Synechocystis sp. PCC 6803
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PROVIDER: PRJNA345038 | ENA |
REPOSITORIES: ENA
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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
Project description:Cyanobacteria are oxygenic photoautotrophs responsible for a substantial proportion of nitrogen fixation and primary production in the hydrosphere. Non-nitrogen fixing cyanobacteria, such as Synechocystis sp. PCC 6803, depend of the availability of nitrogenized species to survive. Therefore, an intricate regulatory network around the transcriptional factor NtcA maintains the homeostasis of nitrogen in these organisms. The mechanisms controlling NtcA activity are well understood but a comprehensive study of its regulon is missing in Synechocystis. To define NtcA regulon during the early stage of nitrogen starvation, we have performed chromatin immunoprecipitation followed by sequencing (ChiP-seq), in parallel with genome level transcriptome analysis (RNA-seq). By combining both methods we assigned 51 activated and 28 repressed genes directly by NtcA. Most of direct targets included genes involved in nitrogen and carbon metabolism and photosynthesis. NtcA regulon also included 8 ncRNAs, of which ncr0710, Syr6 and NsiR7 were experimentally validated. Intriguingly, we identified several NtcA intragenic binding sites suggesting that NtcA can modulate transcriptional expression by binding along the whole transcript and not only in the promoter region as previously though. Finally, the transcriptional implication of PipX was analyzed in some NtcA-targets genes, revealing that PipX assists NtcA in the global nitrogen regulation in Synechocystis.
2017-10-01 | GSE97282 | GEO
Project description:Cyanobacteria are oxygenic photoautotrophs responsible for a substantial proportion of nitrogen fixation and primary production in the hydrosphere. Non-nitrogen fixing cyanobacteria, such as Synechocystis sp. PCC 6803, depend of the availability of nitrogenized species to survive. Therefore, an intricate regulatory network around the transcriptional factor NtcA maintains the homeostasis of nitrogen in these organisms. The mechanisms controlling NtcA activity are well understood but a comprehensive study of its regulon is missing in Synechocystis. To define NtcA regulon during the early stage of nitrogen starvation, we have performed chromatin immunoprecipitation followed by sequencing (ChiP-seq), in parallel with genome level transcriptome analysis (RNA-seq). By combining both methods we assigned 51 activated and 28 repressed genes directly by NtcA. Most of direct targets included genes involved in nitrogen and carbon metabolism and photosynthesis. NtcA regulon also included 8 ncRNAs, of which ncr0710, Syr6 and NsiR7 were experimentally validated. Intriguingly, we identified several NtcA intragenic binding sites suggesting that NtcA can modulate transcriptional expression by binding along the whole transcript and not only in the promoter region as previously though. Finally, the transcriptional implication of PipX was analyzed in some NtcA-targets genes, revealing that PipX assists NtcA in the global nitrogen regulation in Synechocystis.
2017-10-01 | GSE97289 | GEO
Project description:Cyanobacteria have shaped the earth’s biosphere as the first oxygenic photoautotrophs and still play an important role in many ecosystems. The ability to adapt to changing environmental conditions is an essential characteristic in order to ensure survival. To this end, numerous studies have shown that bacteria use protein post-translational modifications such as Ser/Thr/Tyr phosphorylation in cell signalling, adaptation and regulation. Nevertheless, our knowledge of cyanobacterial phosphoproteomes and their dynamic response to environmental stimuli is relatively limited. In this study, we applied gel-free methods and high accuracy mass spectrometry towards the unbiased detection of Ser/Thr/Tyr phosphorylation events in the model cyanobacterium Synechocystis sp. PCC 6803. We could identify over 300 phosphorylation events in cultures grown on nitrate as exclusive nitrogen source. Chemical dimethylation labelling was applied to investigate proteome and phosphoproteome dynamics during nitrogen starvation. Our dataset describes the most comprehensive (phospho)proteome of Synechocystis to date, identifying 2,382 proteins and 183 phosphorylation events and quantifying 2,111 proteins and 148 phosphorylation events during nitrogen starvation. Global protein phosphorylation levels were increased in response to nitrogen depletion after 24 hours. Among the proteins with increased phosphorylation, the PII signalling protein showed the highest fold-change, serving as positive control. Other proteins with increased phosphorylation levels comprised functions in photosynthesis and in carbon and nitrogen metabolism. This study reveals dynamics of Synechocystis phosphoproteome in response to environmental stimuli and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of homeostatic control in cyanobacteria.
