DNA-methylation of GGCC motifs via M.Ssp6803II is linked to DNA repair in the cyanobacterium Synechocystis sp. PCC 6803 [sll0729 mutant]
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ABSTRACT:
PROVIDER: PRJNA521475 | ENA |
REPOSITORIES: ENA
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Project description:DNA methylation plays a crucial role for gene regulation among eukaryotes, but its regulatory function is less understood in bacteria. In the cyanobacterium Synechocystis sp. PCC 6803 five DNA methyltransferases have been identified. Among them, M.Ssp6803II is responsible for the specific methylation of the first cytosine in the frequently occurring motif GGCC, leading to N4-methylcytosine (GGm4CC). The mutation of the corresponding gene sll0729 led to a strong phenotype, including a lowered chlorophyll/phycocyanin ratio, impaired growth, and alterations of the expression of two genes encoding hypothetical proteins. However, prolonged cultivation revealed instability of the initially obtained phenotype, with colonies showing normal pigmentation and wild-type-like growth appearing regularly and in high frequencies on agar plates. These colonies represent suppressor mutants, since the sll0729 gene was still completely inactivated and the GGCC sites remained un-methylated. Two suppressor clones were further characterized and showed a smaller cell size and lowered DNA content per cell. Moreover, they exhibited a decreased tolerance against UV stress compared to wild type. Proteomics revealed the reduction of DNA topoisomerase in suppressor mutant cells. Collectively, these results indicate that GGm4CC methylation is involved in the regulation of gene expression, in the fine-tuning of DNA replication, and DNA repair mechanisms.
2019-07-02 | GSE126282 | GEO
Project description:DNA-methylation of GGCC motifs via M.Ssp6803II is linked to DNA repair in the cyanobacterium Synechocystis sp. PCC 6803
| PRJNA521473 | ENA
Project description:DNA methylation plays a crucial role for gene regulation among eukaryotes, but its regulatory function is less understood in bacteria. In the cyanobacterium Synechocystis sp. PCC 6803 five DNA methyltransferases have been identified. Among them, M.Ssp6803II is responsible for the specific methylation of the first cytosine in the frequently occurring motif GGCC, leading to N4-methylcytosine (GGm4CC). The mutation of the corresponding gene sll0729 led to a strong phenotype, including a lowered chlorophyll/phycocyanin ratio, impaired growth, and alterations of the expression of two genes encoding hypothetical proteins. However, prolonged cultivation revealed instability of the initially obtained phenotype, with colonies showing normal pigmentation and wild-type-like growth appearing regularly and in high frequencies on agar plates. These colonies represent suppressor mutants, since the sll0729 gene was still completely inactivated and the GGCC sites remained un-methylated. Two suppressor clones were further characterized and showed a smaller cell size and lowered DNA content per cell. Moreover, they exhibited a decreased tolerance against UV stress compared to wild type. Proteomics revealed the reduction of DNA topoisomerase in suppressor mutant cells. Collectively, these results indicate that GGm4CC methylation is involved in the regulation of gene expression, in the fine-tuning of DNA replication, and DNA repair mechanisms.
2019-07-02 | GSE126283 | GEO
Project description:DNA-methylation of GGCC motifs via M.Ssp6803II is linked to DNA repair in the cyanobacterium Synechocystis sp. PCC 6803 [sll0729 suppressor mutant]
| PRJNA521476 | ENA
Project description:The small protein AtpΘ (encoded by gene atpT) identified in cyanobacteria becomes maximum expressed during low-energy conditions such as during darkness. In the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803), AtpΘ was demonstrated to inhibit the ATP hydrolysis activity of the F0F1 ATP synthase. Here, the regulation of atpT gene expression was studied in greater detail. The darkness-induced activation of the atpT promoter indicated the existence of regulatory factors. To identify such factors, DNA-protein affinity precipitation was performed using biotinylated DNA fragments. These fragments contained either the promoter-5’UTR (PatpT66-5’UTR) as bait or, as negative control, only the 5’UTR (atpT 5’UTR). Each DNA fragment was incubated with total protein samples isolated from exponential phase Synechocystis 6803 which had been kept in the light or 12 h in darkness prior to protein preparation. The resulting protein samples were then analyzed by mass spectrometry.
