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. 2013 Oct;195(19):4506–4516. doi: 10.1128/JB.00758-13

Table 3.

Proteins that interact with ClpCtrap identified by GeLC-MS/MS

Functional group and gene ORFa Identified protein Mass (kDa) IDb Normalized count (expt 1/2)c
 P value Fold change
ClpCtrap Vector
Regulatory functions
    ccpA 1629 Catabolite control protein A 36 A6QHR9 8.0/8.7 0.00/1.5 0.006 11.3
    codY 1165 GTP-sensing transcriptional pleiotropic repressor CodY 29 A6QGF5 19.0/28.3 11.0/7.9 0.050 2.5
    agrA 1946 Staphylococcal accessory gene regulator A 28 A6QIN6 31.0/31.8 10.0/14.2 0.006 2.6
    rsbW 1971 Serine-protein kinase RsbW 18 A6QIR1 27.0/23.1 11.0/8.3 0.011 2.6
    rex 1953 Redox-sensing transcriptional repressor Rex 24 A6QIP3 5.0/4.6 0.0/1.0 0.007 9.8
    hprK 0728 HPr kinase/phosphorylase 34 A6QF68 3.0/4.0 0.0/0.0 0.011 infd
Protein fate
    clpC 0487 Clp protease, ATP binding subunit ClpC 91 A6QEH7 5028.0/3263.6 49.0/0.0 0.021 169.2
    clpB 0845 Clp protease, ATP binding subunit ClpB 98 A6QFI5 363.0/266.8 112.0/177.1 0.050 2.2
    clpP 0736 ATP-dependent Clp protease proteolytic subunit 22 A6QF76 29.0/19.6 10.0/5.4 0.043 3.2
    dnaK 1483 Chaperone protein DnaK 66 A6QHC3 158.0/181.9 33.0/29.0 0.004 5.5
    dnaJ 1482 Chaperone protein DnaJ 42 A6QHC2 34.0/46.2 6.0/3.9 0.015 8.1
    groL 1937 60-kDa chaperonin 58 A6QIM7 50.0/60.1 11.0/16.2 0.009 4.0
    trfA 0868* Adaptor protein MecA/TrfA 28 A6QFK8 1.0/4.6 0.0/0.0 0.130 inf
    —e 0495* Conserved hypothetical protein 20 A6QEI5 3.0/0.6 0.0/0.0 0.139 inf
    — 1187* Conserved hypothetical protein 49 A6QGH7 3.0/1.2 0.0/0.0 0.077 inf
Biosynthesis of cofactors, prosthetic groups, and carriers
    lipA 0796 Lipoyl synthase 35 A6QFD6 21.0/16.2 8.0/6.9 0.023 2.5
    ispD1 0185 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase 1 27 A6QDM5 8.0/6.4 0.0/0.0 0.006 inf
    sufC 0785 FeS assembly ATPase SufC 28 A6QFC5 37.0/43.9 8.0/8.3 0.006 3.6
    sufD 0786 FeS assembly protein SufD 49 A6QFC6 15.0/18.5 4.0/7.9 0.027 2.5
    folD 0932 Bifunctional protein FolD 31 A6QFS2 6.0/7.5 0.0/0.5 0.007 27.5
    hemE 1725 Uroporphyrinogen decarboxylase 39 A6QI15 2.0/2.9 0.0/1.0 0.049 5.0
    hemL 1756 Glutamate-1-semialdehyde 2,1-aminomutase 2 47 A6QI46 2.0/3.5 0.0/0.0 0.032 inf
    thiD 0543 Phosphomethylpyrimidine kinase 30 A6QEN3 10.0/15.6 0.0/3.9 0.043 6.5
Amino acid metabolism
    sbnB 0061 Ornithine cyclodeaminase 38 A6QDA1 4.0/3.5 0.0/1.5 0.031 5.1
