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. 2016 Apr 14;15(6):2125–2140. doi: 10.1074/mcp.M115.056440

Table I. Thioredoxin targets identified in a ΔtrxAΔtrxC E. coli strain. The proteins in this table were identified in two independent experiments with at least two peptides found in the indicated spot. They all contain cysteine residues. The full list of identified proteins for Experience 1 can be found in Table S3 and those for Experience 2 in Table S4. #PSM, number of peptide-spectrum matches; #pept, number of peptides; #cys, number of cysteines; MW, molecular weight. See supplemental Fig. S4A for the gel of Experience 2.

Gene Uniprot ID Description Experience 1
 Experience 2
 #cys MW (kDa)
spot #PSM #pept spot #PSM #pept
Energy metabolism
    ATP-proton motive force interconversion
        atpAb,c P0ABB0 ATP synthase subunit alpha 15 14 11 14 3 3 4 55.2
        atpDb,c P0ABB4 ATP synthase subunit beta 14 44 22 12 17 13 1 50.3
        atpGb P0ABA6 ATP synthase gamma chain 8 8 8 7 2 2 2 31.6
        nuoE P0AFD1 NADH-quinone oxidoreductase subunit E 4 10 5 6 3 3 5 18.6
    Glycolysis
        fbaAb,c P0AB71 Fructose-bisphosphate aldolase class 2 12 18 11 10 12 7 4 39.1
        gapAb,c P0A9B2 Glyceraldehyde-3-phosphate dehydrogenase A 11 13 7 9 33 10 3 35.5
        lpdA P0A9P0 Dihydrolipoyl dehydrogenase 15 24 13 14 15 9 5 50.7
        pfkAb P0A796 ATP-dependent 6-phosphofructokinase isozyme 1 11 4 3 9 4 4 6 34.8
        pgkb P0A799 Phosphoglycerate kinase 13 8 8 11 23 13 3 41.1
        pykFb,c P0AD61 Pyruvate kinase I 15 3 3 14 4 4 6 50.7
    Gluconeogenesis
        sdaA P16095 l-serine dehydratase 1 15 2 2 14 4 4 9 48.9
    Pentose phosphate pathway
        gndb P00350 6-phosphogluconate dehydrogenase, decarboxylating 13 10 9 11 16 10 2 51.4
        talBb,c P0A870 Transaldolase B 11 23 12 9 13 10 3 35.2
    TCA cycle
        gltAb P0ABH7 Citrate synthase 14 9 9 12 4 4 7 48
        icdb,c P08200 Isocitrate dehydrogenase [NADP] 14 6 5 12 7 7 6 45.7
        mdhb P61889 Malate dehydrogenase 10 25 16 8 16 13 3 32.3
        sucCb,c P0A836 Succinyl-CoA ligase [ADP-forming] subunit beta 13 18 13 11 2 2 5 41.4
        sucDb,c P0AGE9 Succinyl-CoA ligase [ADP-forming] subunit alpha 9 13 10 7 4 4 5 29.8
    Carbohydrate metabolism (other)
        ackA P0A6A3 Acetate kinase 13 8 7 11 4 4 6 43.3
        aldA P25553 Lactaldehyde dehydrogenase 15 4 4 14 3 3 3 52.2
        deoB P0A6K6 Phosphopentomutase 13 9 8 11 8 8 6 44.3
        deoC P0A6L0 Deoxyribose-phosphate aldolase 8 62 14 7 5 5 4 27.7
        galF P0AAB6 UTP–glucose-1-phosphate uridylyltransferase 10 2 2 8 2 2 3 32.8
        garR P0ABQ2 2-hydroxy-3-oxopropionate reductase 8 9 7 7 2 2 2 30.4
        gatY B1X7I7 Tagatose-1,6-bisphosphate aldolase GatY 9 12 4 7 22 6 4 30.8
