91 1.10 ± 0.0001 –   13C 48.3 ± 1.41 1.81 ± 0.0013 0.27 ± 0.0007 H16∆cbbLS p 12C 50.0 ± 2.49 1.13 ± 0.0002 –   13C 48.3 ± 2.48 2.11 ± 0.0022 0.38 ± 0.0012 H16∆∆cbbLS 12C 27.8 ± 0.17 1.11 ± 0.0003 –   13C 30.0 ± 0.48 1.25 ± 0.0005 0.05 ± 0.0004 aP(3HB) biosynthesis was performed by 2-stage Microbiology inhibitor cultivation as described in the text. bAdded periodically during the second stage. cMeans of 13C/12C ratios calculated from isotopomer abundances of the three fragments

(m/z 45, 87, and 103) derived from 3HB methyl ester. Conclusion This study applied the RNA-seq technique to analyze the genome-wide transcriptional dynamics of PHA-producing R. eutropha H16. The mRNA enrichment using a commercially available probe specific to bacterial rRNA was incomplete for R. eutropha even after two repeated operations, but the greater depth of new sequencing technology could overcome this problem by giving sufficient numbers of reads from mRNA. A comparison of the transcriptomes detected several WH-4-023 ic50 phase-depending changes in the expression of genes responsible for shifts in the physiological state of R. eutropha throughout cultivation on fructose. In the growth phase, there was high level induction of genes related

to transcription, translation, cell division, peptidoglycan biosynthesis, pilus and flagella assembly, energy conservation, and fatty acid biosynthesis; while the genes related to central metabolism were repressed in the PHA production phase. Interestingly, the CBB cycle genes and several β-oxidation genes were transcriptionally activated in the PHA production phase compared with that in the growth phase, Autophagy Compound Library ic50 when fructose was supplied as the sole carbon source. We further found that 13CO2 was incorporated into P(3HB) when R. eutropha H16 was incubated in the fructose-containing Meloxicam medium in the presence of NaH13CO3. The incorporation of 13C was significantly reduced by the double disruption

of both Rubisco genes, which demonstrated that the CO2 fixation was mediated by Rubisco, i.e., the transcriptionally activated CBB cycle was functional during heterotrophic PHA biosynthesis. To the best of our knowledge, this is the first report to demonstrate CO2 fixation into PHA under a heterotrophic condition. The results of our study will facilitate further metabolic engineering of R. eutropha for improved production of PHAs from non-fossil resources, such as the increased metabolic flux from sugars to PHA, the provision of mcl-(R)-3-hydroxyacyl-CoA monomers from sugars through lipid turnover, and fixation of CO2 into the polymer materials. Methods Cultivation, RNA isolation, and mRNA enrichment R. eutropha wild strain H16 (DSM428) was cultivated in a 500 ml flask on a reciprocal shaker (115 strokes/min) at 30°C with 100 ml of a nitrogen-limited mineral salts (MB) medium, which was composed of 9 g/l Na2HPO4 · 12H2O, 1.5 g/l KH2PO4, 2.0 g/l NH4Cl, 0.2 g/l MgSO4 · 7H2O, and 1 ml/l trace element solution [46] in deionized water.