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. 2005 Dec;187(23):7996–8005. doi: 10.1128/JB.187.23.7996-8005.2005

TABLE 2.

Identified proteins involved in cellular processes outside of aromatic and C1 catabolisma

Functional class Annotation (EC number) Specific functionb Gene Scorec #Pd SCd Normalized volumee
Succ-ML Benz-ML Benz-TP Biph-ML Biph-TP
Stress response AhpC alkyl hydroperoxide reductase (1.11.1.7) Detoxification of organic hydroperoxides 2448 118 10 68 0.07 0.10 0.03 0.25 0.20
Stress response AhpF alkyl hydroperoxide reductase (1.8.1.9) Detoxification of organic hydroperoxides 2449 86 9 29 0.05 0.07 0.02 0.15 0.05
Stress response GroEL chaperonin Involved in degradation of abnormal proteins 7732 142 13 30 6.1 10 6.1 9.9 6.0
Stress response Heat shock protein HsIU Proteolysis of abnormal proteins 8238 53 8 18 0.06 0.25 0.20 0.18 0.08
Stress response Stringent starvation protein A Unknown 4794 61 7 53 ND 0.08 LR 0.25 0.15
Stress response PrkA serine kinase Regulation 6208 109 12 18 0.02 ND 0.16 0.03 0.12
Purine metabolism PurF (2.4.2.14) PRPP + Gln → 5′-phosphoribosylamine + Glu 3945 85 14 30 ND 0.03 0.04 0.01 0.01
Purine metabolism PurA (6.3.4.4) GTP + IMP = l-aspartate → GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP 5861 74 8 25 0.09 0.24 0.15 0.13 0.01
Amino acid metabolism Aspartyl tRNA synthetase (6.1.1.12) Asp + tRNA → Asp-tRNA 7923 61 7 15 ND 0.09 ND 0.05 ND
Amino acid metabolism Glutamine synthetase (6.3.1.2) ATP + Glu → ADP + Gln 5786 110 12 30 0.19 0.22 LR 0.42 LR
Amino acid metabolism Aspartate transaminase (2.6.1.1) 2-Oxoglutarate + Asp → oxaloacetate + Glu 7794 71 11 24 ND 0.01 0.01 ND 0.12
Amino acid metabolism Histidyl-tRNA synthetase (6.1.1.21) His + tRNA → His-tRNA 5852 55 11 28 ND 0.13 0.09 0.09 0.05
Amino acid metabolism IlvC ketol-acid reductoisomerase (1.1.1.86) 2,3-diOH-3-methylbutanoate → 2-OH-2-methyl-3-oxobutanoate 7236 67 7 26 0.15 0.41 LR 0.18 0.02
Aminosugar metabolism N-Acetylglucosamine-6-P deacetylase (3.5.1.25) N-Acetylglucosamine-6-P → d-glucosamine-6-P + acetate 8032 80 8 28 ND 0.04 0.09 ND ND
Outer membrane protein Porin (OmpC) Outer membrane permeability 2049 114 8 40 0.02 0.02 0.04 0.08 0.87
Protein biosynthesis Ribosomal protein L1 Structural constituent of ribosome 4689 56 5 24 LR LR LR 0.12 LR
Outer membrane protein Porin Outer membrane permeability 7389 157 14 61 0.01 ND ND 0.02 0.50
Outer membrane protein Porin (OmpC) Outer membrane permeability 4849 121 10 32 0.03 ND ND ND 9.6
TCA cycle Isocitrate dehydrogenase (1.1.1.42) Isocitrate → 2-oxoglutarate + CO2 5150 71 13 31 0.10 0.05 0.29 0.06 0.17
TCA cycle Citrate synthase (1.7.99.5) Oxaloacetate + acetyl CoA → citrate + CoA 2385 109 12 32 0.08 1.3 0.66 ND ND
Fatty acid metabolism Acetyl-CoA carboxylase, alpha subunit (6.4.1.2) ATP + acetyl-CoA + HCO3 → malonyl-CoA 5882 59 7 32 LR 0.04 LR 0.02 0.01
Fatty acid metabolism Hypothetical dehydrogenase (1.1.1.100) 3-OH-acyl-ACP → 3-oxoacyl-ACP 6307 66 5 33 0.01 0.04 0.14 0.02 0.02
Fatty acid metabolism Acyltransferase Acyl-carrier + reactant = acyl-reactant + carrier 6659 61 6 40 0.01 0.03 0.01 0.21 0.20
DNA replication DNA polymerase III, beta subunit (2.7.7.7) Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n + 1) 8311 120 18 58 ND 0.14 0.27 0.11 0.11
Other 5,10 methylene THF reductase (1.7.99.5) 5-methyl-THF → 5,10-methylene-THF 4607 69 7 38 LR 0.05 LR 0.01 0.04
Other Phasin (granule-associated protein) Unknown 5805 79 7 43 ND ND ND 0.04 0.02
Other Putative Amidase (3.5.1.4) Monocarboxylic acid amide → monocarboxylate + NH3 0365 58 7 22 ND 0.16 0.23 0.03 0.03
Other Acyl-carrier protein (ACP) phosphodiesterase (3.1.4.14) ACP + H2O → 4-P-pantetheine + apoprotein 4830 101 6 44 0.005 0.01 0.10 0.16 0.36
Other Hypothetical hydrolase Unknown 4637 113 8 34 ND 0.10 0.04 0.09 0.03
a

Abbreviations are as used in Table 1, plus: TCA, tricarboxylic acid; P, phosphate; PRPP, 5-phosphoribosyl 1-pyrophosphate; diOH, dihydroxy; ACP, acyl carrier protein. Normalized volumes in boldface type were at least twofold higher than in control samples (Succ-ML; Progenesis analysis, P < 0.05). Singly and doubly underlined values indicate significant up- and down-regulation, respectively, of the corresponding transcript in previous microarray experiments (Genespring; Silicon Genetics); Student t test, P < 0.10 (8). No microarray data were available for genes 2448, 5150, or 5805 or for any gene in Benz-TP samples.

b

For enzymes, the reaction catalyzed is indicated.

c

Probability-based Mowse score generated by MASCOT. In the LB400 protein database, scores greater than 52 are significant (P < 0.05).

d

Number of peptides matched (#P) and sequence coverage (SC) in MASCOT analysis.

e

Average normalized volumes over the three biological replicates under each of the tested growth conditions.