        gatZ P0C8J8 Putative tagatose 6-phosphate kinase GatZ 14 14 10 14 14 6 8 47.1
        glpK P0A6F3 Glycerol kinase 15 9 9 14 13 11 5 56.2
        nanA P0A6L4 N-acetylneuraminate lyase 10 6 6 8 4 4 4 32.6
Processes
    Cell division/cellular structure
        mreBc P0A9X4 Rod shape-determining protein MreB 12 5 5 10 2 2 3 36.9
    Chaperones
        groLb P0A6F5 60 kDa chaperonin 16 6 6 14 2 2 3 57.3
    Detoxification/oxidative stress response
        ahpCb P0AE08 Alkyl hydroperoxide reductase subunit C 4 136 16 6 175 13 2 20.7
        bcpa,b P0AE52 Putative peroxiredoxin bcp 1 3 3 3 9 6 3 17.6
        katGb,c P13029 Catalase-peroxidase 16 10 9 14 4 4 1 80
        msrBa,b P0A746 Peptide methionine sulfoxide reductase MsrB 1 6 3 3 5 5 6 15.4
        msrCa,b P76270 Free methionine-R-sulfoxide reductase 3 9 5 4 7 4 3 18.1
        sodB P0AGD3 Superoxide dismutase [Fe] 4 20 7 6 3 3 1 21.3
        tpxa,b,c P0A862 Thiol peroxidase 3 41 10 4 139 8 3 17.8
        trxBa,b P0A9P4 Thioredoxin reductase 10 4 4 9 6 5 4 34.6
        ucpA P37440 Oxidoreductase UcpA 9 6 5 8 2 2 4 27.8
    Regulatory functions
        arcA P0A9Q1 Aerobic respiration control protein ArcA 8 12 9 7 2 2 2 27.3
        furc P0A9A9 Ferric uptake regulation protein 2 2 2 3 4 3 4 16.8
    Transport/binding proteins
        araG P0AAF3 Arabinose import ATP-binding protein AraG 15 5 4 14 2 2 3 55
        ppab P0A7A9 Inorganic pyrophosphatase 4 8 5 6 2 2 2 19.7
Small molecules biosynthesis and degradation
    Amino acid biosynthesis
        aspA P0AC38 Aspartate ammonia-lyase 15 5 5 14 13 11 11 52.3
        cysKb P0ABK5 Cysteine synthase A 11 6 5 9 6 6 1 34.5
        glnAb P0A9C5 Glutamine synthetase 15 3 2 14 12 8 4 51.9
        glyAb P0A825 Serine hydroxymethyltransferase 13 5 5 11 2 2 3 45.3
        iscS P0A6B7 Cysteine desulfurase IscS 13 8 8 11 5 5 3 45.1
        metKb P0A817 S-adenosylmethionine synthase 13 7 6 11 2 2 4 41.9
    Amino acid degradation
        tnaAb,c P0A853 Tryptophanase 14 53 22 12 67 18 7 52.7
    Fatty acid biosynthesis
        accC P24182 Biotin carboxylase 14 4 4 12 2 2 8 49.3
        fabAc P0A6Q3 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase 2 11 5 4 2 2 2 19
        fabB P0A953 3-oxoacyl-[acyl-carrier-protein] synthase 1 13 10 7 12 3 3 6 42.6
        fabDb P0AAI9 Malonyl CoA-acyl carrier protein transacylase 10 4 3 9 5 3 5 32.4
        fabH P0A6R0 3-oxoacyl-[acyl-carrier-protein] synthase 3 10 3 3 8 2 2 5 33.5
        fabZc P0A6Q6 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ 1 4 4 3 3 3 2 17
    Deoxyribonucleotide/nucleoside metabolism
        cddb P0ABF6 Cytidine deaminase 9 3 3 8 2 2 5 31.5
    Purine/pyrimidine ribonucleotide biosynthesis
        preT P76440 NAD-dependent dihydropyrimidine dehydrogenase subunit PreT 13 4 4 11 4 4 13 44.3
        prs P0A717 Ribose-phosphate pyrophosphokinase 10 2 2 9 2 2 4 34.2
