Table 2.
Differentially expressed proteins between L. plantarum CCFM8610 and CCFM191 in Cd-free conditions.
| Categorya | Accessionb | Descriptionc | FCd | |
|---|---|---|---|---|
| Global Stress Response | DNA repair, metabolism, regulation | F9UQY3 | lp_2444; Prophage P2a protein 13 | −3.30 |
| F9ULA4 | lp_0641; Prophage P1 protein 18, DNA single-strand annealing protein RecT | −1.87 | ||
| Q6LWF5 | traI; DNA topoisomerase | 6.30 | ||
| F9URZ6 | endA; DNA-entry nuclease | 1.58 | ||
| Q88V16 | mutS2; Endonuclease MutS2 | −1.70 | ||
| Q88W97 | recU; Holliday junction resolvase RecU | −1.52 | ||
| Oxidoreductase | F9UUA8 | lp_3430; Peroxidase | 5.14 | |
| F9USL4 | lp_3100; Aldo/keto reductase family protein | 3.41 | ||
| F9UPP0 | lp_1918; NAD(P)(H)-dependent oxidoreductase, quinone oxidoreductase (QOR) family | 2.10 | ||
| F9URK6 | lp_2732; NADPH-dependent FMN reductase family protein | −1.50 | ||
| F9UQD7 | lp_2212; NADH-flavin reductase | −1.51 | ||
| F9UQI9 | trxA2; Thioredoxin | −1.56 | ||
| F9UPR0 | lp_1939; Oxidoreductase, medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family | −1.64 | ||
| F9USA2 | lp_2968; Nitroreductase | −1.65 | ||
| F9UTJ8 | lp_3318; Aldo/keto reductase family protein | −1.65 | ||
| F9USK5 | lp_3091; Short-chain dehydrogenase/oxidoreductase, atypical SDR family, subgroup 1 | −2.83 | ||
| F9UT37 | trxA1; Thioredoxin | 2.04 | ||
| F9UTD6 | lp_3236; Short-chain dehydrogenase/oxidoreductase, atypical SDR family, TMR-like | 1.70 | ||
| F9URB2 | lp_2604; NAD(P)-dependent oxidoreductase | 1.53 | ||
| F9US17 | nrdG; Anaerobic ribonucleoside-triphosphate reductase-activating protein | 1.55 | ||
| F9UTT1 | acdH; Acetaldehyde dehydrogenase | 1.55 | ||
| F9UNI0 | ribB; Riboflavin synthase, alpha chain | −5.89 | ||
| F9UR64 | npr2; NADH peroxidase | −4.38 | ||
| F9ULD3 | cat; Catalase | −3.76 | ||
| F9UN44 | gshR2; glutathione reductase | −4.67 | ||
| F9UUC2 | nox5; NADH oxidase | −2.30 | ||
| F9UTJ6 | pflA; Pyruvate formate-lyase-activating enzyme | −2.09 | ||
| F9UUK7 | lp_3545; D-arabitol-phosphate dehydrogenase | −3.08 | ||
| F9USK6 | gabD; succinate-semialdehyde dehydrogenase (NAD(P) + ) | −2.06 | ||
| Protein repair | F9UPH1 | msrA; Peptide methionine sulfoxide reductase MsrA | −6.02 | |
| Q88W33 | msrB; Peptide methionine sulfoxide reductase MsrB | −2.67 | ||
| Protease | F9UTF5 | lp_3259; Zinc-dependent proteinase | −1.96 | |
| F9UT31 | pepD1; Dipeptidase | −1.54 | ||
| Other | F9US30 | lp_2952; Bacteriocin immunity protein | −1.58 | |
| F9URC0 | lp_2616; Bacteriocin immunity protein | −1.96 | ||
| F9USV1 | hsp1; Small heat shock protein | −2.32 | ||
| Q88V03 | ruvB; Holliday junction ATP-dependent DNA helicase RuvB | 1.92 | ||
| Regulation network | Transcriptional regulation | F9UT59 | treR; Trehalose operon transcriptional repressor, GntR family | −1.91 |
| F9UM95 | lp_0892; Transcription regulator, MarR family | −1.70 | ||
| Q88X36 | argR1; Arginine regulator | −1.65 | ||
| F9UNC5 | lp_1360; Transcription regulator, MarR family | 2.06 | ||
| F9USP8 | lp_3138; Bifunctional protein: transcriptional antiterminator, BglG family PTS system, EIIA component | 1.87 | ||
