.82 ± 0.01NN
    Q5F9Z6Periplasmic proteinNGO02381.1 ± 0.041.23 ± 0.071.31 ± 0.15YN
    Q5F9M1Putative ABC transporter, periplasmic binding protein, amino acidNGO03720.85 ± 0.050.97 ± 0.11.04 ± 0YY
    Q5F6Q5Putative ABC transporter, periplasmic binding protein, polyamineNGO14940.79 ± 0.020.74 ± 01.24 ± 0.03YN
    Q5F7C5Putative ABC transporter, periplasmic binding protein, polyamineNGO12531.14 ± 0.020.93 ± 0.21.79 ± 0.01NN
    Q5FA28Putative ABC transporter, periplasmic binding protein, polyamineNGO02060.64 ± 00.83 ± 0.011.5 ± 0.12YN
    Q5F574Putative ABC transporter, thiamine-binding periplasmic proteinNGO20561.43 ± 0.290.84 ± 0.231.41 ± 0YN
    Q5FAB9Putative carboxypeptidase, penicillin binding proteinpbp3/NGO01071.05 ± 0.281.43 ± 0.180.83 ± 0.17YN
    Q5F718Putative cytochrome c oxidase subunitNGO13711.15 ± 0.171.1 ± 0.461.01 ± 0.12NN
    Q5F598Putative cytochrome C1NGO20311.16 ± 0.011.3 ± 0.011.66 ± 0.04YN
    Q5F8Y3Putative murein hydrolasemltB/NGO06261.4 ± 0.061.43 ± 0.011.05 ± 0.16YN
    Q5FA91Putative serine proteaseNGO01381.06 ± 0.110.98 ± 0.41.11 ± 0.06YN
    Q5F515Putative thioredoxinNGO21240.9 ± 0.051.02 ± 0.181.12 ± 0.04NN
    Q5F5C7Putative uncharacterized proteinNGO20021.29 ± 01.06 ± 0.071.34 ± 0.23NN
    Q5F6P4Putative uncharacterized proteinNGO15051.18 ± 0.111.28 ± 0.141.71 ± 0.08NN
    Q5F7W0Putative uncharacterized proteinNGO10561.17 ± 0.151.18 ± 0.450.95 ± 0.07NY
    Q5F7X1Putative uncharacterized proteinNGO10440.94 ± 0.411.02 ± 0.111.27 ± 0.1NN
    Q5F7X2Putative uncharacterized proteinNGO10431.07 ± 0.011.06 ± 0.20.84 ± 0.11YN
    Q5F8C4Putative uncharacterized proteinNGO08611.17 ± 0.191.4 ± 0.421.23 ± 0.16YN
    Q5F571Putativeptide methionine sulfoxide reductasemsrAB, pilB/NGO20591.36 ± 0.311.19 ± 0.361.29 ± 0.33YN
    Q5F649Thiol:disulphide interchange proteindsbA/NGO17170.98 ± 0.021.14 ± 0.131.28 ± 0.02YY
    Q5F6V7Thiol:disulphide interchange proteindsbC/NGO14381.37 ± 0.031.01 ± 0.11.03 ± 0.1YN
    Q5F505TransglycosylaseNGO21351.62 ± 0.221.29 ± 0.170.98 ± 0.12YN
    Q5F912Type IV pilus assembly proteinpilF/NGO05951.3 ± 0.11.01 ± 0.091.07 ± 0.08NN
Inner membrane
    Q5F4Z4ATP synthase subunit batpF/NGO21461.23 ± 0.031.04 ± 01.17 ± 0.18NN
    Q5F9L1ATP-dependent zinc metalloprotease FtsHftsH/NGO03821.04 ± 0.051.14 ± 0.421.29 ± 0.03NN
    Q5F6M1Cell division protein FtsQftsQ/NGO15300.95 ± 0.050.7 ± 0.31.01 ± 0.09NN
    Q5F6L1Division cell wall proteindcaA/NGO15400.97 ± 0.090.88 ± 0.161 ± 0.06NN
