Table 5

R. eutropha H16 gene expression during growth on fructose compared to gene expression during growth on intracellular PHB

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 biogenesis7 (3.9)3 (1.7)30 (16.7)5 (2.8)
    KTranscription26 (3.3)5 (0.6)34 (4.3)10 (1.3)
    LDNA replication, recombination, and repair2 (1.2)1 (0.6)22 (13.6)3 (2.7)
Cellular processes
    DCell division and chromosomal partitioning1 (3.6)0 (0.0)6 (21.7)1 (3.6)
    OPosttranslational modification, protein turnover, chaperones8 (5.1)3 (1.9)11 (7.0)5 (3.2)
    MCell envelope biogenesis, outer membrane3 (1.3)0 (0.0)21 (9.0)19 (8.2)
    NCell motility and secretion3 (1.7)2 (1.1)18 (10.0)9 (5.0)
    PInorganic ion transport and metabolism7 (6.8)11 (10.7)19 (18.6)3 (2.9)
    TSignal transduction mechanisms5 (0.6)10 (1.3)16 (2.0)4 (0.5)
Metabolism
    CEnergy production and conversion17 (3.5)15 (3.1)24 (4.9)28 (5.8)
    GCarbohydrate metabolism and transport5 (3.3)5 (3.3)24 (16.1)27 (18.0)
    EAmino acid metabolism and transport10 (3.4)8 (2.7)52 (17.6)27 (9.1)
    FNucleotide metabolism and transport8 (10.7)0 (0.0)15 (20.0)2 (2.7)
    HCoenzyme metabolism6 (3.8)3 (1.9)18 (9.1)5 (3.2)
    ILipid metabolism (includes genes in the PHB cycle)12 (3.6)8 (2.4)30 (6.4)10 (7.0)
    QSecondary metabolite biosynthesis, transport, and catabolism1 (1.0)4 (4.1)6 (6.1)4 (4.1)
Uncharacterized or poorly characterized
    RGeneral function prediction only38 (5.2)19 (2.6)86 (11.7)30 (4.1)
    SFunction unknown89 (4.9)76 (4.1)88 (4.8)33 (1.8)
Total248173520225
  • 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 utilization compared to growth using fructose as a carbon source. Genes in the “downregulated” category underwent a downregulation of expression during PHB utilization 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 levels 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.