GEO DataSets

(Submitter supplied) In many habitats, microorganisms are exposed to high or fluctuating salinities and evolved specific acclimation strategies to thrive in those environments. Euryhaline microorganisms can grow in a broad range of salinities, from low ionic strength like freshwater up to twofold seawater salinities. Here, we analyzed the salt acclimation process of the euryhaline model cyanobacterium Synechocystis sp. PCC 6803 in a multi-omics approach by combining transcriptomic, proteomic and metabolomic analyses. The Overall, the comparison of salt-induced proteome and transcriptome changes revealed a good correleation between the proteome and transcriptome that as most the majority of stably up-regulated proteins also showed elevated mRNA transcript levels. However, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably also involves the action of small regulatory RNAs acting at the post-transcriptional level. In addition to the rapid and stable steady upregulation of compatible solute biochemistry, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably involves the action of small regulatory RNAs. Moreover, the coordinated induction of several stress proteins known to be involved in iron and oxidative stress responses as well as of mechano-sensitive channels was observed. Based on these data, an extended salt stimulon can be defined comprising many proteins directly or indirectly related to compatible solute metabolism, ion and water movements as well as a defined set of small regulatory RNAs. Moreover, the massive accumulation of the compatible solute glucosylglycerol had large impact on the overall carbon and nitrogen metabolism. Our comprehensive data set provides the basis for future attempts to engineer cyanobacterial salt tolerance and to search for processes regulating this important environmental acclimation process.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

(Submitter supplied) Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the post-transcriptional regulation of gene expression. A key endoribonuclease in many bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria such as E. coli have evolved a tightly functioning feedback regulation of RNase E, which is mediated in cis by the rne 5′-untranslated region (5′UTR); however, the mechanisms involved in the control of RNase E in other bacteria have largely remained unknown. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

(Submitter supplied) The cyanobacterial phytochrome Cph2 is a light-dependent diguanylate cyclase producing the second messenger c-di-GMP. Under blue light, the Cph2-dependent increase in the cellular c-di-GMP concentration leads to inhibition of motility in the cyanobacterium Synechocystis 6803. However, the targets of c-di-GMP in this cyanobacterium and its mechanism of action remained unclear. Here, we determined the cellular concentrations of three cyclic nucleotides in wild-type and Δcph2 cells after blue- and green light illumination. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

(Submitter supplied) Ethylene is a gaseous signal sensed by plants and bacteria. Heterologous expression of the ethylene-forming enzyme (EFE) from Pseudomonas syringae in cyanobacteria leads to the production of ethylene under photoautotrophic conditions. The recent characterization of an ethylene responsive signaling pathway affecting phototaxis in the cyanobacterium Synechocystis sp. PCC 6803 implies that biotechnologically relevant ethylene synthesis may induce regulatory processes which are not related to changes in the metabolism. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

4 Samples

Download data: TXT

(Submitter supplied) Carbohydrate metabolism is a tightly regulated process in photosynthetic organisms. The ability to utilize glucose for growth and to regulate storage carbohydrate (i.e. glycogen) metabolisms requires a number of regulatory elements. In the cyanobacterium Synechocystis sp. PCC 6803, the photomixotrophic growth protein A (PmgA), a putative serine/threonine kinase, is involved in governing these abilities; however its downstream regulatory elements are not well studied. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

5 Samples

Download data: TXT

(Submitter supplied) Oxygenic photosynthesis contains multiple proteins that possess Fe2+ or Fe/S complexes as co-factors or prosthetic groups. Accordingly, its composition is heavily re-organized when iron becomes limiting as a nutrient factor, a situation that is frequently encountered in nature. However, the molecular mechanisms controlling the reorganization of the photosynthetic system upon iron deprivation have remained enigmatic. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

32 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

16 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

16 Samples

Download data: TXT

(Submitter supplied) Regulation of gene expression is a sophisticated process leading to the activation or suppression of genes due to adaptation to environmental stimuli. The membrane-embedded FtsH proteases conserved in bacteria, chloroplasts and mitochondria, are involved in such regulation. The genome of the cyanobacterium Synechocystis sp. PCC 6803 encodes four FtsH homologues FtsH1-4, functioning in the form of oligomeric complexes. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

(Submitter supplied) Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellular Synechocystis sp. PCC 6803 and in the filamentous, nitrogen-fixing Anabaena sp. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

(Submitter supplied) Functional analysis of engineered carbon limitation in the ∆ndhD3/ndhD4/cmpA/sbtA (= ∆4) Synechocystis mutant reveals a global phenocopy of wild type acclimation to low CO2 and multi-layered Ci-regulation.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

12 Samples

Download data: TXT

(Submitter supplied) The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms, and, hence it is tightly controlled. We studied the Ci-dependent transcriptional and metabolic regulation in the Synechocystis sp. PCC 6803 wild type compared to a DndhR mutant that is defective in the main transcriptional repressor for Ci acquisition genes, NdhR (CcmR). more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

13 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

12 Samples

Download data: TXT

(Submitter supplied) The production of biofuels in photosynthetic microalgae and cyanobacteria is considered a promising alternative to the generation of fuels from fossil resources. However, to be economically competitive, producer strains need to be established that synthesize the targeted product at high yield and over a long time. Engineering cyanobacteria to forced fuel producers should considerably interfere with overall cell homeostasis, which in turn might counteract productivity and sustainability of the process. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

16 Samples

Download data: TXT

(Submitter supplied) Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

10 Samples

Download data: TXT

(Submitter supplied) The NDH1 complex fulfils numerous tasks in the cyanobacterial cell such as respiration, cyclic electron flow, and inorganic carbon concentration. Despite the immense progress in our understanding of structure/function relation of the cyanobacterial NDH1 complex, the subunits catalysing the NAD(P)H docking and oxidation are still missing. The gene sml0013 of Synechocystis 6803 encodes for a small protein of unknown function for that homologs exist in all completely known cyanobacterial genomes. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

(Submitter supplied) We investigated Synechocystis high-density microarray data of three high-resolution time-series experiments with alternating light/dark rhythm, transition to continuous light, and transition to continuous darkness. Using ‘least oscillating set’ normalization and a clustering approach we found a daily temporal program for rhythmic expression of protein-coding and non-coding genes under light/dark conditions. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

62 Samples

Download data: TXT

(Submitter supplied) Quantification of circadian gene expression in WT Synechocystis sp. PCC 6803 cells

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

12 Samples

Download data: TXT

(Submitter supplied) Comparison of gene expression of WT Synechocystis cells with cells overexpressing the sRNA PsrR1 in order to detect direct targets of the sRNA PsrR1.

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

10 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

12 Samples

Download data: TXT