| F9UPQ9 | lp_1938; Transcription regulator, LysR family | 1.82 | ||
| F9USH9 | lp_3060; Transcription regulator, AraC family | 1.53 | ||
| F9UMJ7 | lp_1020; Transcription regulator, TetR family | 1.57 | ||
| F9UL40 | tex; Transcription accessory protein, contains S1 RNA binding domain | −1.82 | ||
| Other regulation proteins | Q88XG5 | recX; Regulatory protein RecX | 2.02 | |
| F9UM52 | spx1; RNA polymerase (RNAP)-binding regulatory protein, arsenate reductase (ArsC) family, Spx subfamily | −1.59 | ||
| F9ULW6 | lp_0737; Sigma 54 modulation protein/ribosomal protein S30EA | −1.53 | ||
| Carbohydrate metabolism | TCA cycle | F9UMS1 | fum; fumarate hydratase | −3.81 |
| F9UQ90 | pdhD; pyruvate dehydrogenase complex, E3 component; dihydrolipoamide dehydrogenase | −1.90 | ||
| F9UQ91 | pdhC; pyruvate dehydrogenase complex, E2 component; dihydrolipoamide S-acetyltransferase | −2.30 | ||
| F9UQ92 | pdhB; pyruvate dehydrogenase complex, E1 component, beta subunit | −2.21 | ||
| F9UQ93 | pdhA; pyruvate dehydrogenase complex, E1 component, alpha subunit | −2.12 | ||
| Pyruvate metabolism | F9UTR4 | ack2; acetate kinase | −1.59 | |
| F9UM63 | pox1; pyruvate oxidase | −2.79 | ||
| P59390 | ldhL2; L-lactate dehydrogenase | −3.36 | ||
| Q88VJ2 | ldhD; D-lactate dehydrogenase | 1.69 | ||
| F9URC8 | pox3; pyruvate oxidase | −8.87 | ||
| F9UTJ5 | pflB; formate C-acetyltransferase | −1.85 | ||
| P37063 | pox5; pyruvate oxidase | −4.19 | ||
| Pentose phosphate pathway | F9UN42 | gntK; gluconokinase | −1.99 | |
| F9URA8 | tal1; Transaldolase | −5.21 | ||
| F9UN43 | lp_1251;6-phosphogluconate dehydrogenase | −7.13 | ||
| Q88S87 | xfp; xylulose-5-phosphate phosphoketolase | −1.64 | ||
| F9ULK7 | rbsK1; ribokinase | −1.72 | ||
| Glycolysis | Q88YY8 | pgm2; phosphoglycerate mutase family protein | 2.56 | |
| F9URP6 | pbg4; 6-phospho-beta-glucosidase | −1.94 | ||
| F9URP7 | pbg5; 6-phospho-beta-glucosidase | −2.03 | ||
| Other | F9US84 | pgmB2; Beta-phosphoglucomutase | −2.71 | |
| F9USZ1 | malS; Alpha-amylase, maltodextrins and cyclomaltodextrins | −1.61 | ||
| F9USY2 | dak3; Dihydroxyacetone phosphotransferase, phosphoryl donor protein | −1.66 | ||
| F9UP85 | mapA; Maltose phosphorylase | −2.73 | ||
| Q88RZ2 | rbsD; D-ribose mutarotase | −1.78 | ||
| Q88S51 | rhaA; L-rhamnose isomerase | −1.56 | ||
| PTS system | PTS system | F9UT61 | pts4ABC; PTS system trehalose-specific transporter subunit IIBC | −1.86 |
| F9UL45 | pts9AB; PTS system, mannose-specific EIIAB component | 1.73 | ||
| F9UL47 | pts9D; PTS system, mannose-specific EIID component | 1.82 | ||
| F9UL56 | pts10A; PTS system, mannose-specific EIIA component | −1.52 | ||
| F9UL57 | pts10B; PTS system, mannose-specific EIIB component | −3.91 | ||
| F9URE1 | pts19D; PTS system, N-acetylglucosamine–specific EIID component | −1.79 | ||
| F9URE3 | pts19B; PTS system, N-acetylglucosamine–specific EIIB component | −1.70 | ||
| F9URP8 | pts20A; PTS system, cellobiose-specific EIIA component | −2.47 | ||
| F9URP9 | pts20B; PTS system, cellobiose-specific EIIB component | −2.99 | ||
