CyAbrB2 Contributes to the Transcriptional Regulation of Low CO2 Acclimation in Synechocystis sp. PCC 6803.

Acclimation to low CO2 conditions in cyanobacteria involves the co-ordinated regulation of genes mainly encoding components of the carbon-concentrating mechanism (CCM). Making use of several independent microarray data sets, a core set of CO2-regulated genes was defined for the model strain Synechocystis sp. PCC 6803. On the transcriptional level, the CCM is mainly regulated by the well-characterized transcriptional regulators NdhR (= CcmR) and CmpR. However, the role of an additional regulatory protein, namely cyAbrB2 belonging to the widely distributed AbrB regulator family that was originally characterized in the genus Bacillus, is less defined. Here we present results of transcriptomic and metabolic profiling of the wild type and a ΔcyabrB2 mutant of Synechocystis sp. PCC 6803 after shifts from high CO2 (5% in air, HC) to low CO2 (0.04%, LC). Evaluation of the transcriptomic data revealed that cyAbrB2 is involved in the regulation of several CCM-related genes such as sbtA/B, ndhF3/ndhD3/cupA and cmpABCD under LC conditions, but apparently acts supplementary to NdhR and CmpR. Under HC conditions, cyAbrB2 deletion affects the transcript abundance of PSII subunits, light-harvesting components and Calvin-Benson-Bassham cycle enzymes. These changes are also reflected by down-regulation of primary metabolite pools. The data suggest a role for cyAbrB2 in adjusting primary carbon and nitrogen metabolism to photosynthetic activity under fluctuating environmental conditions. The findings were integrated into the current knowledge about the acquisition of inorganic carbon (Ci), the CCM and parts of its regulation on the transcriptional level.

Integrated Analysis of Engineered Carbon Limitation in a Quadruple CO2/HCO3- Uptake Mutant of Synechocystis sp. PCC 6803.

Cyanobacteria have efficient carbon concentration mechanisms and suppress photorespiration in response to inorganic carbon (Ci) limitation. We studied intracellular Ci limitation in the slow-growing CO2/HCO3 (-)-uptake mutant ΔndhD3 (for NADH dehydrogenase subunit D3)/ndhD4 (for NADH dehydrogenase subunit D4)/cmpA (for bicarbonate transport system substrate-binding protein A)/sbtA (for sodium-dependent bicarbonate transporter A): Δ4 mutant of Synechocystis sp. PCC 6803. When cultivated under high-CO2 conditions, ∆4 phenocopies wild-type metabolic and transcriptomic acclimation responses after the shift from high to low CO2 supply. The ∆4 phenocopy reveals multiple compensation mechanisms and differs from the preacclimation of the transcriptional Ci regulator mutant ∆ndhR (for ndhF3 operon transcriptional regulator). Contrary to the carboxysomeless ∆ccmM (for carbon dioxide concentrating mechanism protein M) mutant, the metabolic photorespiratory burst triggered by shifting to low CO2 is not enhanced in ∆4. However, levels of the photorespiratory intermediates 2-phosphoglycolate and glycine are increased under high CO2. The number of carboxysomes is increased in ∆4 under high-CO2 conditions and appears to be the major contributing factor for the avoidance of photorespiration under intracellular Ci limitation. The ∆4 phenocopy is associated with the deregulation of Ci control, an overreduced cellular state, and limited photooxidative stress. Our data suggest multiple layers of Ci regulation, including inversely regulated modules of antisense RNAs and cognate target messenger RNAs and specific trans-acting small RNAs, such as the posttranscriptional PHOTOSYNTHESIS REGULATORY RNA1 (PsrR1), which shows increased expression in ∆4 and is involved in repressing many photosynthesis genes at the posttranscriptional level. In conclusion, our insights extend the knowledge on the range of compensatory responses of Synechocystis sp. PCC 6803 to intracellular Ci limitation and may become a valuable reference for improving biofuel production in cyanobacteria, in which Ci is channeled off from central metabolism and may thus become a limiting factor.

Integrated Transcriptomic and Metabolomic Characterization of the Low-Carbon Response Using an ndhR Mutant of Synechocystis sp. PCC 6803.

