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Table 1 Differentially expressed proteins under ex vivo conditions in BALF model

From: Quantitative proteomic analysis of host—pathogen interactions: a study of Acinetobacter baumannii responses to host airways

Protein description AbH12O-A2 locus Sec.a BALF model/controlb BALF model/control p-valuec
Pathogenesis and virulence
Molecular chaperone DnaK AIS05048.1 NO 1.77 (0.65) 0.027
Clp protease ClpX AIS05265.1 NO 1.51 (0.61) 0.024
Amino acid ABC transporter substrate-binding protein (NfuA-like) AIS05727.1 YES 2.38 (1.76) 0.031
Enoyl-CoA hydratase (PaaZ) AIS06043.1 NO 0.30 (0.11) 0.012
Peptidase M16 AIS06751.1 NO 0.29 (0.16) 0.007
Aminopeptidase N AIS06953.1 NO 0.39 (0.21) 0.023
Protein CsuC AIS07073.1 YES 2.19 (0.76) 0.003
Protein CsuA AIS07075.1 YES 1.87 (0.95) 0.036
Membrane protein (OmpA) AIS07737.1 YES 1.51 (0.65) 0.015
Oligopeptidase A AIS07885.1 NO 0.48 (0.11) 0.001
ABC transporter ATP-binding protein (YjjK) AIS08062.1 NO 1.74 (0.61) 0.038
Amino acid metabolism and transport
Aspartate-semialdehyde dehydrogenase AIS05215.1 NO 0.25 (0.19) 0.038
2-Isopropylmalate synthase AIS05260.1 NO 0.31 (0.11) 0.034
Ketol-acid reductoisomerase AIS05310.1 NO 0.31 (0.05) 0.027
Ornithine carbamoyltransferase AIS06867.1 NO 0.40 (0.17) 0.044
Aspartate aminotransferase AIS07065.1 NO 0.08 (0.07) 0.000
Glutamate synthase AIS08029.1 NO 0.39 (0.20) 0.025
Carbohydrate metabolism and transport
Phosphoglyceromutase AIS05033.1 NO 0.26 (0.14) 0.020
Phosphoenolpyruvate synthase AIS07024.1 NO 0.19 (0.04) 0.000
Glucose dehydrogenase AIS07744.1 NO 0.19 (0.13) 0.009
Cell cycle control and mitosis
Cell division inhibitor MinD AIS05622.1 NO 1.63 (1.55) 0.000
tRNA uridine 5-carboxymethylaminomethyl modification protein AIS07041.1 NO 2.70 (1.89) 0.025
Cell division protein FtsZ AIS08195.1 NO 4.61 (1.68) 0.001
Cell wall/membrane/envelope biogenesis
Membrane protein(OmpW) AIS05087.1 YES 2.25 (0.89) 0.032
UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) AIS05387.1 NO 2.27 (1.47) 0.002
UDP-N-acetylmuramate-alanine ligase (MurC) AIS08199.1 NO 99.08 (0.00) 0.020
Coenzyme metabolism
Coproporphyrinogen III oxidase AIS07950.1 NO 0.31 (0.13) 0.004
3-Phosphoglycerate dehydrogenase AIS07996.1 NO 0.38 (0.09) 0.016
Defense mechanisms (cellular processes and signaling)
RND transporter AIS04803.1 YES 0.30 (0.22) 0.004
Energy production and conversion
Malate dehydrogenase AIS04961.1 NO 0.45 (0.23) 0.038
Inorganic pyrophosphatase AIS05013.1 YES 2.83 (1.43) 0.030
Aconitate hydratase AIS05319.1 NO 0.21 (0.16) 0.000
NAD(P) transhydrogenase subunit alpha AIS05328.1 NO 2.49 (1.37) 0.041
NADH dehydrogenase AIS05456.1 NO 0.44 (0.17) 0.012
Cytochrome C oxidase subunit II AIS07026.1 NO 0.21 (0.23) 0.016
Malic enzyme AIS07199.1 NO 0.46 (0.10) 0.041
Isocitrate dehydrogenase AIS07371.1 NO 0.29 (0.05) 0.004