    — 1421 2-Oxoisovalerate dehydrogenase, E2 component 47 A6QH61 7.0/6.9 4.0/1.5 0.039 2.5
    — 1422 2-Oxoisovalerate dehydrogenase, E1 component 36 A6QH62 6.0/7.5 0.0/0.5 0.007 27.5
    — 0475 Cysteine synthase 33 A6QEG5 6.0/8.1 0.0/0.5 0.012 28.7
    — 1871 Aspartate transaminase 48 A6QIG1 3.0/2.3 0.0/0.5 0.015 10.8
Cell envelope
    atl 0922 Bifunctional autolysin 137 A6QFR2 117.0/106.8 55.0/59.9 0.005 2.0
    murG 2028 UDP-glucose diacylglycerol glucosyltransferase 45 A6QGX0 6.0/10.4 0.0/1.0 0.038 16.7
    femB 1287* Methicillin resistance expression factor FemB 50 A6QGS7 3.0/6.4 0.0/0.0 0.054 inf
    srtA 2426 Sortase A, peptide LPXTG peptidoglycan transferase 24 A6QK16 3.0/2.9 1.0/1.0 0.000 3.0
    clfA 0756 Clumping factor A 97 Q53653 10.0/9.8 0.0/4.9 0.047 4.0
    — 0369 Putative lipoprotein 24 A6QE59 4.0/4.6 1.0/2.0 0.019 2.9
    — 2356 Putative lipoprotein 17 A6QJU6 8.0/5.8 2.0/1.5 0.023 4.0
Cellular processes
    ahpF 0371 Alkyl hydroperoxide reductase subunit F 55 A6QE61 8.0/11.6 0.0/1.5 0.021 13.3
    — 1639 Propeptide, PepSY, and peptidase M4 12 A6QHS9 3.0/2.3 0.0/0.0 0.008 inf
Cell division
    ftsA 1095 Cell division protein FtsA 53 A6QG85 59.0/51.4 22.0/28.5 0.013 2.2
    divIVA 1102* Putative uncharacterized protein 24 A6QG92 8.0/3.5 0.0/0.0 0.064 inf
DNA metabolism
    dnaN 0002 DNA polymerase III subunit beta 42 A6QD42 40.0/25.4 4.0/9.3 0.039 4.9
    recA 1194 Protein RecA 38 A6QGI4 58.0/86.6 16.0/12.8 0.028 5.0
    recN 1425 DNA repair protein RecN 64 A6QH65 7.0/6.4 0.0/2.0 0.016 6.8
    sbcC 1258 Nuclease SbcCD subunit C 117 A6QGP8 9.0/8.7 0.0/3.4 0.027 5.1
    mutS 1204 DNA mismatch repair protein MutS 100 A6QGJ4 8.0/7.5 2.0/4.4 0.033 2.4
Central intermediary metabolism
    glmS 2056 Glucosamine-fructose-6-phosphate aminotransferase, isomerizing 66 A6QIZ6 84.0/56.0 17.0/20.1 0.034 3.8
    — 0584 Hydrolase 31 A6QES4 7.0/4.0 0.0/0.0 0.032 inf
    — 0973 Inositol-1-monophosphatase family protein 30 A6QFW3 6.0/6.4 0.0/2.0 0.017 6.3
    — 2375 NAD-dependent epimerase/dehydratase 25 A6QJW5 2.0/1.2 0.0/0.0 0.032 inf
    — 2434 Conserved hypothetical protein 37 A6QK24 2.0/3.5 0.0/0.5 0.042 11.1
Energy metabolism
    citC 1587 Isocitrate dehydrogenase [NADP] 46 A6QHM7 5.0/5.8 0.0/0.0 0.003 inf
    pycA 0979 Pyruvate carboxylase 129 A6QFW9 5.0/4.6 0.0/0.0 0.001 inf
    gapA 0741 Glyceraldehyde 3-phosphate dehydrogenase 1 36 A6QF81 17.0/22.5 0.0/0.0 0.009 inf