The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms; hence, this process is tightly regulated. We examined the Ci-dependent transcriptional and metabolic regulation in wild-type Synechocystis sp. PCC 6803 compared with a mutant defective in the main transcriptional repressor for Ci acquisition genes, the NAD(P)H dehydrogenase transcriptional regulator NdhR. The analysis revealed that many protein-coding transcripts that are normally repressed in the presence of high CO2 (HC) concentrations were strongly expressed in ∆ndhR, whereas other messenger RNAs were strongly down-regulated in mutant cells, suggesting a potential activating role for NdhR. A conserved NdhR-binding motif was identified in the promoters of derepressed genes. Interestingly, the expression of some NdhR-regulated genes remained further inducible under low-CO2 conditions, indicating the involvement of additional NdhR-independent Ci-regulatory mechanisms. Intriguingly, we also observed that the abundance of 52 antisense RNAs and 34 potential noncoding RNAs was affected by Ci supply, although most of these molecules were not regulated through NdhR. Thus, antisense and noncoding RNAs could contribute to NdhR-independent carbon regulation. In contrast to the transcriptome, the metabolome in ∆ndhR cells was similar to that of wild-type cells under HC conditions. This observation and the delayed metabolic responses to the low-CO2 shift in ∆ndhR, specifically the lack of transient increases in the photorespiratory pathway intermediates 2-phosphoglycolate, glycolate, and glycine, suggest that the deregulation of gene expression in the ΔndhR mutant successfully preacclimates cyanobacterial cells to lowered Ci supply under HC conditions.

Multi-level kinetic model explaining diverse roles of isozymes in prokaryotes.

Current standard methods for kinetic and genomic modeling cannot provide deep insight into metabolic regulation. Here, we developed and evaluated a multi-scale kinetic modeling approach applicable to any prokaryote. Specifically, we highlight the primary metabolism of the cyanobacterium Synechococcus elongatus PCC 7942. The model bridges metabolic data sets from cells grown at different CO2 conditions by integrating transcriptomic data and isozymes. Identification of the regulatory roles of isozymes allowed the calculation and explanation of the absolute metabolic concentration of 3-phosphoglycerate. To demonstrate that this method can characterize any isozyme, we determined the function of two glycolytic glyceraldehyde-3-phosphate dehydrogenases: one co-regulates high concentrations of the 3-phosphoglycerate, the other shifts the bifurcation point in hexose regulation, and both improve biomass production. Moreover, the regulatory roles of multiple phosphoglycolate phosphatases were defined for varying (non-steady) CO2 conditions, suggesting their protective role against toxic photorespiratory intermediates.

Effects of Inorganic Carbon Limitation on the Metabolome of the Synechocystis sp. PCC 6803 Mutant Defective in glnB Encoding the Central Regulator PII of Cyanobacterial C/N Acclimation.

Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis. Non-diazotrophic strains such as the model Synechocystis sp. PCC 6803 depend on a balanced uptake and assimilation of inorganic carbon and nitrogen sources. The internal C/N ratio is sensed via the PII protein (GlnB). We analyzed metabolic changes of the DglnB mutant of Synechocystis sp. PCC 6803 under different CO2 availability. The identified metabolites provided a snapshot of the central C/N metabolism. Cells of the DglnB mutant shifted to carbon-limiting conditions, i.e. a decreased C/N ratio, showed changes in intermediates of the sugar storage and particularly of the tricarboxylic acid cycle, arginine, and glutamate metabolism. The changes of the metabolome support the notion that the PII protein is primarily regulating the N-metabolism whereas the changes in C-metabolism are probably secondary effects of the PII deletion.

The gene sml0013 of Synechocystis species strain PCC 6803 encodes for a novel subunit of the NAD(P)H oxidoreductase or complex I that is ubiquitously distributed among Cyanobacteria.

The NAD(P)H oxidoreductase or complex I (NDH1) complex participates in many processes such as respiration, cyclic electron flow, and inorganic carbon concentration in the cyanobacterial cell. Despite immense progress in our understanding of the structure-function relation of the cyanobacterial NDH1 complex, the subunits catalyzing NAD(P)H docking and oxidation are still missing. The gene sml0013 of Synechocystis 6803 encodes for a small protein of unknown function for which homologs exist in all completely known cyanobacterial genomes. The protein exhibits weak similarities to the NDH-dependent flow6 (NDF6) protein, which was reported from Arabidopsis (Arabidopsis thaliana) chloroplasts as a NDH subunit. An sml0013 inactivation mutant of Synechocystis 6803 was generated and characterized. It showed only weak differences regarding growth and pigmentation in various culture conditions; most remarkably, it exhibited a glucose-sensitive phenotype in the light. The genome-wide expression pattern of the Δsml0013::Km mutant was almost identical to the wild type when grown under high CO2 conditions as well as after shifts to low CO2 conditions. However, measurements of the photosystem I redox kinetic in cells of the Δsml0013::Km mutant revealed differences, such as a decreased capability of cyclic electron flow as well as electron flow into respiration in comparison with the wild type. These results suggest that the Sml0013 protein (named NdhP) represents a novel subunit of the cyanobacterial NDH1 complex, mediating its coupling either to the respiratory or the photosynthetic electron flow.

