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. 2008 Jan 18;190(8):2739–2758. doi: 10.1128/JB.01683-07

TABLE 7.

Genes repressed in NO2−-containing medium

Functional category or metabolic pathway Genes activated in NO2−-containing medium
Genes in P. aeruginosa genome
P value
No. of genes identified % of genes identified No. of genes % of genes
COG functional category
    Energy production and conversion 15 38.46 320 5.16 3.18E-08*
    Translation, ribosomal structure, and biogenesis 5 12.82 198 3.19 0.02457*
    Unclassified 3 7.69 1,054 16.99 0.08562
    Lipid metabolism 3 7.69 190 3.06 0.2134
    Carbohydrate transport and metabolism 2 5.13 222 3.58 1
    Posttranslational modification, protein turnover, chaperones 2 5.13 191 3.08 0.721
    Amino acid transport and metabolism 1 2.56 486 7.83 0.2134
    Cell envelope biogenesis, outer membrane 1 2.56 254 4.09 1
    Coenzyme metabolism 1 2.56 204 3.29 1
    DNA replication, recombination, and repair 1 2.56 132 2.13 1
    Defense mechanisms 1 2.56 77 1.24 0.6212
    General function prediction only 1 2.56 604 9.74 0.0818
    Secondary metabolite biosynthesis, transport, and catabolism 1 2.56 158 2.55 1
    Signal transduction mechanisms 1 2.56 337 5.43 0.721
    Transcription 1 2.56 482 7.77 0.2134
    Function unknown 0 0 498 8.03 0.006755*
PseudoCyc metabolic pathways
    Unclassified 15 25.42 4,701 77.64 4.28E−13*
    Citrate cycle (TCA cycle) 7 11.86 22 0.36 0.00194*
    Pyruvate metabolism 4 6.78 33 0.55 0.06486
    Glyoxylate and dicarboxylate metabolism 3 5.08 18 0.3 0.05938
    Oxidative phosphorylation 3 5.08 24 0.4 0.05938
    Aminoacyl-tRNA biosynthesis 2 3.39 20 0.33 0.2462
    C5 branched dibasic acid metabolism 2 3.39 4 0.07 0.2462
    Fatty acid biosynthesis (path 1) 2 3.39 10 0.17 0.2462
    Glycolysis/gluconeogenesis 2 3.39 21 0.35 0.2462
    Lysine degradation 2 3.39 10 0.17 0.2462
    Reductive carboxylate cycle (CO2 fixation) 2 3.39 8 0.13 0.2462
    Valine, leucine, and isoleucine biosynthesis 2 3.39 14 0.23 0.2462
    Aminophosphonate metabolism 1 1.69 1 0.02 0.4975
    Amino sugar metabolism 1 1.69 5 0.08 0.4975
    Butanoate metabolism 1 1.69 11 0.18 0.4975
    Glutathione metabolism 1 1.69 8 0.13 0.4975
    Glycerolipid metabolism 1 1.69 17 0.28 0.4975
    Lysine biosynthesis 1 1.69 10 0.17 0.4975
    Methionine metabolism 1 1.69 11 0.18 0.4975
    Propanoate metabolism 1 1.69 9 0.15 0.4975
    Purine metabolism 1 1.69 37 0.61 1
    Pyrimidine metabolism 1 1.69 27 0.45 0.4975
    Selenoamino acid metabolism 1 1.69 10 0.17 0.4975
    Tryptophan metabolism 1 1.69 8 0.13 0.4975
    Urea cycle and metabolism of amino groups 1 1.69 16 0.26 0.4975

aSignificantly greater proportions of genes were classified as being involved in energy production and conversion (P = 3.18E−08) and translation, ribosomal structure, and biogenesis (P = 0.025). A significantly greater proportion of genes were involved in the TCA cycle (P = 0.0019) than that for the genome, supporting the above COG data showing that significantly more genes are involved in energy production and conversion. Also, note that many genes are involved in pathways related to translation, ribosomal structure, and biogenesis, but similar to the case in Table 5, they are spread out among multiple categories and did not reach statistical significance.

bPearson's chi-square test with Yates's continuity correction. For those categories with small values (<5), Fisher's exact test was performed instead. Asterisks indicate statistical significance (P < 0.05).