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The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 [dacA]

ABSTRACT: Gene expression changes were followed in cultures of the cyanobacterium Synechocystis sp. PCC 6803 three and 24 hours after shift from high carbon (HC) to low carbon (LC) concentrations. The acclimation to fluctuating inorganic carbon (Ci) concentrations is crucial for photoautotrophic organisms living in aquatic environments such as cyanobacteria. The PII-like regulator protein SbtB binds the second messengers cAMP or c-diAMP and is involved in the acclimation to LC. Here, we investigated the impact of SbtB and of second messengers on gene expression changes during this acclimation response. We analyzed cultures of the wild type (WT), the ΔsbtB mutant lacking the PII-like regulator protein SbtB, the ΔcyaI mutant, lacking the main soluble adenylate cyclase for cAMP production and ΔdacA, lacking the diadenylate cyclase for c-diAMP production. The majority of LC-induced genes behaved in these mutants like in wild type. However, a defined subset of LC-regulated genes in WT was found to be changed in mutant ΔsbtB already under high CO2. Collectively, the results indicate that SbtB regulates a particular subset of genes during the LC acclimation response.

ORGANISM(S): Synechocystis sp. PCC 6803

PROVIDER: GSE185297 | GEO | 2022/09/28

REPOSITORIES: GEO

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The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 [sbtB]

Project description:Gene expression changes were followed in cultures of the cyanobacterium Synechocystis sp. PCC 6803 three and 24 hours after shift from high carbon (HC) to low carbon (LC) concentrations. The acclimation to fluctuating inorganic carbon (Ci) concentrations is crucial for photoautotrophic organisms living in aquatic environments such as cyanobacteria. The PII-like regulator protein SbtB binds the second messengers cAMP or c-diAMP and is involved in the acclimation to LC. Here, we investigated the impact of SbtB and of second messengers on gene expression changes during this acclimation response. We analyzed cultures of the wild type (WT), the ΔsbtB mutant lacking the PII-like regulator protein SbtB, the ΔcyaI mutant, lacking the main soluble adenylate cyclase for cAMP production and ΔdacA, lacking the diadenylate cyclase for c-diAMP production. The majority of LC-induced genes behaved in these mutants like in wild type. However, a defined subset of LC-regulated genes in WT was found to be changed in mutant ΔsbtB already under high CO2. Collectively, the results indicate that SbtB regulates a particular subset of genes during the LC acclimation response.

2022-09-28 | GSE185294 | GEO

The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 [cyal]

2022-09-25 | GSE185296 | GEO

Comparison of carboxysomal (ccmM) and photorespiratory (glcD1/D2) mutants of Synechocystis sp. PCC 6803 using metabolic and transcriptomic phenotyping

Project description:The general acclimation of cyanobacteria to low carbon (LC) conditions includes coordinated alterations of gene expression and metabolism. To analyze possible signals for LC sensing and compensating reactions, we compared wild-type (WT) cells with two mutants of Synechocystis, the carboxysome-less mutant ccmM and the photorespiratory mutant ΔglcD1/D2. Metabolic phenotyping revealed that the mutant ΔccmM accumulated high 2-phosphoglycolate (2PG) levels while the ΔglcD1/D2 mutant accumulated glycolate, indicating oxygenase activity of RubisCO at high carbon (HC). The changes in the metabolite spectrum were compared to alterations in the global gene expression pattern. Cells of HC-grown mutants ΔccmM and ΔglcD1/D2 showed altered mRNA levels for many genes involved in photosynthesis, high light stress, and N-assimilation, while LC-specific genes such as those for inorganic carbon (Ci) transporters were not increased. After a shift to LC, mutant ΔglcD1/D2 revealed gene expression changes similar to WT cells, while mutant ΔccmM showed no differential expression of most LC-induced genes under identical conditions. In fact, none of the genes for Ci transporters or other components of the carbon concentrating mechanism (CCM) displayed higher transcript levels in the ΔccmM mutant. This finding renders a direct role for 2PG as a metabolic signal component for the induction of CCM during LC acclimation less likely. Because, the transcription pattern of ΔglcD1/D2 under LC showed specific differences compared to WT, a potential role for glycolate as a signal molecule that may trigger expression of parts of the CCM is proposed. Transcriptional profiling of carboxysomal and photorespiratory mutants of Synechocystis sp. PCC 6803 under high carbon (HC) and low carbon (LC) conditions relative to the wildtype response.

2011-12-30 | E-GEOD-31672 | biostudies-arrayexpress

Comparison of carboxysomal (ccmM) and photorespiratory (glcD1/D2) mutants of Synechocystis sp. PCC 6803 using metabolic and transcriptomic phenotyping

2011-12-30 | GSE31672 | GEO

Therapeutic melanoma inhibition by local micelle-mediated cyclic nucleotide repression

Project description:The acidic tumor microenvironment in melanoma drives immune evasion by up-regulating cyclic adenosine monophosphate (cAMP) in tumor-infiltrating monocytes..Melanoma growth can be suppressed by releasing non-toxic concentrations of an adenylate cyclase (AC) inhibitor from polypept(o)id micelles at the tumor site in an immune cell-dependent manner.

