title: Integrated metabolic flux and omics analysis of Synechocystis sp. PCC 6803 under mixotrophic and photoheterotrophic conditions.
abstract: Cyanobacteria have flexible metabolic capability that enables them to adapt to various environments. To investigate their underlying metabolic regulation mechanisms, we performed an integrated analysis of metabolic flux using transcriptomic and metabolomic data of a cyanobacterium Synechocystis sp. PCC 6803, under mixotrophic and photoheterotrophic conditions. The integrated analysis indicated drastic metabolic flux changes, with much smaller changes in gene expression levels and metabolite concentrations between the conditions, suggesting that the flux change was not caused mainly by the expression levels of the corresponding genes. Under photoheterotrophic conditions, created by the addition of the photosynthesis inhibitor atrazine in mixotrophic conditions, the result of metabolic flux analysis indicated the significant repression of carbon fixation and the activation of the oxidative pentose phosphate pathway (PPP). Moreover, we observed gluconeogenic activity of upstream of glycolysis, which enhanced the flux of the oxidative PPP to compensate for NADPH depletion due to the inhibition of the light reaction of photosynthesis. 'Omics' data suggested that these changes were probably caused by the repression of the gap1 gene, which functions as a control valve in the metabolic network. Since metabolic flux is the outcome of a complicated interplay of cellular components, integrating metabolic flux with other 'omics' layers can identify metabolic changes and narrow down these regulatory mechanisms more effectively.
authors: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871 Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (JST, CREST).
authors: Tsubasa
authors: T
authors: Nakajima
authors: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871 Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (JST, CREST).
authors: Shuichi
authors: S
authors: Kajihata
authors: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871 Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (JST, CREST).
authors: Katsunori
authors: K
authors: Yoshikawa
authors: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871 Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (JST, CREST).
authors: Fumio
authors: F
authors: Matsuda
authors: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871 Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (JST, CREST) Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874 Japan.
authors: Chikara
authors: C
authors: Furusawa
authors: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871 Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (JST, CREST) Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan.
authors: Takashi
authors: T
authors: Hirasawa
authors: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871 Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (JST, CREST) shimizu@ist.osaka-u.ac.jp.
authors: Hiroshi
authors: H
authors: Shimizu
mesh_terms: D001280:Atrazine / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D057486:Carbon Cycle; D002247:Carbon Isotopes / Q000032:analysis; D020869:Gene Expression Profiling; D005947:Glucose / Q000378:metabolism; D006019:Glycolysis; D006540:Herbicides / Q000494:pharmacology; D052836:Heterotrophic Processes; D008027:Light; D064688:Metabolic Flux Analysis; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D055432:Metabolomics; D010788:Photosynthesis; D052817:Phototrophic Processes; D046939:Synechocystis / Q000235:genetics / Q000254:growth & development / Q000378:metabolism / Q000528:radiation effects; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D002247:Carbon Isotopes; D006540:Herbicides; D005947:Glucose; D001280:Atrazine
keywords: Cyanobacteria; Integrated omics analysis; Metabolic flux; Metabolomics; Synechocystis sp. PCC 6803; Transcriptomics