        purAb P0A7D4 Adenylosuccinate synthetase 13 3 2 12 2 2 4 47.3
    Salvage of nucleotides and nucleosides
        deoA P07650 Thymidine phosphorylase 14 3 3 12 3 3 2 47.2
    Molybdenum cofactor biosynthesis
        moaB P0AEZ9 Molybdenum cofactor biosynthesis protein B 2 9 5 4 2 2 2 18.7
    Iron-sulfur cluster assembly
        iscUb P0ACD4 Iron-sulfur cluster assembly scaffold protein IscU 1 4 3 3 3 3 3 13.8
Macromolecules
    DNA transcription
        hns P0ACF8 DNA-binding protein H-NS 1 11 6 3 2 2 1 15.5
        rho P0AG30 Transcription termination factor Rho 14 11 11 12 3 3 1 47
    Protein translation and modification
        asnS P0A8M0 Asparagine–tRNA ligase 14 2 2 14 2 2 4 52.5
        gltX P04805 Glutamate–tRNA ligase 15 12 9 14 14 9 7 53.8
        hisS P60906 Histidine—tRNA ligase 14 2 2 12 2 2 5 47
        infC P0A707 Translation initiation factor IF-3 4 6 4 6 4 3 1 20.6
        prfB P07012 Peptide chain release factor 2 14 2 2 14 2 2 2 41.2
        rplB P60422 50S ribosomal protein L2 8 5 5 8 3 3 2 29.8
        rplE P62399 50S ribosomal protein L5 3 64 15 4 13 5 1 20.3
        rplFb P0AG55 50S ribosomal protein L6 3 30 10 6 3 2 1 18.9
        rplJ P0A7J3 50S ribosomal protein L10 1 23 7 3 3 3 1 17.7
        rplK P0A7J7 50S ribosomal protein L11 1 19 5 3 7 4 1 14.9
        rplN P0ADY3 50S ribosomal protein L14 1 22 5 3 3 3 2 13.5
        rplQ P0AG44 50S ribosomal protein L17 1 19 5 3 11 4 1 14.4
        rpsAb P0AG67 30S ribosomal protein S1 16 60 28 11 2 2 2 61.1
        rpsBb P0A7V0 30S ribosomal protein S2 8 42 11 7 3 2 1 26.7
        rpsKb P0A7R9 30S ribosomal protein S11 1 17 7 3 3 3 2 13.8
        rpsLb P0A7S3 30S ribosomal protein S12 1 15 4 3 3 2 4 13.7
        rpsM P0A7S9 30S ribosomal protein S13 1 29 6 2 9 5 1 13.1
        serS P0A8L1 Serine–tRNA ligase 15 8 8 14 6 5 5 48.4
        tsfc P0A6P1 Elongation factor Ts 10 35 13 8 9 8 2 30.4
        tufBb P0CE48 Elongation factor Tu 13 99 20 11 87 17 3 43.3
    t-RNA and r-RNA processing
        miaB P0AEI1 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase 15 3 3 14 4 4 6 53.6
        mnmA P25745 tRNA-specific 2-thiouridylase MnmA 13 11 8 11 6 5 7 40.9
    ATP binding
        ychF P0ABU2 Ribosome-binding ATPase YchF 13 26 15 11 37 14 6 39.6
    Protein degradation/proteases
        clpXb P0A6H1 ATP-dependent Clp protease ATP-binding subunit ClpX 14 3 3 12 6 6 7 46.3
        pepD P15288 Cytosol non-specific dipeptidase 15 8 7 14 4 4 4 52.9
Unknown proteins
    yfeX P76536 Probable deferrochelatase/peroxidase YfeX 10 6 6 8 3 3 4 33

a Genes encoding known substrates of Trx1 in E. coli (39).

b Genes encoding known substrates of Trx1 in other organisms a (18–31, 33–37, 39, 105–112).

c Genes encoding proteins that copurify with Trx1 in E. coli (17).