2022-04-14 | PXD027801 | Pride
Project description: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. Homologue FtsH3 is bound in two hetero-oligomeric complexes, FtsH1/FstH3 and/or FtsH2/FtsH3, respectively. Previous data showed that the FtsH1/FtsH3 complex is involved in the acclimation of cells to iron deficiency by controlling the availability of the transcriptional regulator Fur (Sll0567). To gain more comprehensive insight into the physiological role of FtsH hetero-complexes, we carried out genome-wide expression profiling of a mutant conditionally depleted in FtsH3, grown under nutrient sufficiency and iron depletion. Our results show, that besides Fur, also the SufR and Pho regulons belong to the set of genes controlled by FtsH. Moreover, by combining the transcriptome data with in silico prediction we identified novel targets of Fur in Synechocystis PCC 6803. Fur tends to evoke mostly repression, but also appears to activate some target genes. We monitored the global gene expression in a conditional Synechocystis PCC6083 ftsH knockdown strain (FtsHdown) (Boehm et al., 2012) and a control strain (WT) at standard conditions and at iron depletion. The presence of ammonia to induced the conditional knockdown. Each sample was done in biological replicates.
2016-06-14 | E-GEOD-83303 | biostudies-arrayexpress
Project description:Cyanobacteria, photoautotrophic prokaryotes, contribute significantly to the global photosynthesis and require large amounts of the essential micronutrient iron in order to maintain their Fe-rich photosynthetic apparatus. Here we use the model organism Synechocystis sp. PCC 6803 (later referred to Synechocystis) in both, standard and iron stress conditions, to study transcription and post-transcription regulation in iron deprivation. Although iron is one of the most abundant metals on earth, it is not soluble under aerobic conditions. Thus Synechocystis had to find ways to overcome iron deficiency. At the same time, however, free intracellular iron needs to be kept at permissive levels, as it becomes toxic under aerobic conditions by producing reactive oxygen species. For these reasons, complex regulatory networks have evolved to tightly control intracellular iron concentrations, ensuring its essential function yet avoiding cellular damage (Pierre Cornelis et al). In a previous study, we investigated iron deprivation in Synechocystis using customised amplification library for the analysis of global gene expression in the unicellular cyanobacterium (Hernández-Prieto et al, 2012; Georg et al, 2017),(Georg et al, 2017) but it is still little known about RNA stability in this organism. We now extend this study through a transcriptome wide half-life analysis in Synechocystis grown under standard and iron-limiting conditions using oligonucleotide microarrays that detect both protein-coding and non-coding transcripts (ncRNA). We used the antibiotic Rifampicin to stop the transcription. Samples were taken at time points 0 min (before the addition of rifampicin) and in a time series of 2 min, 4 min, 8 min, 16 min, 32 min and 64 min after its addition.
2022-07-30 | GSE209879 | GEO
Project description: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. Homologue FtsH3 is bound in two hetero-oligomeric complexes, FtsH1/FstH3 and/or FtsH2/FtsH3, respectively. Previous data showed that the FtsH1/FtsH3 complex is involved in the acclimation of cells to iron deficiency by controlling the availability of the transcriptional regulator Fur (Sll0567). To gain more comprehensive insight into the physiological role of FtsH hetero-complexes, we carried out genome-wide expression profiling of a mutant conditionally depleted in FtsH3, grown under nutrient sufficiency and iron depletion. Our results show, that besides Fur, also the SufR and Pho regulons belong to the set of genes controlled by FtsH. Moreover, by combining the transcriptome data with in silico prediction we identified novel targets of Fur in Synechocystis PCC 6803. Fur tends to evoke mostly repression, but also appears to activate some target genes.
2016-06-14 | GSE83303 | GEO
Project description:CO2-neutral isoprene production using the cyanobacterium Synechocystis sp. PCC 6803
| PRJNA301973 | ENA
Project description:The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey of differential expression with a focus on antisense (as)RNAs and non-coding (nc)RNAs. A microarray was constucted with on average 5 probes for each transcript known thus far, including ncRNAs and asRNAs. The resulting 20,431 individual probes are duplicated on the array (Agilent 4x44k custom array) representing a technical replicate. Hybridization of this array with total RNA isolated from cultures raised under different growth conditions identified transcripts from intergenic spacers and in antisense orientation to known genes (natural cis-asRNAs) with differential expression compared to control hybridizations. This shows the involvement of such transcripts in the regulation of adaptation to various stresses. 12 RNA hybridizations (1 control & 3 stress conditions, 3 times each)
2010-05-18 | E-GEOD-16162 | biostudies-arrayexpress