| F9UUH8 | pts30BCA; PTS system, beta-glucoside–specific EIIBCA component | −1.71 | ||
| F9UUK9 | pts35B; PTS system, galactitol-specific EIIB component | −2.50 | ||
| F9ULA5 | pts35A; PTS system, galactitol-specific EIIA component | −1.54 | ||
| F9UUH6 | lp_3510; PTS-associated protein | −1.80 | ||
| Amino acid metabolism | Lysine biosynthesis | F9UPP5 | dapE1; succinyl-diaminopimelate desuccinylase | 2.86 |
| F9URV7 | dapE2; succinyl-diaminopimelate desuccinylase | 1.95 | ||
| F9UT53 | cblB; cystathionine beta-lyase/cystathionine gamma-lyase | −3.54 | ||
| Sulfur amino acid metabolism | F9UQB3 | iscS; Cysteine desulfurase | 1.64 | |
| F9UTH2 | lp_3283; Methonine synthase (Cobalamine-independent), C-terminal domain | −2.40 | ||
| Q88UW5 | gshAB; glutathione biosynthesis bifunctional protein: glutamate-cysteine ligase; glutathione synthetase | 1.50 | ||
| F9UR58 | oahS; O-acetylhomoserine sulfhydrylase | −2.44 | ||
| Other | Q88UT5 | glyA; glycine hydroxymethyltransferase | 1.53 | |
| Q88WI3 | trpD; anthranilate phosphoribosyltransferase | 4.58 | ||
| Nucleic acid metabolism | F9UT41 | ndk; nucleoside-diphosphate kinase | −1.72 | |
| F9UM77 | gmk2; guanylate kinase | 1.64 | ||
| F9URN3 | lp_2762; phosphohydrolase | 1.87 | ||
| F9US18 | nrdD; anaerobic ribonucleoside-triphosphate reductase | 2.16 | ||
| P71479 | pyrR1; pyrimidine operon regulator | 1.62 | ||
| F9UNA0 | dgk2; Deoxynucleoside kinase | 2.04 | ||
| Lipid metabolism | Fatty acid biosynthesis | F9UP42 | accC2; acetyl-CoA carboxylase, biotin carboxylase subunit | 1.90 |
| Q88WG0 | accD2; acetyl-CoA carboxylase, carboxyl transferase subunit beta | 1.84 | ||
| F9UP44 | accA2; acetyl-CoA carboxylase, carboxyl transferase subunit alpha | 1.98 | ||
| Glycerol lipid metabolism | F9USY0 | dak1B; dihydroxyacetone phosphotransferase, dihydroxyacetone binding subunit | −1.70 | |
| F9USY1 | dak2; dihydroxyacetone phosphotransferase, ADP-binding subunit | −1.70 | ||
| Q88ZF1 | glpK; glycerol kinase | −5.69 | ||
| F9UTW9 | glpF3; Glycerol uptake facilitator protein | −3.30 | ||
| Q88YD9 | glpK2; Glycerol kinase 2 | −3.04 | ||
| F9UT65 | tagF1; CDP-glycerol glycerophosphotransferase | −2.15 | ||
| F9UT64 | tagD1; glycerol-3-phosphate cytidylyltransferase | −5.85 | ||
| F9UPG2 | tarL; Ribitolphosphotransferase | 4.22 | ||
| F9UTW8 | glpD; glycerol-3-phosphate dehydrogenase, FAD-dependent | −6.09 | ||
| Terpenoid backbone biosynthesis | Q88W46 | tarI; D-ribitol-5-phosphate cytidylyltransferase | 6.81 | |
| F9URB5 | dxs; 1-deoxy-D-xylulose-5-phosphate synthase | 2.46 | ||
| Other | F9UT87 | cfa2; Cyclopropane-fatty-acyl-phospholipid synthase | 1.67 | |
| F9UMC4 | lp_0925; Acyltransferase | 2.30 | ||
| Two-component system | F9UMR7 | citC; [citrate (pro-3S)-lyase] ligase | −1.52 | |
| Q88XS8 | citD; citrate lyase, gamma chain, acyl carrier protein | −2.43 | ||
| F9UMR9 | citE; citrate lyase, beta chain | −1.82 | ||
| F9UMS0 | citF; citrate lyase, alpha chain | −1.95 | ||
| Q88VM8 | dltC1; D-alanine–poly(phosphoribitol) ligase subunit 2-1 | −1.65 | ||
| Transporter | F9USY7 | mdxE; maltodextrin ABC transporter, substrate binding protein | −1.91 | |
