title: Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses.
abstract: BACKGROUND
  Ralstonia eutropha H16 is well known to produce polyhydroxyalkanoates (PHAs), which are potential bio-based biodegradable plastics, in an efficient manner as an energy storage material under unbalanced growth conditions. To obtain further knowledge of PHA biosynthesis, this study performed a quantitative transcriptome analysis based on deep sequencing of the complementary DNA generated from the RNA (RNA-seq) of R. eutropha H16.
  
  
  RESULTS
  Total RNAs were extracted from R. eutropha cells in growth, PHA production, and stationary phases on fructose. rRNAs in the preparation were removed by repeated treatments with magnetic beads specific to bacterial rRNAs, and then the 36 bp sequences were determined using an Illumina high-throughput sequencer. The RNA-seq results indicated the induction of gene expression for transcription, translation, cell division, peptidoglycan biosynthesis, pilus and flagella assembly, energy conservation, and fatty acid biosynthesis in the growth phase; and the repression trends of genes involved in central metabolisms in the PHA production phase. Interestingly, the transcription of genes for Calvin-Benson-Bassham (CBB) cycle and several genes for β-oxidation were significantly induced in the PHA production phase even when the cells were grown on fructose. Moreover, incorporation of 13C was observed in poly(3-hydroxybutyrate) synthesized by R. eutropha H16 from fructose in the presence of NaH13CO3, and further gene deletion analyses revealed that both of the two ribulose 1,5-bisphosphate carboxylase (Rubiscos) in CBB cycle were actually functional in CO2 fixation under the heterotrophic condition.
  
  
  CONCLUSIONS
  The results revealed the phase-dependent transcriptomic changes and a CO2 fixation capability under heterotrophic conditions by PHA-producing R. eutropha.
authors.forename: Rie
authors.initials: R
authors.lastname: Shimizu
authors.forename: Kenta
authors.initials: K
authors.lastname: Chou
authors.forename: Izumi
authors.initials: I
authors.lastname: Orita
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nakamura
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Fukui
mesh_terms: D002245:Carbon Dioxide / Q000378:metabolism*; D002247:Carbon Isotopes / Q000032:analysis; D020118:Cupriavidus necator / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial; D052836:Heterotrophic Processes; D006885:Hydroxybutyrates / Q000378:metabolism*; D011091:Polyesters / Q000378:metabolism*; D012329:RNA, Bacterial / Q000235:genetics; D012273:Ribulose-Bisphosphate Carboxylase / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D000094122:Polyhydroxybutyrates
chemical_list: D002245:Carbon Dioxide; D002247:Carbon Isotopes; D006885:Hydroxybutyrates; D011091:Polyesters; D012329:RNA, Bacterial; D012273:Ribulose-Bisphosphate Carboxylase; C003182:poly-beta-hydroxybutyrate; D000094122:Polyhydroxybutyrates