2021-08-19 | GSE166028 | GEO

The Novel PII-Interacting Regulator PirC (Sll0944) Identifies 3-Phosphoglycerate Mutase (PGAM) as Central Control Point of Carbon Storage Metabolism in Cyanobacteria

Project description:Nitrogen limitation imposes a major transition in the life-style of non-diazotrophic cyanobacteria, which is regulated via a complex interplay of regulatory factors, involving, the nitrogen-specific transcription factor NtcA and the pervasive signal processor PII. Immediately upon nitrogen-limitation, newly fixed carbon is re-directed towards glycogen synthesis. How operation of the metabolic switch for distributing fixed carbon to either glycogen or cellular building blocks was poorly understood. Here we identify from Synechocystis sp. PCC 6803 a novel PII interactor, PirC, (Sll0944) that controls 3-phosphoglycerate mutase (PGAM), the enzyme that deviates newly fixed CO2 towards lower glycolysis. PirC acts as competitive inhibitor of PGAM and this interaction is tuned by PII/2-oxoglutarate. High oxoglutarate release PirC from PII-complex to inhibit PGAM. Accordingly, PirC deficient mutant, as compared to the wild-type, shows strongly reduced glycogen levels upon nitrogen deprivation whereas polyhydroxybutyrate granules are over-accumulated. Metabolome analysis revealed an imbalance in 3-phosphoglycerate to pyruvate levels in the PirC mutant, conforming that PirC controls the carbon flux in cyanobacteria via mutually exclusive interaction with either PII or PGAM.

2020-12-17 | PXD021415 | Pride

Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the Cyanobacterium Synechocystis sp. Strain PCC 6803

Project description: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 CO2 (5% in air) into conditions of low CO2 (LC; ambient air with 0.035% CO2). 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 CO2 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.

2015-09-14 | MTBLS5 | MetaboLights

Transcription profiling by array of adenylylation of mycobacterial Glnk (PII) protein induced by nitrogen limitation

Project description:PII proteins are pivotal regulators of nitrogen metabolism in most prokaryotes, controlling the activities of many targets, including nitrogen assimilation enzymes, two component regulatory systems and ammonium transport proteins. Escherichia coli contains two PII-like proteins, PII (product of glnB) and GlnK, both of which are uridylylated under nitrogen limitation at a conserved Tyrosine-51 residue by GlnD (a uridylyl transferase). PII-uridylylation in E. coli controls glutamine synthetase (GS) adenylylation by GlnE and mediates the NtrB/C transcriptomic response. Mycobacteria contain only one PII protein (GlnK) which in environmental Actinomycetales is adenylylated by GlnD under nitrogen limitation. However in mycobacteria, neither the type of GlnK (PII) covalent modification nor its precise role under nitrogen limitation is known. In this study, we used LC-Tandem MS to analyse the modification state of mycobacterial GlnK (PII), and demonstrate that during nitrogen limitation GlnK from both non-pathogenic Mycobacterium smegmatis and pathogenic Mycobacterium tuberculosis is adenylylated at the Tyrosine-51 residue; we also show that GlnD is the adenylyl transferase enzyme responsible. Further analysis shows that in contrast to E. coli, GlnK (PII) adenylylation in M. tuberculosis does not regulate GS adenylylation, nor does it mediate the transcriptomic response to nitrogen limitation. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-135]

2013-05-10 | E-BUGS-135 | biostudies-arrayexpress

Diatom acclimation to elevated CO2 via novel gene clusters and cAMP-signaling

Project description:Diatoms are responsible for ~40% of marine primary productivity1, fueling the oceanic carbon cycle and contributing to natural carbon sequestration in the deep ocean2. Diatoms rely on energetically expensive carbon concentrating mechanisms (CCMs) to fix carbon efficiently at modern levels of CO23–5. How diatoms may respond over the short and long-term to rising atmospheric CO2 remains an open question. Here we use nitrate-limited chemostats to show that the model diatom Thalassiosira pseudonana rapidly responds to increasing CO2 by differentially expressing gene clusters that regulate transcription and chromosome folding and subsequently reduces transcription of photosynthesis and respiration gene clusters under steady-state elevated CO2. These results suggest that exposure to elevated CO2 first causes a shift in regulation and then a metabolic rearrangement. Genes in one CO2-responsive cluster included CCM and photorespiration genes that share a putative cyclic-AMP responsive cis-regulatory sequence, implying these genes are co-regulated in response to CO2 with cAMP as an intermediate messenger. We verified cAMP-induced down-regulation of CCM gene δ-CA3 in nutrient-replete diatom cultures by inhibiting the hydrolysis of cAMP. These results indicate an important role for cAMP in down-regulating CCM and photorespiration genes under elevated CO2 and provide insights into mechanisms of diatom acclimation in response to climate change.

2015-04-17 | GSE67971 | GEO

Overexpression of the adenylate cyclase gene cyaC facilitates current generation by Shewanella oneidensis in bioelectrochemical systems

Project description:Electrochemically active bacteria (EAB) are capable of electrochemical interactions with electrodes via extracellular electron transfer (EET) pathways and serve as essential components in bioelectrochemical systems. Previous studies have suggested that EAB, such as Shewanella oneidensis MR-1, use cyclic AMP (cAMP) receptor proteins for coordinately regulating the expression of catabolic and EET-related genes, allowing us to hypothesize that the intracellular cAMP concentration is an important factor determining electrochemical activities of EAB. The present study constructed an MR-1 mutant, cyaC-OE that overexpressed cyaC, a gene encoding a membrane-bound class III adenylate cyclase, and examined its electrochemical and transcriptomic characteristics. We show that intracellular cAMP concentration in cyaC-OE is more than double that in wild-type MR-1, and cya-OE generates approximately two-fold higher current in BES than the wild type. In addition, the expression of genes involved in EET and anaerobic carbon catabolism is up-regulated in cya-OE as compared to that in the wild type. These results suggest that enhancement of the intracellular cAMP level is a promising approach for constructing an EAB with high catabolic and electrochemical activities.

2019-11-01 | GSE129679 | GEO

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