    sucB 1325 Dihydrolipoamide succinyltransferase E2 component of 2-oxoglutarate dehydrogenase complex 47 A6QGW5 2.0/4.0 0.0/0.0 0.049 inf
    sucC 1155 Succinyl coenzyme A ligase (ADP-forming) subunit beta 42 A6QGE5 9.0/12.7 0.0/0.0 0.014 inf
    zwf 1412 Glucose-6-phosphate 1-dehydrogenase 57 A6QH52 15.0/9.2 3.0/2.0 0.041 4.9
    glk 1451 Glucokinase 35 A6QH91 5.0/4.0 0.0/0.0 0.006 inf
    pgk 0742 Phosphoglycerate kinase 43 A6QF82 8.0/6.9 3.0/0.0 0.032 5.0
    ackA 1605 Acetate kinase 44 A6QHP5 46.0/38.7 14.0/10.3 0.009 3.5
    fbaA 2029 Fructose-bisphosphate aldolase 31 A6QIW9 1.0/1.7 0.0/0.0 0.032 inf
    — 2210 Formate dehydrogenase homolog 111 A6QJF0 7.0/6.9 4.0/1.5 0.039 2.5
    — 1672* Transaldolase 26 A6QHW2 3.0/0.6 0.0/0.0 0.139 inf
Fatty acid and phospholipid metabolism
    accC 1431 Biotin carboxylase subunit of acetyl-CoA carboxylase 50 A6QH71 9.0/6.4 0.0/2.0 0.028 7.8
    gpsA 1383 Glycerol-3-phosphate dehydrogenase 36 A6QH23 3.0/4.6 0.0/0.0 0.021 inf
Protein synthesis
    rsmH 1089 rRNA small subunit methyltransferase H 36 A6QG79 5.0/4.0 0.0/1.5 0.025 6.1
    rplA 0500 50S ribosomal protein L1 25 A6QEJ0 18.0/18.5 7.0/6.4 0.001 2.7
    rpsA 1385 30S ribosomal protein S1 43 A6QH25 29.0/20.8 13.0/9.8 0.046 2.2
    rpsP 1148 30S ribosomal protein S16 10 A6QGD8 8.0/6.4 4.0/2.0 0.043 2.4
    rpsD 1613 30S ribosomal protein S4 23 A6QHQ3 65.0/50.2 22.0/33.9 0.044 2.1
    gatA 1838 Glutamyl-tRNA(Gln) amidotransferase subunit A 53 A6QIC8 40.0/65.3 6.0/16.2 0.046 4.7
    gatB 1837 Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B 54 A6QIC7 42.0/27.1 4.0/11.3 0.041 4.5
    tyrS 1622 Tyrosine-tRNA ligase 48 A6QHR2 2.0/1.7 0.0/0.5 0.014 7.6
    ileS 1103* Isoleucyl-tRNA ligase 48 A6QG93 1.0/3.5 0.0/0.0 0.106 inf
    — 0721 Sigma 54 modulation protein 22 A6QF61 31.0/26.6 15.0/13.7 0.012 2.0
    — 1408 SpoU rRNA methylase family protein 27 A6QG38 3.0/3.5 0.0/1.0 0.019 6.6
Purine, pyrimidine, nucleoside, nucleotides, purine ribonucleotide synthesis
    guaB 0380 Inosine-5′-monophosphate dehydrogenase 53 A6QE70 42.0/27.1 4.0/11.3 0.041 4.5
    prs 0463 Ribose-phosphate pyrophosphokinase 35 A6QEF3 44.0/40.4 4.0/15.2 0.016 4.4
    pyrH 1168 Uridylate kinase 26 A6QGF8 7.0/5.8 1.0/1.0 0.006 6.4
    pyrR 1109 Bifunctional protein PyrR 20 A6QG99 15.0/25.4 0.0/4.9 0.045 8.2
    nrdE 0700 Ribonucleoside-diphosphate reductase 82 A6QF40 55.0/56.0 27.0/28.5 <0.001 2.0
    — 0284 Conserved hypothetical protein 21 A6QDX4 3.0/2.9 0.0/0.0 <0.001 inf
Transcription