Phosphoglycerate mutases function as reverse regulated isoenzymes in Synechococcus elongatus PCC 7942.

Phosphoglycerate-mutase (PGM) is an ubiquitous glycolytic enzyme, which in eukaryotic cells can be found in different compartments. In prokaryotic cells, several PGMs are annotated/localized in one compartment. The identification and functional characterization of PGMs in prokaryotes is therefore important for better understanding of metabolic regulation. Here we introduce a method, based on a multi-level kinetic model of the primary carbon metabolism in cyanobacterium Synechococcus elongatus PCC 7942, that allows the identification of a specific function for a particular PGM. The strategy employs multiple parameter estimation runs in high CO2, combined with simulations testing a broad range of kinetic parameters against the changes in transcript levels of annotated PGMs. Simulations are evaluated for a match in metabolic level in low CO2, to reveal trends that can be linked to the function of a particular PGM. A one-isoenzyme scenario shows that PGM2 is a major regulator of glycolysis, while PGM1 and PGM4 make the system robust against environmental changes. Strikingly, combining two PGMs with reverse transcriptional regulation allows both features. A conclusion arising from our analysis is that a two-enzyme PGM system is required to regulate the flux between glycolysis and the Calvin-Benson cycle, while an additional PGM increases the robustness of the system.

Recent applications of metabolomics toward cyanobacteria.

Our knowledge on cyanobacterial molecular biology increased tremendously by the application of the "omics" techniques. Only recently, metabolomics was applied systematically to model cyanobacteria. Metabolomics, the quantitative estimation of ideally the complete set of cellular metabolites, is particularly well suited to mirror cellular metabolism and its flexibility under diverse conditions. Traditionally, small sets of metabolites are quantified in targeted metabolome approaches. The development of separation technologies coupled to mass-spectroscopy- or nuclear-magnetic-resonance-based identification of low molecular mass molecules presently allows the profiling of hundreds of metabolites of diverse chemical nature. Metabolome analysis was applied to characterize changes in the cyanobacterial primary metabolism under diverse environmental conditions or in defined mutants. The resulting lists of metabolites and their steady state concentrations in combination with transcriptomics can be used in system biology approaches. The application of stable isotopes in fluxomics, i.e. the quantitative estimation of carbon and nitrogen fluxes through the biochemical network, has only rarely been applied to cyanobacteria, but particularly this technique will allow the making of kinetic models of cyanobacterial systems. The further application of metabolomics in the concert of other "omics" technologies will not only broaden our knowledge, but will also certainly strengthen the base for the biotechnological application of cyanobacteria.

Modulation of the major paths of carbon in photorespiratory mutants of synechocystis.

BACKGROUND: Recent studies using transcript and metabolite profiles of wild-type and gene deletion mutants revealed that photorespiratory pathways are essential for the growth of Synechocystis sp. PCC 6803 under atmospheric conditions. Pool size changes of primary metabolites, such as glycine and glycolate, indicated a link to photorespiration. METHODOLOGY/PRINCIPAL FINDINGS: The (13)C labelling kinetics of primary metabolites were analysed in photoautotrophically grown cultures of Synechocystis sp. PCC 6803 by gas chromatography-mass spectrometry (GC-MS) to demonstrate the link with photorespiration. Cells pre-acclimated to high CO(2) (5%, HC) or limited CO(2) (0.035%, LC) conditions were pulse-labelled under very high (2% w/w) (13)C-NaHCO(3) (VHC) conditions followed by treatment with ambient (12)C at HC and LC conditions, respectively. The (13)C enrichment, relative changes in pool size, and (13)C flux of selected metabolites were evaluated. We demonstrate two major paths of CO(2) assimilation via Rubisco in Synechocystis, i.e., from 3PGA via PEP to aspartate, malate and citrate or, to a lesser extent, from 3PGA via glucose-6-phosphate to sucrose. The results reveal evidence of carbon channelling from 3PGA to the PEP pool. Furthermore, (13)C labelling of glycolate was observed under conditions thought to suppress photorespiration. Using the glycolate-accumulating ΔglcD1 mutant, we demonstrate enhanced (13)C partitioning into the glycolate pool under conditions favouring photorespiration and enhanced (13)C partitioning into the glycine pool of the glycine-accumulating ΔgcvT mutant. Under LC conditions, the photorespiratory mutants ΔglcD1 and ΔgcvT showed enhanced activity of the additional carbon-fixing PEP carboxylase pathway. CONCLUSIONS/SIGNIFICANCE: With our approach of non-steady-state (13)C labelling and analysis of metabolite pool sizes with respective (13)C enrichments, we identify the use and modulation of major pathways of carbon assimilation in Synechocystis in the presence of high and low inorganic carbon supplies.

