Skip to main content

Table 1 Proteins of H.hepaticus identified by LC-MS/MS whose expression was modulated by at least 2-fold in 0.05% human- or 0.1% porcine bile in the growth media

From: Effects of human and porcine bile on the proteome of Helicobacter hepaticus

Protein a Fold change (± SEM) b Gene Function c Spot No. Matching score d Coverage (Peptide) Observed/Theoretical pI e
  Human Porcine    Human Porcine Human Porcine Human Porcine Human Porcine
Amino acid metabolism
Dihydropicolinate reductase* 0.4 ± 0.01 3.5 ± 0.03 dapB Lysine biosynthesis 33 23 438 201 33(7) 26(12) 6.59/6.24 5.7/6.24
Dihydropicolinate reductase* 0.1 ± 0.01 NI    32 - 430 - 44(19) - 6.50/6.24 -
Glycine hydroxymethyltransferase 0.48 ± 0.1 2.5 ± 0.01 glyA Glycine hydroxymethyltransferase 18 17 330 278 26(6) 16(5) 6.57/6.33 6.95/6.33
Ketol-acid reductoisomerase 2.7 ± 0.3 NI ilvN Valine, leucine and isoleucine biosynthesis 27 - 916   49(14) - 6.59/6.05 -
Threonyl-tRNA synthetase NI 4.0 ± 0.01 thrS Glycine, threonine and serine metabolism - 8 - 214 - 12(3) - 5.78/6.06
2-isopropylmalate synthase NI 5.0 ± 0.01 leuA Valine, leucine and isoleucine biosynthesis - 9 - 148 - 26(12) - 5.78/5.86
Phosphoglycerate dehydrogenase NI 0.4 ± 0.02 serA Serine family amino acid biosynthesis - 32 - 583 - 18(9) - 5.70/5.84
Cellular metabolism
ATP-dependent CLP protease* NI 0.3 ± 0.01 clpA Endopeptidase activity - 3 - 941 - 41(19) - 5.92/5.70
ATP-dependent CLP protease* NI 0.2 ± 0.06    - 4 - 1167 - 38(36) - 5.84/5.70
Carbohydrate & energy metabolism
Aconitase* 0.25 ± 0.01 0.4 ± 0.01 acnB Citrate cycle, glyoxylate and dicarboxylate metabolism, reductive carboxylate cycle 2 2 1237 784 48(28) 10(13) 6.65/6.21 6.46/6.21
Aconitase* 0.1 ± 0.03 0.4 ± 0.01    3 1 1491 665 29(20) 29(11) 6.54/6.21 6.54/6.21
Aconitase* 0.1 ± 0.01 NI    1 - 1488 - 43(14) - 6.76/6.21 -
Aconitase* 0.2 ± 0.01 NI    4 - 866 - 34(12) - 6.46/6.21 -
Alkyl hydroperoxide reductase NI 3.0 ± 0.01 tsaA Oxidative phosphorylation - 28 - 288 - 50(17) - 6.3/5.95
ATP synthase subunit A NI 4.0 ± 0.02 atpA   - 12 - 891 - 43(19) - 5.7/5.69
ATP synthase subunit B NI 2.5 ± 0.1 atpB   - 15 - 1509 - 53(12) - 5.12/5.17
dDTP-glucose dehydratase 0.3 ± 0.01 NI rfbB Nucleotide sugar biosynthesis 23 - 549 - 31(5) - 5.57/6.05 -
UDP-glucose 6-dehydrogenase 0.24 ± 0.06 NI kfiD Pentose and glucuronate interconversions; starch & sucrose metabolism, nucleotide sugars metabolism 17 - 384 - 50(17) - 5.51/5.27 -
Ferredoxin oxidoreductase* 3.5 ± 0.02 NI porA Pyruvate metabolism 37 - 514 - 11(4) - 5.92/5.91 -
Ferredoxin oxidoreductase* 2.5 ± 0.3 NI    22 - 900 - 35(20) - 6.38/5.91 -
