Synechocystis sp. PCC 6803
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PROVIDER: PRJNA215900 | ENA |
REPOSITORIES: ENA
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Project description:Acclimation of cyanobacterium Synechocystis sp. PCC6803 to suboptimal conditions is largely dependent on adjustments of gene expression, which is highly controlled by the σ factor subunits of RNA polymerase (RNAP). The SigB and SigD σ factors are close homologues. Here we show that sigB and sigD genes are both induced in bright light and high temperature stresses. Comparison of transcriptomes of the control strain (CS), ΔsigB, ΔsigD, ΔsigBCE (SigD is an only functional group 2 σ factor), and ΔsigCDE (SigD is an only functional group 2 σ factor) strains in standard, bright light and high temperature conditions revealed that the SigB and SigD factors regulate different set of genes, and that SigB and SigD regulons are highly dependent on stress conditions. The SigB regulon is bigger than the SigD regulon at high temperature, whereas in bright light the SigD regulon is bigger the SigB regulon. Furthermore, our results show that favoring the SigB or SigD factor by deleting other group 2 σ factors do not lead to superior acclimation to bright light or high temperature conditions, indicating that all group 2 σ factors play roles in acclimation processes.
2022-01-19 | GSE192357 | GEO
Project description:Deletion of the Synechocystis sp. PCC 6803 kaiAB1C1 gene cluster causes impaired cell growth under light-dark conditions
| PRJNA252913 | ENA
Project description:To investigate acclimation mechanisms employed under extreme high light conditions, gene expression analysis was performed using the model microalgae Synechocystis sp. PCC 6803 (PCC 6803) cultured under various light intensities. From the low to the mid light conditions, the expression of genes related to light harvesting systems was repressed, whereas that of CO2 fixation and of D1 protein turnover-related genes was induced. Gene expression data also revealed that the down-regulation of genes related to flagellum synthesis (pilA2), pyridine nucleotide transhydrogenase (pntA and pntB), and sigma factor (sigA and sigF) represents acclimation mechanisms of PCC 6803 under excessive high light conditions.
2018-03-06 | GSE111408 | GEO
Project description:In vivo recruitment analysis and a mutant strain without any group 2 σ factors reveal roles of different σ factors in cyanobacteria
| PRJNA287323 | 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:ChIP-seq data of sigma factor SigE and SigA in Synechocystis sp. PCC6803
| PRJNA761880 | ENA
Project description:The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is already well-characterized in 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. This study reveals 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. Physiological characterization of a 6S RNA deletion strain (ÎssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation is accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding components of both photosystems, ATP synthase and the phycobilisomes were negatively affected in the ÎssaA mutant. In vivo pull-down studies of the RNA polymerase complex further indicate a promoting effect of 6S RNA on the recruitment of the cyanobacterial housekeeping sigma factor SigA, concurrently supporting dissociation of group II sigma factors during recovery from nitrogen starvation. According to these results, 6S RNA supports a rapid adaptation to changing nitrogen conditions by regulating the switch from group II sigma factors SigB / SigC to SigE / SigA dependent transcription. We performed microarray analysis of total RNA from wild-type and âssaA cultures that were starved for nitrogen for seven days and recovered over a period of 48 hours. Sampling time points were t1 = 1h +N, t2 = 4h +N and t3 = 22h +N after nitrogen recovery. Samples were taken in biological replicates.
2016-06-16 | E-GEOD-83387 | biostudies-arrayexpress
Project description:we obtained a HL tolerant (Tol) strain Synechocystis sp. PCC 6803 by adaptive evolution experiment that the cells were repeatedly subcultured for prolonged periods of time (52 days) under high light stress condition (7000 to 9000 μmol m-2 s-1). Although the growth of the parental strain almost stopped under 9000 μmol m-2 s-1, no growth inhibition was observed in the Tol strain. Furthermore, the growth rate was identical to that of parental strain under low light condition (40 μmol m-2 s-1). To further investigate the high light tolerant mechanisms in the Tol strain, the transcriptome was performed. The transcriptome data suggests the increase of isiA expression in the Tol strain under HL condition. The overexpression of isiA successfully enhanced the HL stress tolerance in the parental strain. The HL tolerant mechanism was different from previous reported mechanisms, such as a reduction of the light-harvesting antenna size. The tolerant strain would be an attractive host for bio-production under high light conditions.
2020-05-06 | GSE149892 | GEO
Project description:Every cyanobacterial species contains gene encoding site-2-protease (S2P) homolog. The studied prokaryotic S2P homologs play essential roles in regulating stress response through intramembrane proteolysis of membrane-bound anti-sigma factors. Here, gene of Slr0643, one of four S2P homologs in Synechocystis sp. PCC 6803, was insertionally disrupted to explore its physiological role. Only a partially segregated mutant was obtained, indicating its indispensability for growth. The partially disrupted mutant could not grow at pH 6.5, while wild type acclimated to pH 6.5 quickly. The slr0643 gene expression was transiently induced after pH transfer from 7.5 to 6.5. Both evidences demonstrated the pivotal role of fully functional Slr0643 in acid acclimation. DNA microarray and quantitative RT-PCR analyses decoded genes involved in early acid acclimation and revealed differentially expressed genes due to slr0643 disruption at both pH conditions. Early acid acclimation to pH 6.5 included upregulation of sigH, hik16 and hik35, and downregulation of pcrR and sigG; as well as downregulation of porins and upregulation of inorganic carbon and nitrogen transporters. Defective photosynthesis and excess expression of NADH dehydrogenase, together with over upregulation of carbon transporter and repression of nitrogen transporter and metabolism gene contributed to the acid lethality of mutant at pH 6.5. Most interestingly, analysis of microarray data revealed the close relationship between slr0643 disruption and expression of sigH operon. Therefore it was implied that Slr0643/Sll0857/SigH might acts through S2P/anti-Sigma factor/Sigma factor mechanism to play a role in acid acclimation.
2012-09-18 | GSE37747 | GEO
Project description:The rpoZ gene encodes the small ω subunit of RNA polymerase (RNAP). A ∆rpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions (constant illumination at 40 µmol photons m-2s-1; 32 °C; ambient CO2) but was heat sensitive and died at 40 °C. In the control strain , 71 genes were at least two-fold up-regulated and 91 genes down-regulated after a 24-h treatment at 40 °C, while in ∆rpoZ 394 genes responded to heat. Only 62 of these heat-responsive genes were similarly regulated in both strains, and 80 % of heat-responsive genes were unique for ΔrpoZ. The RNAP core and the primary σ factor SigA were down-regulated in control strain at 40 °C, but not in ΔrpoZ. In accordance with reduced RNAP content, the total RNA content of mild-heat-stress-treated cells was lower in control strain than in ΔrpoZ. Light-saturated photosynthetic activity decreased more in ΔrpoZ than in control strain upon mild heat stress. The amounts of Photosystem II and Rubisco decreased at 40 °C in both strains while PSI and the phycobilisome antenna protein allophycocyanin remained at the same level as in standard conditions. The phycobilisome rod proteins, phycocyanins, diminished during the heat treatment in ΔrpoZ but not in control strain, and the nblA1 and nblA2 genes (encode NblA proteins required for phycobilisome degradation) were up-regulated only in ΔrpoZ. Our results show that the ω subunit of RNAP is essential in heat stress because it is required for heat acclimation of diverse cellular processes.
2014-11-11 | GSE59451 | GEO