Table 5.
R. eutropha H16 gene expression during growth on fructose compared to gene expression during growth on intracellular PHB
| Functional category | Functional groupa | No. (%) of genesb |
|||
|---|---|---|---|---|---|
| Upregulated |
Downregulated |
||||
| 2- to 4-fold | >4-fold | 2- to 4-fold | >4-fold | ||
| Information storage and processing | |||||
| J | Translation, ribosomal structure, and biogenesis | 7 (3.9) | 3 (1.7) | 30 (16.7) | 5 (2.8) |
| K | Transcription | 26 (3.3) | 5 (0.6) | 34 (4.3) | 10 (1.3) |
| L | DNA replication, recombination, and repair | 2 (1.2) | 1 (0.6) | 22 (13.6) | 3 (2.7) |
| Cellular processes | |||||
| D | Cell division and chromosomal partitioning | 1 (3.6) | 0 (0.0) | 6 (21.7) | 1 (3.6) |
| O | Posttranslational modification, protein turnover, chaperones | 8 (5.1) | 3 (1.9) | 11 (7.0) | 5 (3.2) |
| M | Cell envelope biogenesis, outer membrane | 3 (1.3) | 0 (0.0) | 21 (9.0) | 19 (8.2) |
| N | Cell motility and secretion | 3 (1.7) | 2 (1.1) | 18 (10.0) | 9 (5.0) |
| P | Inorganic ion transport and metabolism | 7 (6.8) | 11 (10.7) | 19 (18.6) | 3 (2.9) |
| T | Signal transduction mechanisms | 5 (0.6) | 10 (1.3) | 16 (2.0) | 4 (0.5) |
| Metabolism | |||||
| C | Energy production and conversion | 17 (3.5) | 15 (3.1) | 24 (4.9) | 28 (5.8) |
| G | Carbohydrate metabolism and transport | 5 (3.3) | 5 (3.3) | 24 (16.1) | 27 (18.0) |
| E | Amino acid metabolism and transport | 10 (3.4) | 8 (2.7) | 52 (17.6) | 27 (9.1) |
| F | Nucleotide metabolism and transport | 8 (10.7) | 0 (0.0) | 15 (20.0) | 2 (2.7) |
| H | Coenzyme metabolism | 6 (3.8) | 3 (1.9) | 18 (9.1) | 5 (3.2) |
| I | Lipid metabolism (includes genes in the PHB cycle) | 12 (3.6) | 8 (2.4) | 30 (6.4) | 10 (7.0) |
| Q | Secondary metabolite biosynthesis, transport, and catabolism | 1 (1.0) | 4 (4.1) | 6 (6.1) | 4 (4.1) |
| Uncharacterized or poorly characterized | |||||
| R | General function prediction only | 38 (5.2) | 19 (2.6) | 86 (11.7) | 30 (4.1) |
| S | Function unknown | 89 (4.9) | 76 (4.1) | 88 (4.8) | 33 (1.8) |
| Total | 248 | 173 | 520 | 225 | |
Functional group categories are based on those described previously by Tatusov et al. (62).
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.