Metabolic and transcriptomic phenotyping of inorganic carbon acclimation in the Cyanobacterium Synechococcus elongatus PCC 7942.

The amount of inorganic carbon is one of the main limiting environmental factors for photosynthetic organisms such as cyanobacteria. Using Synechococcus elongatus PCC 7942, we characterized metabolic and transcriptomic changes in cells that had been shifted from high to low CO(2) levels. Metabolic phenotyping indicated an activation of glycolysis, the oxidative pentose phosphate cycle, and glycolate metabolism at lowered CO(2) levels. The metabolic changes coincided with a general reprogramming of gene expression, which included not only increased transcription of inorganic carbon transporter genes but also genes for enzymes involved in glycolytic and photorespiratory metabolism. In contrast, the mRNA content for genes from nitrogen assimilatory pathways decreased. These observations indicated that cyanobacteria control the homeostasis of the carbon-nitrogen ratio. Therefore, results obtained from the wild type were compared with the MP2 mutant of Synechococcus 7942, which is defective for the carbon-nitrogen ratio-regulating PII protein. Metabolites and genes linked to nitrogen assimilation were differentially regulated, whereas the changes in metabolite concentrations and gene expression for processes related to central carbon metabolism were mostly similar in mutant and wild-type cells after shifts to low-CO(2) conditions. The PII signaling appears to down-regulate the nitrogen metabolism at lowered CO(2), whereas the specific shortage of inorganic carbon is recognized by different mechanisms.

Metabolome phenotyping of inorganic carbon limitation in cells of the wild type and photorespiratory mutants of the cyanobacterium Synechocystis sp. strain PCC 6803.

The amount of inorganic carbon represents one of the main environmental factors determining productivity of photoautotrophic organisms. Using the model cyanobacterium Synechocystis sp. PCC 6803, we performed a first metabolome study with cyanobacterial cells shifted from high CO(2) (5% in air) into conditions of low CO(2) (LC; ambient air with 0.035% CO(2)). Using gas chromatography-mass spectrometry, 74 metabolites were reproducibly identified under different growth conditions. Shifting wild-type cells into LC conditions resulted in a global metabolic reprogramming and involved increases of, for example, 2-oxoglutarate (2OG) and phosphoenolpyruvate, and reductions of, for example, sucrose and fructose-1,6-bisphosphate. A decrease in Calvin-Benson cycle activity and increased usage of associated carbon cycling routes, including photorespiratory metabolism, was indicated by synergistic accumulation of the fumarate, malate, and 2-phosphoglycolate pools and a transient increase of 3-phosphoglycerate. The unexpected accumulation of 2OG with a concomitant decrease of glutamine pointed toward reduced nitrogen availability when cells are confronted with LC. Despite the increase in 2OG and low amino acid pools, we found a complete dephosphorylation of the PII regulatory protein at LC characteristic for nitrogen-replete conditions. Moreover, mutants with defined blocks in the photorespiratory metabolism leading to the accumulation of glycolate and glycine, respectively, exhibited features of LC-treated wild-type cells such as the changed 2OG to glutamine ratio and PII phosphorylation state already under high CO(2) conditions. Thus, metabolome profiling demonstrated that acclimation to LC involves coordinated changes of carbon and interacting nitrogen metabolism. We hypothesize that Synechocystis has a temporal lag of acclimating carbon versus nitrogen metabolism with carbon leading.