    Q5F8I5Genome-derived Neisseria antigen 1220NGO07881.43 ± 0.031.27 ± 01.52 ± 0NN
    Q5F573Integral membrane proteinNGO20571.28 ± 0.091.32 ± 0.021.26 ± 0.02NN
    Q5F5L3Integral membrane proteinNGO19100.82 ± 0.061.1 ± 0.140.94 ± 0.03YN
    Q5F795Integral membrane proteinNGO12881.15 ± 0.021.06 ± 0.021.27 ± 0.03NN
    Q5F4X8Lipid A export ATP-binding/permease protein MsbAmsbA/NGO21651.07 ± 0.021.05 ± 0.161.13 ± 0.11NN
    Q5F6V6Macrolide export ATP-binding/permease protein MacBmacB/NGO14391.25 ± 0.140.94 ± 0.40.85 ± 0.09NN
    Q5F4W6Membrane protein insertase YidCyidC/NGO21781.2 ± 0.070.99 ± 0.051.2 ± 0.03NN
    Q5F6K9Penicillin-binding protein 2penA/NGO15421.15 ± 00.79 ± 0.211 ± 0.1NN
    Q5F7H2Phosphatidylserine decarboxylase proenzymepsd/NGO12061.09 ± 0.021.31 ± 0.31.32 ± 0.04NN
    Q5F693Pilus assembly proteinpilG/NGO16691.33 ± 0.051.17 ± 01.44 ± 0.01NN
    Q5FAD0Pilus assembly proteinpilO/NGO00961.28 ± 0.151.03 ± 0.211.35 ± 0.11NN
    Q5F6W9Probable ubiquinone biosynthesis protein UbiBubiB/NGO14241.26 ± 0.11.18 ± 0.131.39 ± 0.18NY
    Q5FA43Protein translocase subunit SecDsecD/NGO01891.24 ± 0.071.08 ± 01.21 ± 0.11NN
    Q5F567Putative 1-acyl-SN-glycerol-3-phosphate acyltransferasenlaB/NGO20691.03 ± 0.081.06 ± 0.21.48 ± 0.06NN
    Q5F523Putative ABC transporter, ATP-binding proteinNGO21160.98 ± 0.031.12 ± 0.241.27 ± 0.05NN
    Q5F634Putative ABC transporter, ATP-binding proteinNGO17321.22 ± 0.061.23 ± 0.031.5 ± 0.05NN
    Q5F969Putative acyl-CoA ligaseNGO05301.13 ± 0.111 ± 0.391.02 ± 0.06NN
    Q5F7V3Putative carbon starvation proteincstA/NGO10641.01 ± 0.041.44 ± 0.021.55 ± 0.02NN
    Q5F823Thiol:disulfide interchange protein DsbDdsbD/NGO09781.11 ± 0.041.1 ± 0.211.06 ± 0.12NN
    Q5F952Putative dnaJ-family proteinNGO05511.29 ± 0.230.93 ± 0.351 ± 0.12NN
    Q5F7Y5Putative ferredoxinNGO10260.99 ± 00.89 ± 0.031.02 ± 0.04NY
    Q5F7V7Putative fimbrial assembly proteinfimB/NGO10601.14 ± 0.031.01 ± 0.041.35 ± 0.09NY
    Q5F916Putative ftsK-like cell division/stress response proteinNGO05901.07 ± 0.020.98 ± 0.191.04 ± 0.08NN
    Q5F8K3Putative lipoprotein releasing system transmembrane proteinNGO07691.19 ± 0.111.17 ± 0.121.43 ± 0.05NN
    Q5F9U8Putative Na+/H+ antiporterNGO02911.29 ± 0.21.2 ± 0.291.53 ± 0.02NN
    Q5F6S7Putative NADP transhydrogenase, alpha subunitNGO14701.38 ± 0.011.14 ± 0.031.26 ± 0.02NN
    Q5F7A5Putative nitric oxide reductaseNGO12751.5 ± 0.161.03 ± 0.051 ± 0.19NN