2016-05-09 | PXD001831 | Pride
Project description:Unicellular cyanobacteria that do not fix nitrogen can survive prolonged periods of nitrogen starvation as bleached cells in a non-growing, dormant state. Upon re-addition of a usable nitrogen source, bleached cultures re-green within 48 hours and the cells return to vegetative growth. Here we investigated the process of resuscitation at the physiological and molecular level. Almost immediately upon nitrate addition, the cells initiate an amazingly organized resuscitation program: they first turn on respiration, gaining energy and activating the genes of the entire translational apparatus, genes for ATP synthesis and nitrate assimilation. Only after about 12 hours, the cells rebuild the photosynthetic apparatus and switch on photosynthesis. Analysis of the transcriptome in recovering cells shows a perfect match to the physiological processes and reveals a paramount dynamics of non-coding RNAs in awaking cells. This genetically encoded program ensures rapid colonization of habitats, in which nitrogen starvation imposes a recurring growth limitation.
2016-06-15 | GSE83363 | GEO
Project description:Unicellular cyanobacteria that do not fix nitrogen can survive prolonged periods of nitrogen starvation as bleached cells in a non-growing, dormant state. Upon re-addition of a usable nitrogen source, bleached cultures re-green within 48 hours and the cells return to vegetative growth. Here we investigated the process of resuscitation at the physiological and molecular level. Almost immediately upon nitrate addition, the cells initiate an amazingly organized resuscitation program: they first turn on respiration, gaining energy and activating the genes of the entire translational apparatus, genes for ATP synthesis and nitrate assimilation. Only after about 12 hours, the cells rebuild the photosynthetic apparatus and switch on photosynthesis. Analysis of the transcriptome in recovering cells shows a perfect match to the physiological processes and reveals a paramount dynamics of non-coding RNAs in awaking cells. This genetically encoded program ensures rapid colonization of habitats, in which nitrogen starvation imposes a recurring growth limitation. Synechocstis PCC 6803 WT cells were subjected to nitrogen limitation for 14d, then nitrogen was re-added to monitor recovery of the cells. Samples were taken before nitrogen depletion, after 14d of nitrogen depletion and 4h, 13h, 24h and 48h after nitrogen re-addition. Samples were taken in biological replicates for all timepoints besides 48h nitrogen recovery.
2016-06-15 | E-GEOD-83363 | biostudies-arrayexpress
Project description:Small proteins are an underinvestigated class of gene products in all domains of life. Here we describe the role of NsiR6/NblD, a cysteine-rich 66 amino acid small protein in the acclimation response of cyanobacteria to nitrogen starvation. Phycobilisomes, the macromolecular pigment-protein complexes for photosynthetic light harvesting, are rapidly degraded upon shift to low nitrogen. Deletion of nblD in Synechocystis sp. strain PCC 6803 prevents this degradation, indicated by the non-bleaching (nbl) phenotype. Complementation by a plasmid-localized gene copy fully restored the phenotype of the wild type, while overexpression of NblD under nitrogen-replete conditions did not lead to any phenotypical effect, different from the unrelated proteolysis adaptors NblA1 and NblA2, which can trigger phycobilisome degradation ectopically. However, transcriptome analysis revealed that nitrogen starvation induced nblA1/2 transcription in the ΔnblD strain, which excluded the possibility that the nbl phenotype was due to a possible NblD function as transcriptional co-regulator. In contrast, fractionation experiments indicated the presence of NblD in the phycobilisome fraction and pull-down experiments with NblD containing a triple FLAG tag identified the α and β phycocyanin subunits as the only two co-purifying proteins. Homologs of NblD exist in all cyanobacteria that use phycobilisomes but not in the genera Prochlorococcus and Acaryochloris which use alternative light-harvesting mechanisms. These data suggest that NblD plays a crucial role in the coordinated dismantling of phycobilisomes when nitrogen becomes limiting. We performed a microarray, to examine the global expression pattern of wild type and ∆nblD isolated RNA after 0h and 3h past induction of nitrogen depletion (-N) to detect potential differences in the nitrogen acclimation process.
2020-04-29 | GSE149511 | GEO
Project description:The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7
| PRJNA298210 | ENA
Project description:Background: The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles. Results: Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation. Conclusions: The combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 σ factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria.
2016-06-16 | GSE83387 | GEO
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