Abstract
Cyanobacteria Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 show similar changes in the metabolic response to changed CO2 conditions but exhibit significant differences at the transcriptomic level. This study employs a systems biology approach to investigate the difference in metabolic regulation of Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803. Presented multi-level kinetic model for Synechocystis sp. PCC 6803 is a new approach integrating and analysing metabolomic, transcriptomic and fluxomics data obtained under high and ambient CO2 levels. Modelling analysis revealed that higher number of different isozymes in Synechocystis 6803 improves homeostatic stability of several metabolites, especially 3PGA by 275%, against changes in gene expression, compared to Synechococcus sp. PCC 7942. Furthermore, both cyanobacteria have the same amount of phosphoglycerate mutases but Synechocystis 6803 exhibits only ~20% differences in their mRNA levels after shifts from high to ambient CO2 level, in comparison to ~500% differences in the case of Synechococcus sp. PCC 7942. These and other data imply that the biochemical control dominates over transcriptional regulation in Synechocystis 6803 to acclimate central carbon metabolism in the environment of variable inorganic carbon availability without extra cost carried by large changes in the proteome.
Highlights
The handling of large data sets from “omics” experiments, such as transcriptomics, remains challenging
The gene expression analysis revealed that the cyanobacterium Synechococcus 7942 exhibits major changes in expression of genes for many enzymes involved in central carbon metabolism after a shift from HC to AC9
The main goal of this study is to achieve a mathematical description of the response of the central carbon metabolism to different inorganic carbon conditions in Synechocystis 6803, which could help to identify major regulatory processes
Summary
The handling of large data sets from “omics” experiments, such as transcriptomics, remains challenging. In contrast to Synechococcus 7942, Synechocystis 6803 cells did not show significant changes in the expression of enzymes involved in central carbon metabolism[27,28], whereas the principal changes in the metabolome were similar in both cyanobacteria during the AC shift response[29]. These findings may indicate that in Synechocystis 6803 carbon metabolism is rather regulated at the posttranslational, i.e. biochemical, level during the acclimation to different CO2 levels. We focus on three major topics: 1) differences in the metabolic regulation between Synechococcus 7942 and Synechocystis 6803, 2) the role of additional isozymes in Synechocystis 6803, and 3) the influence of gene expression on metabolic fluxes
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