GNPS 7120-HGG1 - Dataset Creation from GNPS Molcular Networking - 8dfc4d60dd644e4a8b1060877fba3687
Ontology highlight
ABSTRACT:
INSTRUMENT(S): micrOTOF-Q II
ORGANISM(S): Heterolobosean Amoeba Hgg1 Anabaena Sp. Pcc 7120
SUBMITTER: 
Pieter C. Dorrestein Ryan Simkovsky
PROVIDER: MSV000086470 | GNPS | Tue Nov 17 11:15:00 GMT 2020
REPOSITORIES: GNPS
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Project description:We found that cyanobacterial RNA polymerase possesses very efficient intrinsic proofreading ability. This ability allows model species of cyanobacteria, Synechocystis sp PCC 6803 to keep in vivo level of transcriptional mistakes close to that of E.coli.
2018-08-15 | GSE115134 | GEO
Project description:We found that cyanobacterial RNA polymerase possesses very efficient intrinsic proofreading ability. This ability allows model species of cyanobacteria, Synechocystis sp PCC 6803 to keep in vivo level of transcriptional mistakes close to that of E.coli.
2018-08-15 | GSE115132 | GEO
Project description:Iron is an essential cofactor in many metabolic reactions. Mechanisms controlling iron homeostasis need to respond to changes in extracellular conditions, but must also keep the concentration of intracellular iron under strict control, as free ferrous iron (Fe2+) can lead to the generation of reactive oxygen species. Due to its role as redox carrier in photosynthesis, the iron quota in cyanobacteria is about 10 times higher than in model enterobacteria, but the molecular details how such high quota is tightly regulated have remained obscure. Here, we measured time-resolved gene expression changes after iron depletion in the cyanobacterium Synechocystis sp. PCC 6803 using a comprehensive microarray platform monitoring both protein-coding and non-coding transcripts. In total, 644 protein-coding genes were differentially expressed during the first 72h. Many of these proteins are associated with iron transport, photosynthesis or ATP synthesis. Comparing our data with three previous studies, we identified a core set of 28 genes involved in the iron stress response. Among them were genes encoding proteins important for assimilation of inorganic carbon, suggesting a previously unknown link between the carbon and iron regulatory networks. Nine of the 28 genes are of unknown function and constitute key targets for detailed functional analysis. Applying identical statistical and clustering criteria as for the protein-coding fraction, we also identified 10 small RNAs, 62 anti-sense RNAs, four 5M-bM-^@M-^YUTRs and 7 intergenic elements as likely to be involved in the iron regulatory network. Hence, our genome-wide profiling results indicate an unprecedented complexity in the iron-related regulatory network of cyanobacteria. We monitored iron limitation stress induced gene expression changes in the cyanobacterial model organism Synechocystis sp. PCC 6803. We included a control sample without iron-stress (0h) and 5 samples from timepoints after stress induction (3h, 12h, 24h, 48h, 72h). Each timepoint was sampled from two independent biological replicates.
2012-07-31 | E-GEOD-39804 | biostudies-arrayexpress
Project description:Cyanobacteria are valuable organisms for studying the physiology of photosynthesis and carbon fixation as well as metabolic engineering for the production of fuels and chemicals. This work describes a novel counter selection method for the cyanobacterium Synechococcus sp. PCC 7002 based on organic acid toxicity. The organic acids acrylate, 3-hydroxypropionate, and propionate were shown to be inhibitory towards PCC 7002 and other cyanobacteria at low concentrations. Inhibition was overcome by a loss of function mutation in the gene acsA. Loss of AcsA function was used as a basis for an acrylate counter selection method. DNA fragments of interest were inserted into the acsA locus and strains harboring the insertion were isolated on selective medium containing acrylate. This methodology was also used to introduce DNA fragments into a pseudogene, glpK. Application of this method will allow for more advanced genetics and engineering studies in PCC 7002 including the construction of markerless gene deletions and insertions. The acrylate counter-selection could be applied to other cyanobacterial species where AcsA activity confers acrylate sensitivity (e.g. Synechocystis sp. PCC 6803).
2013-07-19 | GSE48981 | GEO
Project description:Cyanobacteria are valuable organisms for studying the physiology of photosynthesis and carbon fixation as well as metabolic engineering for the production of fuels and chemicals. This work describes a novel counter selection method for the cyanobacterium Synechococcus sp. PCC 7002 based on organic acid toxicity. The organic acids acrylate, 3-hydroxypropionate, and propionate were shown to be inhibitory towards PCC 7002 and other cyanobacteria at low concentrations. Inhibition was overcome by a loss of function mutation in the gene acsA. Loss of AcsA function was used as a basis for an acrylate counter selection method. DNA fragments of interest were inserted into the acsA locus and strains harboring the insertion were isolated on selective medium containing acrylate. This methodology was also used to introduce DNA fragments into a pseudogene, glpK. Application of this method will allow for more advanced genetics and engineering studies in PCC 7002 including the construction of markerless gene deletions and insertions. The acrylate counter-selection could be applied to other cyanobacterial species where AcsA activity confers acrylate sensitivity (e.g. Synechocystis sp. PCC 6803). Cultures were grown in medium modified with 5mM acrylic acid at pH 8 and compared to cultures grown in unmodified medium. Samples were processed in duplicate.