| F9USZ2 | msmX; maltodextrin ABC transporter, ATP-binding protein | −2.23 | ||
| F9USG5 | lp_3042; Multidrug ABC transporter, ATP-binding and permease protein | −1.97 | ||
| F9UM05 | lp_0783; Oligopeptide ABC transporter, substrate binding protein | 2.77 | ||
| F9UR50 | lp_2525; ABC transporter, ATP-binding protein | 1.75 | ||
| F9UPR5 | lp_1945; Multidrug ABC transporter, ATP-binding protein | 1.65 | ||
| F9USL7 | fhuD; iron chelatin ABC transporter, substrate binding protein | 1.74 | ||
| F9UMR4 | citP; Citrate transport protein | −2.16 | ||
| F9UP84 | malT; Carbohydrate (Maltose)/proton symporttransporter, GPH family | −2.12 | ||
| Membrane protein and cell surface protein | F9URF3 | lp_2663; Hypothetical membrane protein | −1.53 | |
| F9UU92 | lp_3413; Cell surface protein, CscA/DUF916 family | −1.69 | ||
| F9UTN0 | lp_3359; Hypothetical membrane protein, DUF125 family | −2.24 | ||
| F9ULS6 | lp_0689; Cell surface protein, lipoprotein | 2.05 | ||
| F9URZ3 | lp_2901; Hypothetical membrane protein | 1.73 | ||
| F9UU47 | lp_3360; Hypothetical membrane protein, DUF125 family | −3.35 | ||
| Extracellular protein | F9USP4 | lp_3134; Extracellular protein, DUF 1093 family, membrane-bound | −2.04 | |
| F9UR45 | lp_2520; Extracellular protein, NlpC/P60 family, gamma-D-glutamate-meso-diaminopimelate muropeptidase | −1.79 | ||
| F9UQA0 | lp_2162; Extracellular protein, NlpC/P60 family, gamma-D-glutamate-meso-diaminopimelate muropeptidase | 1.55 | ||
| F9URD4 | lp_2636; Extracellular protein | 1.55 | ||
| F9UUA0 | lp_3421; Extracellular protein, gamma-D-glutamate-meso-diaminopimelate muropeptidase | 2.39 | ||
| F9USJ3 | lp_3077; Extracellular protein | 2.37 | ||
| F9UQ85 | lp_2145; Extracellular protein, cell wall–anchored | 1.90 | ||
| F9UNC2 | lp_1357; Extracellular protein, membrane-anchored | 1.88 | ||
| F9UL67 | zmp2; Extracellular zinc metalloproteinase, M10 family | 1.96 | ||
| F9USE1 | lp_3014; Extracellular transglycosylase, with LysM peptidoglycan–binding domain | 1.62 | ||
| F9USH2 | lp_3050; Extracellular transglycosylase, membrane-bound | 3.29 | ||
| Hydrolase | F9UTL5 | lp_3341; Cell surface hydrolase, DUF915 family, membrane-bound | 2.01 | |
| F9UM81 | gph1; Phosphohydrolase | 1.58 | ||
| F9UM42 | lp_0824; Hydrolase, HAD superfamily, Cof family | −3.78 | ||
| F9URL1 | lp_2737; Cell surface hydrolase, DUF915 family, membrane-bound | −2.25 | ||
| F9URQ4 | lp_2787; Hydrolase, HAD superfamily, Cof family | −1.96 | ||
| F9URF0 | xynC; Acetyl xylosidase (Promiscuous) | 1.51 | ||
| F9USG7 | amd; Aminohydrolase/peptidase, M20D family | −2.33 | ||
| Q06115 | cbh; Choloylglycine hydrolase | −2.05 | ||
| F9UTI3 | folQ; Dihydroneopterin triphosphate pyrophosphohydrolase | −1.98 | ||
| F9UPB8 | lp_1767; Glycosyl hydrolase, family 25 | 1.84 | ||
| F9UQI5 | lp_2266; Phosphoesterase | 1.75 | ||
| F9UL25 | lp_0552; Phosphoesterase | −1.62 | ||
| Other | Galactose metabolism and cell wall synthesis | F9UMX4 | glf1; UDP-galactopyranose mutase | 1.72 |
| F9URD9 | acm2; Cell wall hydrolase/muramidase | 1.51 | ||
| Inositol phosphate metabolism | Q88S38 | iolG; myo-inositol 2-dehydrogenase (promiscuous) | −6.86 | |