Fumarase 0.25 ± 0.1 0.4 ± 0.1 fumC Citrate cycle, reductive carboxylate cycle 30 13 566 725 47(8) 23(11) 6.62/5.61 5.7/5.61
Fumarate reductase NI 6.0 ± 0.1 frdA Citrate cycle, oxidative phosphorylation - 6 - 734 - 38(36) - 5.7/7.23
Fructose-bisphosphate aldolase 2.8 ± 0.01 NI fba Glycolysis, gluconogenesis 19 - 975 - 50(13) - 6.59/5.95 -
Isocitrate dehydrogenase NI 5.5 ± 0.02 icd Citrate cycle - 5 - 865 - 23(7) - 5.7/7.10
Malate dehydrogenase NI 2.0 ± 0.01 mdh Pyruvate metabolism - 21 - 710 - 42(9) - 6.89/8.11
Phosphoglycerate kinase 2.5 ± 0.01 NI pgk Glycolysis, glyconogenesis 13 - 699 - 44(10) - 6.0/5.64 -
Rod shape determining protein 2.5 ± 0.2 NI mreB Cell shape determining protein 20 - 455 - 33(7) - 5.27/5.16 -
Cellular oxygen metabolism & stress response
Catalase NI 0.1 ± 0.01 kat Superoxide metabolism - 10 - 715 - 27(5) - 5.7/6.75
Superoxide dismutase 0.1 ± 0.01 0.4 ± 0.3 sodF   16 27 137 411 13(2) 31(9) 6.49/6.24 5.7/6.24
Thioredoxin reductase 0.3 ± 0.01 4.7 ± 0.03 trxB1 Oxygen & ROS metabolism 31 18 470 390 27 (12) 14(5) 5.41/5.34 5.30/5.34
Putative thioredoxin reductase (HH1153) 0.2 ± 0.01 NI trxB2   24 - 381 - 16(5) - 5.95/6.15 -
Chaperone & stress response
Hsp-70 (DnaK cofactor) 2.3 ± 0.03 NI grpE Heat shock protein 26 - 308 - 11(8) - 4.57/4.62 -
Cpn60 NI 3.0 ± 0.01 groEL Chaperonin - 14 - 705 - 42(11) - 5.32/5.19
Lipid metabolism
Acetyl-CoA caroxylase alpha subunit 0.2 ± 0.01 NI accA Fatty acid biosynthesis 41 - 277 - 32(4) - 5.59/5.47 -
7-Alpha-dehydroxysteroid dehydrogenase 2.5 ± 0.01 NI fabG   46 - 629 - 23(11) - 6.19/7.59 -
(3R)-hydroxymyristoyl ACP dehydratase NI 4.0 ± 0.01 fabZ   - 7 - 356 - 28(6) - 6.95/6.31
s-malonyltransferase 0.3 ± 0.01 NI fabD   15 - 311 - 31(5) - 5.49/5.45 -
Motility & chemotaxis
Flagellin* 2.5 ± 0.3 2.0 ± 0.01 flaB Flagella assembly 11 11 946 961 41(16) 60(11) 4.81/6.38 4.57/6.38
Flagellin* 0.3 ± 0.02 NI    10 - 833 - 13(10) - 4.95/6.38 -
Flagellin* 0.4 ± 0.01 NI    9 - 699 - 26(9) - 4.89/6.38 -
Flagellin assembly protein* 0.4 ± 0.01 NI fliH   35 - 474 - 31(5) - 4.86/4.93 -
Flagellin assembly protein* 0.3 ± 0.01 NI    34 - 466 - 57(8) - 4.80/4.93 -
Major flagellin subunit 2.4 ± 0.1 NI flaA   12 - 827 - 47(13) - 4.68/5.56 -
Two-component system response regulator 0.4 ± 0.01 NI ompR Two-component signal regulatory system 36 - 154 - 16(9) - 4.84/5.63 -
Nucleotide metabolism
Adenylate kinase 0.2 ± 0.3 NI adk Purine metabolism 40 - 833 - 35(20) - 5.22/5.09 -
DNA polymerase III subunit beta 3.0 ± 0.01 NI dnaN DNA metabolism 45 - 385 - 24(4) - 5.62/5.33 -