    Q5F8S5Putative P-type cation-transporting ATPaseNGO06851.03 ± 01.22 ± 0.031.39 ± 0.02NN
    Q5F7D2Putative serine proteaseNGO12461.46 ± 0.290.85 ± 0.170.87 ± 0NN
    Q5FAG5Putative thioredoxinNGO00571.26 ± 0.091.13 ± 0.241.12 ± 0.11NN
    Q5F614Putative uncharacterized proteinNGO17521.14 ± 0.111.15 ± 0.340.73 ± 0.1NN
    Q5FA44Putative uncharacterized proteinNGO01881.04 ± 0.081.45 ± 0.351.32 ± 0.25NN
    Q5F5W9RIP metalloprotease RsePrseP/NGO18001.02 ± 0.030.95 ± 0.121.03 ± 0.1NN
    Q5F5K7Transmembrane transporterNGO19170.91 ± 0.121.25 ± 0.211.28 ± 0.59NN
    Q5F711Transport proteinexbB/NGO13781.05 ± 0.030.82 ± 0.20.99 ± 0NN
    Q5F5Q0Two-component system sensor kinaseNGO18671.12 ± 0.011 ± 0.141.23 ± 0.03NN
    Q5FA56Two-component system sensor kinaseNGO01761.14 ± 0.011.13 ± 0.081.26 ± 0.02NN
    Q5FAA1UPF0761 membrane protein NGO0127NGO01271.26 ± 0.141.14 ± 0.11.07 ± 0.2NN
    Q5F9N3Uroporphyrin-III C-methyltransferasehemX/NGO03600.9 ± 0.020.86 ± 0.151.22 ± 0.1NN
    Q5F7H9YhbX/YhjW/YijP/YjdB family proteinNGO11981.06 ± 0.091.18 ± 0.291.12 ± 0NN
Unknown
    Q5F8Z81-acyl-SN-glycerol-3-phosphate acyltransferaseplsC/NGO06111.36 ± 0.111.32 ± 0.021.5 ± 0.22NY
    Q5F5V030S ribosomal protein S11rpsK/NGO18201.14 ± 0.030.99 ± 0.060.92 ± 0.06NY
    Q5F9134-hydroxy-3-methylbut-2-en-1-yl diphosphate synthaseispG/NGO05940.82 ± 0.080.67 ± 0.080.63 ± 0.09NN
    Q5F9Z8Cell division protein zipAzipA/NGO02360.99 ± 0.011.11 ± 0.051.25 ± 0.01NN
    Q5F501Genome-derived Neisserial antigen 1946NGO21391.21 ± 0.041.23 ± 0.051.74 ± 0.03YY
    Q5F9N2HemY proteinhemY/NGO03611.12 ± 0.031.15 ± 0.061.29 ± 0.03NN
    Q5F9W2IgA-specific metalloendopeptidaseiga/NGO02750.93 ± 0.031.39 ± 0.11.05 ± 0YN
    Q5F5I3LipoproteinNGO19420.99 ± 0.051.24 ± 0.061 ± 0.02NN
    Q5F8J5Membrane proteinNGO07781.12 ± 0.010.89 ± 0.271.01 ± 0.06NN
    Q5F7J8Minor pilin ComPcomP/NGO11771.17 ± 0.20.62 ± 0.331.54 ± 0.01NN
    Q5F521Outer membrane transporterNGO21180.96 ± 0.21.07 ± 0.211.05 ± 0.15NN
    Q5F8S7Periplasmic proteinNGO06831.04 ± 0.40.84 ± 0.080.87 ± 0.28YN
    Q5FAD1Pilin assembly proteinpilP/NGO00951.19 ± 0.041.08 ± 0.071.45 ± 0.16YN
    Q5F4Y0Putative 3-oxoacyl-[acyl-carrier protein] reductasefabG/NGO21630.62 ± 0.110.8 ± 0.210.76 ± 0.02NY
    Q5FA61Putative ABC transporter, ATP-binding proteinznuC, troB/NGO01700.87 ± 0.20.77 ± 0.230.7 ± 0.13NN
    Q5F531Putative adhesion and penetration proteinNGO21051.04 ± 0.270.96 ± 0.130.94 ± 0.12NY