| Q88S37 | iolE; 2-keto-myo-inositol dehydratase (promiscuous) | −2.18 | ||
| F9ULG2 | lp_3608; myo-inositol 2-dehydrogenase-like (promiscuous) | −3.25 | ||
| F9ULG4 | lp_3612; myo-inositol 2-dehydrogenase-like (promiscuous) | −2.95 | ||
| Amino sugar and nucleotide sugar metabolism | F9USZ6 | sacK1; fructokinase | 1.61 | |
| Q88SC3 | murQ1; N-acetylmuramic acid 6-phosphate etherase | −1.80 | ||
| Oxidative phosphorylation | Q88UT8 | atpE; H(+)-transporting two-sector ATPase, C subunit | 1.62 | |
| F9UQR9 | atpB; H(+)-transporting two-sector ATPase, A subunit | 1.73 | ||
| Riboflavin metabolism | F9UNI1 | ribA; 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II | −4.71 | |
| Q88X16 | ribH; riboflavin synthase, beta chain | −4.63 | ||
| Other | F9UQZ9 | lp_2463; Prophage P2b protein 18, major capsid protein | 6.88 | |
| F9UQX7 | lp_2437; Prophage P2a protein 20, replication protein DnaD domain | 1.95 | ||
| F9US31 | lp_2953; Esterase | 1.68 | ||
| F9UNU9 | fthC; 5-formyltetrahydrofolate cyclo-ligase | 1.98 | ||
| Q890D7 | lp_0089; UPF0246 protein | 1.71 | ||
| Q88V85 | sepF; Cell division protein SepF | 2.24 | ||
| F9UPG0 | tarJ; ribitol-5-phosphate 2-dehydrogenase | 10.23 | ||
| F9URL0 | cah; Carbonate dehydratase | 1.51 | ||
| F9URA1 | rnh; Ribonuclease H | 1.62 | ||
| F9UPE3 | lp_1796; DegV family protein | 1.50 | ||
| Q6LWH3 | repB; Copy number control protein | −4.51 | ||
| Q88VB0 | lp_2157; UPF0356 protein | −1.52 | ||
| F9UNZ6 | tpk; Thiamin pyrophosphokinase | 2.12 | ||
| F9ULU2 | rsmI; Ribosomal RNA small subunit methyltransferase I | 1.74 | ||
| Uncharacterized protein | F9UQ40 | lp_2093; Uncharacterized protein | −1.51 | |
| F9UNU5 | lp_1566; Uncharacterized protein | −1.61 | ||
| Q6LWD6 | orf41; Uncharacterized protein | −1.79 | ||
| F9UPK2 | lp_1872; Uncharacterized protein | −1.56 | ||
| F9UU56 | lp_3372; Uncharacterized protein | −2.05 | ||
| F9UM53 | lp_0837; Uncharacterized protein | −1.63 | ||
| F9UTZ1 | lp_0402; Uncharacterized protein | −1.69 | ||
| F9UKY5 | lp_0507; Uncharacterized protein | −1.88 | ||
| Q6LWD8 | orf39; Uncharacterized protein | 2.86 | ||
| Q6LWD7 | orf40; Uncharacterized protein | 2.66 | ||
| F9UT92 | lp_3179; Uncharacterized protein | 1.78 | ||
| F9URF7 | lp_2667; Uncharacterized protein | 1.67 | ||
| F9UQN8 | lp_2333; Uncharacterized protein | 1.54 | ||
| F9UN47 | lp_1257; Uncharacterized protein | 1.54 | ||
| F9USX1 | lp_0158; Uncharacterized protein | 1.51 | ||
| F9UQ59 | lp_2112; Uncharacterized protein | 1.66 | ||
| F9UQ60 | lp_2113; Uncharacterized protein | −4.47 | ||
| F9UTE8 | lp_3250; Uncharacterized protein | −3.03 |
aCategory of differently expressed proteins was based on their functions annotated in the database of Uniprot and KEGG. bAccession number of each protein in Uniprot database. cDescription of each differently expressed protein, including corresponding gene name of each protein and full protein name. dFC indicates fold change of each differently expressed protein in the comparison of CCFM8610/CCFM191. Negative values indicate down-regulation of proteins, and positive values indicate up-regulation.