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. 2011 Jul;77(13):4473–4485. doi: 10.1128/AEM.00116-11

Table 1.

Selected genes showing a significant response identified after meta-analysis of microarray data of C. acetobutylicum ATCC 824 exposed to 50 mM butanol compared to nonexposed controls applying the step-down quadratic regression methoda

Product type and substrateb Butanol-downregulated or -upregulated product namec COG EHIPd Locus tag Overall P value
Butanol-downregulated products
    VitB12 Cobyrinic acid a,c-diamide synthase CobB/CbiA (CBIB protein) H CAC0582 0.001301656
Phosphatidylserine synthase I CAC0676 0.00234798
Predicted permease E CAC0875 0.00077822
    Co Cobalt transport (ATPase component) P CAC1368 0.002664104
    VitB12 Precorrin 8X methylmutase H CAC1376 0.000268975
    VitB12 Precorrin 6B methylase CbiT H CAC1378 3.97206E−07
    VitB12 Precorrin 4 methylase CbiF H CAC1380 0.000110082
    THF Enzyme of dihydrofolate reductase family, ortholog YWFD of B. subtilis H CAC1495 0.00520426
    Lipid 3-Ketoacyl-(acyl carrier protein) reductase I CAC2626 0.00025712
Proline/glycine betaine ABC-type transport system, permease component fused to periplasmic component E CAC2849 0.000922292
Proline/glycine betaine ABC-type transport system, ATPase component E CAC2850 1.31008E−05
Oligopeptide ABC transporter, ATPase component P CAC3182 0.0047743
Oligopeptide transport permease protein E CAP0177 0.000635715
Butanol-upregulated products
    Fe Nitrogenase iron protein (nitrogenase component II) gene nifH P CAC0253 0.000816333
Peptidase T E CAC0476 0.001467584
    His ATP phosphoribosyltransferase catalytic subunit E CAC0936 2.40248E−05
    His Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase E CAC0940 7.91786E−05
Lipoprotein, attached to the cytoplasmic membrane, NLPA family P CAC0986 0.003698933
    Lipid Phosphatidylglycerophosphate synthase related protein (fragment) I CAC2024 0.009199846
    Urea N-Acetylornithine aminotransferase E CAC2388 2.72258E−05
    Urea Acetylglutamate kinase E CAC2389 0.000250975
    Urea N-Acetyl-gamma-glutamyl-phosphate reductase E CAC2390 0.003281643
Dipeptidase PepV E CAC2723 0.002038606
    Se Possible selenocysteine lyase (aminotransferase of NifS family) E CAC2805 0.000640894
    Lys Lysine-specific permease E CAC3164 0.003458938
    Met Homocysteine methyltransferase E CAC3348 0.000180346
ABC-type polar amino acid transport system, ATPase component E CAC3618 0.000132942
Amino acid ABC transporter, permease component E CAC3619 0.006894683
a

The meta-analysis includes time course microarray experiments at 0, 10, 30, 45, 60, 120, 360, 720, and 1,440 min). Figure 2A shows the frequencies of genes displaying a kinetic linear pattern of up- and downregulation compared to genes showing a flat pattern (or no regulation) after applying Stromberg analysis (44). The step-down quadratic regression method was applied to normalized data for pattern recognition (44). Data were obtained from cells cultivated in clostridial growth medium (CGM [69]).

b

VitB12, vitamin B12; THF, tetrahydrofolate.

c

CBIB, cobyrinic acid a,c-diamide synthase; YWFD, synonym for bacilysin biosynthesis oxidoreductase BacC; NLPA, family of lipoproteins.

d

COGs, clusters of orthologous groups (http://www.ncbi.nlm.nih.gov/COG/grace/uni.html); EHIP, COG groups E, H, I, and P.