    sigA 1464 RNA polymerase sigma factor 42 A6QHA4 14.0/9.8 0.0/2.0 0.021 12.1
    rpoA 2126 DNA-directed RNA polymerase subunit alpha 35 A6QJ66 13.0/7.5 0.0/0.0 0.032 inf
    nusA 1176 Transcription termination-antitermination factor 44 A6QGG6 14.0/12.1 2.0/7.4 0.049 2.8
    nusG 0498 Transcription antitermination protein NusG 21 P0C1S3 9.0/6.9 4.0/1.5 0.043 2.9
Transport and binding proteins
    — 0581 Iron compound ABC transporter, iron compound binding protein 33 A6QES1 2.0/2.3 0.0/0.0 0.003 inf
    — 2312 Amino acid ABC transporter, permease protein 26 A6QJQ2 2.0/2.3 0.0/0.0 0.003 inf
    — 0705 Ferrichrome ABC transporter lipoprotein 38 A6QF45 10.0/9.8 4.0/3.9 <0.001 2.5
    — 0954 Conserved hypothetical protein 24 A6QFU4 3.0/2.3 0.0/0.0 0.008 3.00
Unknown
    — 0272 Putative uncharacterized protein 21 A6QDW2 6.0/4.6 0.0/0.0 0.008 inf
    — 0632 Putative uncharacterized protein 24 A6QEX2 7.0/6.4 1.0/2.9 0.022 3.4
    — 0737 Putative uncharacterized protein 34 A6QF77 4.0/3.5 0.0/1.5 0.031 5.1
    — 0976 Putative uncharacterized protein 19 A6QFW6 7.0/4.6 1.0/1.5 0.032 4.7
    — 1265* Putative uncharacterized protein 11 A6QGQ5 3.0/1.2 0.0/0.0 0.077 inf
    — 1381 Putative uncharacterized protein 22 A6QH21 2.0/1.7 0.0/0.0 0.003 inf
    — 1730 Putative uncharacterized protein 13 A6QI20 7.0/5.8 1.0/2.0 0.012 4.3
    — 1820* Putative uncharacterized protein 10 A6QIB0 5.0/1.2 0.0/0.0 0.125 inf
    — 2067 ATP binding Mrp/Nbp35 family protein 38 A6QJ07 3.0/5.8 0.0/0.0 0.044 inf
    — 2002* Putative uncharacterized protein 19 A6QIU2 1.0/2.9 0.0/0.0 0.088 inf
    — 2201* Dehydrogenase family protein 41 A6QJE1 25.0/6.4 0.0/0.0 0.117 inf
    — 2209 Putative uncharacterized protein 17 A6QJE9 2.0/2.3 0.0/0.0 0.003 inf
    — 2405 Putative uncharacterized protein 27 A6QJZ5 1.0/1.2 0.0/0.0 0.003 inf
    — 2468 Acetyltransferase, GNAT family protein 19 A6QK58 3.0/2.3 0.0/0.0 0.008 inf
    — 2511* Putative uncharacterized protein 22 A6QKA1 4.0/1.7 0.0/0.0 0.064 inf
a

ORF numbers are based on strain Newman. ORF numbers followed by an asterisk indicate proteins with a P value of >0.05 but that were specifically captured by ClpCtrap.

b

The ID number is the UniProt accession number.

c

Two biological replicates were used to identify substrates of ClpC. The spectral counts were normalized based on total counts.

d

inf, the fold change could not be accurately estimated due to no detection in the negative-control samples.

e

—, a gene name has not yet been designated.