    Q5F6P7Putative amidaseamiC/NGO15021.56 ± 0.091.47 ± 01.32 ± 0.14NY
    Q5F932Putative carboxy-terminal processing proteaseNGO05720.82 ± 0.060.98 ± 0.360.84 ± 0.04YN
    Q5F759Putative cytochromeNGO13281.16 ± 0.011.2 ± 0.121.28 ± 0.23NY
    Q5FA09Putative MafB-like proteinNGO02251.18 ± 0.171.2 ± 0.461.02 ± 0.01YN
    Q5F6X8Putative Na(+)-translocating NADH-ubiquinone reductase subunit CnqrC/NGO14151.1 ± 0.191.04 ± 0.161.11 ± 0.19NN
    Q5F674Putative outer membrane protein OmpUompU/NGO16881.73 ± 0.171.44 ± 01.54 ± 0.31YN
    Q5F8E6Putative oxidoreductaseNGO08311.17 ± 0.11.33 ± 0.161.28 ± 0.25NN
    Q5F766Putative paraquat-inducible protein BNGO13201.01 ± 0.020.98 ± 0.131 ± 0.01NN
    Q5FAC8Putative pilus assembly proteinpilM/NGO00981.11 ± 0.041.34 ± 0.171.48 ± 0.09NN
    Q5F520Putative uncharacterized proteinNGO21191.27 ± 0.051.03 ± 0.050.7 ± 0.18YN
    Q5F5E5Putative uncharacterized proteinNGO19840.9 ± 0.040.98 ± 0.141.04 ± 0.04NN
    Q5F5P4Putative uncharacterized proteinNGO18731.34 ± 0.281.34 ± 0.10.94 ± 0.08NN
    Q5F5W7Putative uncharacterized proteinNGO18021.06 ± 0.181.45 ± 0.021.06 ± 0.19YY
    Q5F657Putative uncharacterized proteinNGO17091.22 ± 0.031.3 ± 0.071.44 ± 0.01NY
    Q5F676Putative uncharacterized proteinNGO16861.11 ± 0.011.22 ± 0.031.29 ± 0NN
    Q5F6K2Putative uncharacterized proteinNGO15491.15 ± 0.091.1 ± 0.291.31 ± 0.03NY
    Q5F6P5Putative uncharacterized proteinNGO15040.95 ± 0.081.38 ± 0.221.45 ± 0.09NN
    Q5F7A6Putative uncharacterized proteinNGO12741.41 ± 0.021.62 ± 0.11.46 ± 0.01NY
    Q5F7C7Putative uncharacterized proteinNGO12510.94 ± 0.060.88 ± 0.390.62 ± 0.05NN
    Q5FAK6Putative uncharacterized proteinNGO00281.07 ± 0.171.44 ± 0.091.31 ± 0.36NN
    Q5F9Q0Signal peptidase IlepB/NGO03431.01 ± 0.091.07 ± 0.121.21 ± 0.1NN
    Q5F9E3Type IV pilus assembly protein PilXpilX/NGO04550.57 ± 0.060.74 ± 0.030.67 ± 0.12NN
    O87406UPF0070 protein NGO0425NGO04251.11 ± 0.071.12 ± 0.220.98 ± 0.01NN
  • a Average ratios and standard deviations were calculated for proteins ubiquitously expressed in biological replica experiments.

  • b Predictions of signal peptide cleavage site using SignalP (47).

  • c Presence of twin-arginine signal peptide as determined by TatP (48).

  • d The surface localization of AniA was verified experimentally (97).

  • e The outer membrane localization of Ng-MIP was verified experimentally (78).