Pathogenesis & virulence
Cytolethal distending toxin 0.1 ± 0.01 NI cdtC Virulence 44 - 444 - 20(9) - 4.81/5.23 -
Urease subunit A NI 0.3 ± 0.03 ureA Urease activity, virulence - 24 - 393 - 52(8) - 5.32/5.93
Protein translation & modification
Translation elongation factor Ts 3.2 ± 0.01 2.0 ± 0.1 ef-ts Protein translation 14 30 53 717 16(17) 36(12) 6.0/5.31 5.3/5.31
Translation elongation factor Tu 2.5 ± 0.01 2.0 ± 0.1 ef-tu   43 26 64 173 11(6) 15(13) 6.81/4.93 5.49/5.12
Signal transduction
GTP-binding protein* 3.5 ± 0.01 NI yihK Signal transduction 5 - 948 - 50(12) - 5.38/5.26 -
GTP-binding protein* 3.0 ± 0.02 NI    6 - 706 - 42(11) - 5.43/5.26 -
GTP-binding protein* 2.7 ± 0.01 NI    7 - 954 - 31(11) - 5.49/5.26 -
GTP-binding protein* 3.5 ± 0.01 NI    8 - 638 - 37(9) - 5.54/5.26 -
Putative ATP/GTP-binding protein 3.5 ± 0.02 NI mpr   38 - 700 - 26(17) - 6.08/5.77 -
Amino-acid ABC transporter periplasmic solute-binding protein 0.3 ± 0.1 NI pbpB ABC transporter protein 39 - 396 - 24(4) - 4.97/5.17 -
Putative ABC transporter protein 0.4 ± 0.01 NI yaeC   29 - 494 - 57(5) - 4.81/5.16 -
Single-stranded DNA-binding protein NI 0.3 ± 0.1 ssb Single strand binding protein/primosomal replication - 25 - 238 - 27(4) - 5.38/5.91
Putative protein function
HH1212 0.1 ± 0.03 NI hh1212 Hypothetical protein 25 - 349 - 14(5) - 6.34/6.98 -
HH0952 0.3 ± 0.02 NI hh0952   28 - 267 - 9(3) - 4.27/4.52 -
HH1514 0.4 ± 0.01 NI hh1514   42 - 286 - 17(9) - 5.97/5.62 -
HH1023 0.2 ± 0.01 0.2 ± 0.01 hh1023   21 16 1312 410 43(21) 31(6) 5.86/6.15 5.86/6.15
HH1098 NI 4.0 ± 0.01 hh1098   - 31 - 156 - 10(2) - 5.7/5.71
HH1376 NI 0.3 ± 0.01 hh1376   - 19 - 121 - 11(3) - 5.89/5.62
HH1034 NI 2.5 ± 0.1 hh1034   - 20 - 410 - 53(9) - 6.73/6.22
HH1426 NI 0.4 ± 0.1 hh1426   - 22 - 348 - 28(6) - 6.49/6.12
HH0243 NI 2.5 ± 0.01 hh0243   - 29 - 297 - 22(4) - 5.59/5.63
  1. aProteins were identified by LC-MS/MS and MASCOT searches of the NCBI nr database. bProteins that were differentially expressed in the presence of 0.05% human bile or 0.1% porcine bile by at least 2-fold level of expression. A fold change value of > 2 indicates up-regulation, while a value of < 0.5 indicates down-regulation. cProteins were classified into functional categories based on KEGG pathway classification and DAVID gene ontology, and by comparison with the published literature. dProteins with peptides with matching scores of > 49 were considered to be identified. ePredicted isoelectric point of each protein was obtained from the Comprehensive Microbial Resource of the Institute of Genomic Research. NI = Not identified.