2013-07-19 | E-GEOD-48981 | biostudies-arrayexpress
Project description:we aimed to investigate the unique contributions and regulatory network of ClpX in a model cyanobacterium Synechocystis sp. PCC 6803 by quantitative proteomic strategy
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Project description:In contrast to Synechococcus elongatus PCC 7942, which has been the model cyanobacterium for the study of the prokaryotic circadian clock for more than 20 years, only few data exist on the circadian behaviour of the widely used cyanobacterium Synechocystis sp. PCC 6803. The standard kaiABC operon present in this organism was shown to encode a functional KaiC protein which interacts with KaiA, similar to the Synechococcus elongatus PCC 7942 clock. Inactivation of this operon in Synechocystis sp. PCC 6803 resulted in a mutant with a strong growth defect in light-dark cycles, which was even more pronounced when glucose was added to the growth medium. In addition, mutants showed a bleaching phenotype. No effects were detected in mutant cells grown in constant light. Microarray experiments performed with cells grown for one day in a light-dark cycle revealed many differentially regulated genes with known functions in the M-NM-^TkaiABC mutant in comparison to the wild type. Most interestingly, we identified genes like the gene encoding the cyanobacterial phytochrome Cph1 and the light repressed protein LrtA as well as several hypothetical open reading frames with a complete inverse behaviour in the light cycle. These transcripts showed a stronger accumulation in the light but a weaker accumulation in the dark in M-NM-^TkaiABC cells in comparison to the wild type. In addition, we found a considerable overlap with microarray data obtained for hik31 and sigE mutants. These genes are known to be important regulators of cell metabolism in the dark. Three timepoints with two samples (WT and Mutant). Two replicates for each timepoint/sample. RNA hybridization.
2014-06-18 | E-GEOD-58572 | biostudies-arrayexpress
Project description:In contrast to Synechococcus elongatus PCC 7942, which has been the model cyanobacterium for the study of the prokaryotic circadian clock for more than 20 years, only few data exist on the circadian behaviour of the widely used cyanobacterium Synechocystis sp. PCC 6803. The standard kaiABC operon present in this organism was shown to encode a functional KaiC protein which interacts with KaiA, similar to the Synechococcus elongatus PCC 7942 clock. Inactivation of this operon in Synechocystis sp. PCC 6803 resulted in a mutant with a strong growth defect in light-dark cycles, which was even more pronounced when glucose was added to the growth medium. In addition, mutants showed a bleaching phenotype. No effects were detected in mutant cells grown in constant light. Microarray experiments performed with cells grown for one day in a light-dark cycle revealed many differentially regulated genes with known functions in the ΔkaiABC mutant in comparison to the wild type. Most interestingly, we identified genes like the gene encoding the cyanobacterial phytochrome Cph1 and the light repressed protein LrtA as well as several hypothetical open reading frames with a complete inverse behaviour in the light cycle. These transcripts showed a stronger accumulation in the light but a weaker accumulation in the dark in ΔkaiABC cells in comparison to the wild type. In addition, we found a considerable overlap with microarray data obtained for hik31 and sigE mutants. These genes are known to be important regulators of cell metabolism in the dark.
2014-06-18 | GSE58572 | GEO
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:Extracellular proteins are involved in a remarkable number of fundamental processes in cyanobacteria. Yet, there is limited knowledge regarding the identity and function of these proteins. Here, we introduce a solid-phase enhanced protein aggregation workflow that enables description of the cyanobacterial exoproteome with unprecedented depth. Application to cyanobacteria from three distinct habitats, Synechocystis sp. PCC 6803, Synechcoccus sp. PCC 11901 and Nostoc punctiforme PCC 73102, allowed the identification of up to 62% of all predicted secreted proteins. The approach was then extended to compare the Synechocystis sp. PCC 6803 wild-type secretome with that of a bloom-like aggregated state and a secretion-impaired mutant. Finally, we demonstrate that the workflow can be miniaturized and adapted to a 96-well format for high-throughput secretome analysis. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and point to a functional conservation of the secretome across species from different environments. Our approach can be applied to microbes from a wide range of habitats, with the potential to open new avenues of investigation in microbial exoproteomics.
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