Phosphoenolpyruvate carboxykinase AIS07529.1 NO 2.23 (0.66) 0.000
Succinyl-CoA synthetase subunit beta AIS07559.1 NO 0.41 (0.06) 0.035
Energy production and conversion
2-Oxoglutarate dehydrogenase AIS07562.1 NO 0.20 (0.04) 0.000
Succinate dehydrogenase AIS07563.1 NO 1.98 (0.64) 0.017
Type II citrate synthase AIS07567.1 NO 0.22 (0.05) 0.002
Oxidoreductase AIS07724.1 NO 0.31 (0.22) 0.001
Malate dehydrogenase AIS07865.1 NO 0.47 (0.06) 0.040
Acetyl-CoA hydrolase AIS08069.1 NO 2.05 (0.67) 0.008
Pyruvate dehydrogenase AIS08191.1 NO 0.36 (0.06) 0.000
Unknown function
Hypothetical protein AIS05481.1 YES 0.07 (0.10) 0.013
Peptidoglycan-binding protein LysM AIS05521.1 YES 0.05 (0.03) 0.003
Hypothetical protein AIS06125.1 YES 0.17 (0.07) 0.027
DNA-binding protein AIS07086.1 YES 0.08 (0.07) 0.006
Peptidase AIS07285.1 YES 4.57 (3.14) 0.000
Glyoxalase AIS07740.1 YES 0.39 (0.45) 0.015
Hypothetical protein AIS07742.1 YES 1.84 (1.06) 0.048
General functional prediction only (typically, prediction of biochemical activity)
Alpha/beta hydrolase AIS06658.1 YES 0.09 (0.07) 0.001
GTPase obg AIS07390.1 NO 2.58 (1.05) 0.025
Hypothetical protein AIS07569.1 NO 3.47 (1.83) 0.027
Inorganic ion transport and metabolism
Bacterioferritin AIS05502.1 NO 0.25 (0.18) 0.013
Hydroperoxidase AIS06129.1 YES 0.26 (0.10) 0.000
Inorganic ion transport and metabolism
Superoxide dismutase AIS07203.1 YES 0.49 (0.14) 0.013
Sulfurtransferase AIS07821.1 NO 0.37 (0.28) 0.006
Intracellular trafficking and secretion
RNA-binding protein AIS05494.1 NO 2.07 (0.97) 0.001
Lipid metabolism
3-Ketoacyl-CoA thiolase AIS05097.1 NO 0.35 (0.18) 0.049
Multifunctional fatty acid oxidation complex subunit alpha AIS05098.1 NO 0.29 (0.08) 0.000
Acetyl-CoA carboxylase AIS05368.1 NO 2.01 (0.67) 0.000
3-Hydroxyacyl-CoA dehydrogenase AIS06051.1 NO 0.32 (0.22) 0.023
Beta-ketoadipyl CoA thiolase AIS06052.1 NO 0.28 (0.10) 0.000
3-Methylcrotonyl-CoA carboxylase AIS06111.1 NO 0.11 (0.04) 0.002
Short-chain dehydrogenase AIS06130.1 YES 0.04 (0.05) 0.040
Acetyl-CoA acetyltransferase AIS06469.1 YES 0.09 (0.13) 0.027
Acetyl-CoA carboxylase AIS06900.1 NO 0.42 (0.17) 0.001
3-Hydroxy-2-methylbutyryl-CoA dehydrogenase AIS07009.1 NO 0.25 (0.18) 0.031
Acetyl-CoA acetyltransferase AIS07739.1 YES 0.24 (0.26) 0.017
Acyl-CoA dehydrogenase AIS07780.1 NO 0.22 (0.16) 0.000
Nucleotide metabolism and transport
GMP synthase AIS04952.1 NO 0.31 (0.17) 0.000
Formyltetrahydrofolate deformylase AIS05238.1 NO 1.64 (1.02) 0.012
Deoxyuridine 5′-triphosphate nucleotidohydrolase AIS05628.1 NO 4.45 (6.37) 0.039
Dihydroorotase AIS05812.1 NO 1.79 (1.15) 0.043
Nucleotide metabolism and transport
Orotate phosphoribosyltransferase AIS08207.1 NO 2.73 (1.78) 0.004
Post-translational modification, protein turnover, chaperone functions
Peroxidase AIS07758.1 YES 0.25 (0.21) 0.033
Replication and repair
Chromosomal replication initiation protein AIS04811.1 NO 81.66 (31.26) 0.017
