Table 2

R. eutropha H16 gene expression microarray experiment comparing samples of cells growing in the presence of nitrogen to samples with PHB production (without nitrogen)

Functional categoryFunctional groupaNo. (%) of genesb
UpregulatedDownregulated
2- to 4-fold>4-fold2- to 4-fold>4-fold
Information storage and processing
    JTranslation, ribosomal structure, and biogenesis3 (1.7)2 (1.1)20 (11.2)101 (56.4)
    KTranscription42 (5.3)21 (2.7)30 (3.8)21 (2.7)
    LDNA replication, recombination, and repair5 (3.1)3 (1.9)27 (16.7)25 (15.5)
Cellular processes
    DCell division and chromosomal partitioning1 (3.6)1 (3.6)10 (36.1)4 (14.5)
    OPosttranslational modification, protein turnover, chaperones9 (5.7)25 (15.9)24 (15.3)24 (15.3)
    MCell envelope biogenesis, outer membrane4 (1.7)6 (2.6)26 (11.2)39 (16.8)
    NCell motility and secretion8 (4.4)6 (3.3)23 (12.8)32 (17.8)
    PInorganic ion transport and metabolism12 (11.7)34 (33.2)14 (13.7)32 (31.3)
    TSignal transduction mechanisms9 (1.1)29 (3.7)13 (1.7)7 (0.9)
Metabolism
    CEnergy production and conversion35 (7.2)82 (16.9)13 (2.7)53 (10.9)
    GCarbohydrate metabolism and transport13 (8.7)57 (38.1)16 (10.7)26 (17.4)
    EAmino acid metabolism and transport28 (9.5)53 (17.9)35 (11.8)66 (22.3)
    FNucleotide metabolism and transport2 (2.7)12 (16.0)19 (25.3)23 (30.7)
    HCoenzyme metabolism3 (1.9)7 (4.4)21 (13.3)15 (9.5)
    ILipid metabolism (includes genes in the PHB cycle)20 (6.0)16 (4.8)21 (6.4)23 (7.0)
    QSecondary metabolite biosynthesis, transport, and catabolism8 (8.2)8 (8.2)5 (5.1)9 (9.2)
Uncharacterized or poorly characterized
    RGeneral function prediction only51 (6.9)105 (14.5)85 (11.5)66 (9.0)
    SFunction unknown121 (6.6)266 (14.5)87 (4.7)101 (5.5)
Total374733489667
  • a Functional group categories are based on those described previously by Tatusov et al. (62).

  • b Genes in the “upregulated” category underwent an upregulation of expression during PHB production compared to growth using fructose as a carbon source. Genes in the “downregulated” category underwent a downregulation of expression during PHB production compared to growth using fructose as a carbon source. The percentage of genes affected per functional group was based on the number of genes in each group exhibiting significant changes in expression as a percentage of the total number of R. eutropha genes in a given functional group based on data reported previously (40). For all genes represented in this table, the P value was <0.01.