Integrated functional analysis of engineered carbon limitation in the CO2/HCO3-uptake deficient ∆ndhD3/ndhD4/cmpA/sbtA mutant of Synechocystis sp. PCC 6803
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ABSTRACT:
ORGANISM(S): Synechocystis sp. PCC 6803
PROVIDER: GSE68250 | GEO | 2015/10/20
SECONDARY ACCESSION(S): PRJNA282136
REPOSITORIES: GEO
Similar Datasets
Project description:Cyanobacteria are phototrophic prokaryotes that can convert inorganic carbon as CO2 into organic carbon compounds at the expense of light energy. In addition, they need only a few inorganic nutrients and can be cultivated in high densities using non-arable land and seawater. This features qualified cyanobacteria as attractive organisms for the production of third generation biofuels as part of the development of future CO2-neutral energy production. Synechocystis sp. PCC 6803 represents one of the most widely used cyanobacterial model strains. On the basis of its available genome sequence and genetic tools, many strains of Synechocystis have been generated that produce different biotechnological products. Efficient isoprene production is an attractive goal, since this compound represents not only an energy-rich biofuel but is also used as chemical feedstock. Here, we report on our attempts to generate isoprene-producing strains of Synechocystis. The cDNA of a codon-optimized plant isoprene synthase (IspS) was cloned under the control of different Synechocystis promoters, which ensure strong constitutive or light-regulated ispS expression. The expression of the ispS gene was quantified by qPCR, whereas the amount of isoprene was quantified using GC-MS. Incubation of our strains at different salt conditions had marked impact on the isoprene production rates. Under low salt conditions, a good correlation was found between ispS expression and isoprene production rate. However, the cultivation of isoprene production strains under salt-supplemented conditions decreased isoprene production despite the fact that ispS expression was salt-stimulated. The characterization of the metabolome of isoprene producing strains indicated that isoprene production might be limited by insufficient precursor levels. Our isoprene production rates under low salt conditions were 2 - 6.5times higher compared to the previous report of Lindberg et al. (2010). These results can be used to guide future attempts establishing the isoprene production with cyanobacterial host systems.
2015-11-13 | GSE74940 | GEO
Project description:Acclimation to low CO2 conditions in cyanobacteria involves the coordinated regulation of genes mainly encoding components of the carbon concentration mechanism (CCM). Making use of several independent microarray datasets 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 and CmpR, whereas 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 transcript 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 the main regulators. Under HC conditions, cyAbrB2 deletion changes the expression of photosystem II subunits, light-harvesting components, and Calvin-Benson-Bassham cycle enzymes.
2016-09-19 | GSE82120 | GEO
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 | GSE185297 | GEO
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.
2022-09-25 | GSE185296 | GEO
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
Project description:Identification of Components Associated with Thermal Acclimation of Photosystem II in Synechocystis sp. PCC6803
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Project description:CyAbrB2 contributes to the transcriptional regulation of low CO2 acclimation in Synechocystis sp. PCC 6803
| PRJNA324092 | ENA
Project description:Slr0643, a S2P Homolog, Is Essential for Acid Acclimation in Cyanobacterium Synechocystis sp. PCC 6803
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Project description:Synechocystis 6803 cells was grown photoautotrophically at 32 °C buffered in BG-11 and bubbled with 3% CO2. A relatively mild Ci stress was applied by switching the aeration from 3% CO2 to air alone. After incubation under designated conditions, a 100-ml aliquot of culture was immediately combined with an equal volume of ice-cold mixture of phenol and ethanol (1:10, w/v) in an ice bath. The resultant cells were collected by centrifugation at 1000 x g for 10 min at 4 °C. Total RNA was isolated with RNeasy Midi Kit (Qiagen, Valencia, CA) and further treated with the DNA-free kit (Ambion, Austin, TX). Fluorescently labeled cDNA was produced via a two-step indirect procedure involving cDNA synthesis from 16 µg of total RNA in a reverse transcriptase reaction incorporating aminoallyl-modified deoxynucleotide, followed by the second step involving chemical coupling of fluorescent dye to the introduced amino moieties of the synthesized cDNA. Labeled cDNA were adjusted to 14.75 µl, and the remainder of the hybridization components containing 2.5 µl of 10 µg µl-1 salmon sperm DNA, 8.75 µl of 20x SSC, 0.25 µl of 10% SDS, and 8.75 µl of formamide were added. The mixture was then heated for 2 min at 99 °C and maintained at 42 °C until hybridization. Hybridizations were preformed in a static incubator at 42 °C for 12-16 h then washed by placing in a 250-ml solution of 2x SSC and 0.1% SDS at 42 °C for 5 min with gentle agitation provided by rotation of a magnetic stir bar. The slide was transferred quickly to a 250-ml solution of 0.1x SSC and 0.1% SDS, incubated for 10 min at room temperature with gentle agitation, and washed five additional times in 0.1x SSC for 1 min at room temperature. Hybridization signals from the microarray were quantified using GenePix Pro 4.1 (Axon Instruments, Union City, CA). The quality control procedures were conducted in the image analysis software, and then data were saved to Acuity 3.1 (Axon Instruments). Keywords: time-course
2004-08-24 | GSE1695 | GEO
Project description:Cyanobacteria are the only prokaryotes that perform plant-like oxygenic photosynthesis. They evolved an inorganic carbon-concentrating mechanism to adapt to low CO2 conditions. Quantitative phospho-proteomics was applied to analyze regulatory features during the acclimation to low CO2 conditions in the model cyanobacterium Synechocystis sp. PCC 6803. Overall, more than 2500 proteins were quantified, equivalent to approximately 70% of the Synechocystis theoretical proteome. Proteins with changing abundances correlated largely with mRNA expression levels. Functional annotation of the non-correlating proteins revealed an enrichment of key metabolic processes fundamental for maintaining cellular homeostasis. Furthermore, 105 phospho-proteins harboring over 200 site-specific phosphorylation events were identified. Subunits of the bicarbonate transporter BCT1 and the redox switch protein CP12 were among phospho-proteins with significantly reduced phosphorylation levels at lower CO2, whereas the serine/threonine protein kinase SpkC revealed increased phosphorylation levels. The corresponding spkC mutant was characterized and showed decreased ability to acclimate to low CO2 conditions. Possible phosphorylation targets of SpkC including a BCT1 subunit were identified by phospho-proteomics. Collectively, our study highlights the importance of post-transcriptional regulation of protein abundances as well as post-translational regulation by protein phosphorylation for the successful acclimation towards low CO2 conditions in Synechocystis and possibly among cyanobacteria.
2021-07-14 | PXD022283 | Pride