DNA gyrase subunit A AIS07481.1 NO 0.09 (0.16) 0.004
Transcription
Antitermination protein NusG AIS05075.1 NO 2.00 (0.81) 0.010
DNA-directed RNA polymerase subunit beta AIS05080.1 NO 0.26 (0.05) 0.000
DNA-directed RNA polymerase subunit beta’ AIS05081.1 NO 0.10 (0.04) 0.000
RNA polymerase sigma factor RpoD AIS07572.1 NO 1.92 (1.40) 0.042
Translation
Isoleucine-tRNA ligase AIS04850.1 NO 0.28 (0.09) 0.001
Arginine-tRNA ligase AIS04960.1 NO 0.47 (0.16) 0.019
50S ribosomal protein L1 AIS05077.1 YES 3.40 (0.93) 0.000
30S ribosomal protein S15 AIS05149.1 NO 15.56 (6.87) 0.045
50S ribosomal protein L28 AIS05235.1 YES 1.85 (0.68) 0.042
Leucyl-tRNA synthetase AIS05306.1 NO 0.39 (0.16) 0.029
Threonyl-tRNA synthetase AIS05352.1 NO 0.09 (0.16) 0.000
30S ribosomal protein S7 AIS05609.1 NO 9.91 (4.58) 0.000
Elongation factor Tu AIS05611.1 NO 0.34 (0.05) 0.002
Cysteinyl-tRNA synthetase AIS05938.1 NO 0.18 (0.11) 0.015
30S ribosomal protein S6 AIS07031.1 NO 3.56 (0.80) 0.004
Translation
50S ribosomal protein L9 AIS07033.1 NO 4.70 (2.06) 0.000
30S ribosomal protein S21 AIS07108.1 YES 4.33 (3.26) 0.040
50S ribosomal protein L21 AIS07586.1 NO 4.45 (2.38) 0.029
Valyl-tRNA synthetase AIS07599.1 NO 0.17 (0.14) 0.000
30S ribosomal protein S9 AIS07845.1 YES 6.19 (2.19) 0.005
50S ribosomal protein L17 AIS07895.1 YES 15.14 (7.44) 0.025
30S ribosomal protein S11 AIS07898.1 YES 3.40 (1.58) 0.002
50S ribosomal protein L15 AIS07902.1 NO 5.06 (1.54) 0.000
50S ribosomal protein L6 AIS07906.1 YES 5.35 (2.12) 0.000
30S ribosomal protein S8 AIS07907.1 YES 7.52 (1.56) 0.007
50S ribosomal protein L5 AIS07909.1 NO 7.18 (2.38) 0.000
50S ribosomal protein L14 AIS07911.1 NO 5.20 (1.87) 0.002
50S ribosomal protein L22 AIS07916.1 NO 2.03 (0.76) 0.012
50S ribosomal protein L23 AIS07919.1 YES 1.77 (0.58) 0.043
Aminoglycoside phosphotransferase AIS08113.1 NO 2.88 (4.81) 0.015
  1. The protein profiles produced by A. baumannii grown in modified BALF were performed using iTRAQ reagents and LC-MS/MS. Differential expression was defined by a relative abundance ratio >1.5 and <0.5
  2. aSecretion prediction are based on (SignalP 4.1 (http://www.cbs.dtu.dk/services/SignalP/), Phobius (http://phobius.sbc.su.se/), PrediSi (http://www.predisi.de/), TatP 1.0 (www.cbs.dtu.dk/services/TatP-1.0), Tatfind 1.4 (http://signalfind.org/tatfind.html), SecretomeP 2.0 (www.cbs.dtu.dk/services/SecretomeP), TMHMM (http://www.cbs.dtu.dk/services/TMHMM/), DAS-TMfilter (http://www.enzim.hu/DAS/DAS.html), LipoP 1.0 (www.cbs.dtu.dk/services/LipoP), DOLOP (http://www.mrc-lmb.cam.ac.uk/genomes/dolop/), and LIPO (http://services.cbu.uib.no/tools/lipo))
  3. bAverage relative protein expression level ratio in sample and control, with the standard deviation in parentheses, quantified by Protein Pilot 4.0 software (ABSciex).
  4. cDetermined by Student’s t test. Values of less than 0.05 are considered significant