Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression changes in group 2 sigma factor mutant, M-NM-^TsigCDE, in standard growth conditions and after high-light treatment

ABSTRACT: Adjustment of gene expression during acclimation to stress conditions, such as bright light, in the cyanobacterium Synechocystis sp. PCC 6803 depends on four group 2 M-OM-^C factors (SigB, SigC, SigD, SigE). A M-bM-^HM-^FsigCDE strain containing the stress responsive SigB as an only functional group 2 M-OM-^C factor appears twice as resistant to photoinhibition of photosystem II (PSII) as the control strain. Microarray analyzes of the M-bM-^HM-^FsigCDE strain indicated that 77 genes in standard conditions and 79 genes in high light were differently expressed compared to the control strain. Analysis of possible photoprotective mechanisms revealed that high carotenoid content and up-regulation of the photoprotective flavodiiron operon flv4-sll0218-flv2 protected PSII in M-bM-^HM-^FsigCDE, while up-regulation of pgr5-like, hlipB or isiA genes in the mutant strain did not offer particular protection against photoinhibition. The photoinhibition resistance was lost if M-bM-^HM-^FsigCDE was grown in high CO2 where carotenoid and Flv4-Sll0218-Flv2 contents were low. Additionally, photoinhibition resistance of the M-bM-^HM-^FrpoZ strain (lacking the omega subunit of RNA polymerase) with very high carotenoid but only low Flv4-Sll0218-Flv2 content supported the importance of carotenoids in PSII protection. Carotenoids likely protect mainly via quenching of singlet oxygen but efficient non-photochemical quenching in M-bM-^HM-^FsigCDE might offer some additional protection. Comparison of photoinhibition kinetics in control, M-bM-^HM-^FsigCDE and M-bM-^HM-^FrpoZ strains showed that protection by the flavodiiron operon was most efficient during the first minutes of high-light illumination. Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and group 2 sigma factor mutant M-NM-^TsigCDE (A730=1, 40 mL) were harvested directly from standard growth conditions (continuous illumination at the PPFD of 40 M-BM-5mol m-2s-1, 32M-BM-0C, ambient CO2) or after 30-min illumination a PPFD 750 M-BM-5mol m-2s-1. From three to four independent experiments were performed at each conditions.

ORGANISM(S): Synechocystis sp. PCC 6803

SUBMITTER: Taina Tyystjarvi

PROVIDER: E-GEOD-50060 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The catalytic core of the RNA polymerase of most eubacteria is composed of two M-NM-1 subunits and M-NM-2, M-NM-2M-bM-^@M-^Y and M-OM-^I subunits. In Escherichia coli, the M-OM-^I subunit (encoded by the rpoZ gene) has been suggested to assist M-NM-2M-bM-^@M-^Y during RNA polymerase core assembly. The function of the M-OM-^I subunit is particularly interesting in cyanobacteria because the cyanobacterial M-NM-2M-bM-^@M-^Y is split to N-terminal M-NM-3 and C-terminal M-NM-2M-bM-^@M-^Y subunits. The M-bM-^HM-^FrpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions although the mutant cells showed low light-saturated photosynthetic activity, low Rubisco content and accumulated high quantities of protective carotenoids and M-NM-1-tocopherol. The M-bM-^HM-^FrpoZ strain contained 15% less of the primary M-OM-^C factor, SigA, than the control strain, and recruitment of SigA to the RNA polymerase core was inefficient in M-bM-^HM-^FrpoZ. Thus, a cyanobacterial RNA polymerase holoenzyme lacking the M-OM-^I subunit contains less frequently the primary M-OM-^C factor. A DNA microarray analysis revealed that this leads to specific down-regulation of highly expressed genes, like genes encoding subunits for Rubisco, ATP synthase, NADH-dehydrogenase and carbon concentrating mechanisms. On the contrary, many genes showing only low or moderate expression in the control strain were up-regulated in M-bM-^HM-^FrpoZ. A conserved -10 region was detected in promoters showing up or down-regulation in M-bM-^HM-^FrpoZ, but -35 regions of down-regulated genes completely differed from -35 regions of up-regulated genes. Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and RNA polymerase omega subunit inactivation strain, M-NM-^TrpoZ, were harvested (A730=1, 40 mL) directly from standard growth conditions (continuous illumination at the PPFD of 40 M-BM-5mol m-2s-1, 32M-BM-0C, ambient CO2). From three to four independent experiments were performed at each conditions.

Project description:Photosystem II (PSII) is the most thermally sensitive component of photosynthesis. Thermal acclimation of this complex activity is likely to be critically important to the ability of photosynthetic organisms to tolerate temperature changes in the environment. We have analysed gene expression using whole-genome microarrays and monitored alterations in physiology during acclimation of PSII to elevated growth temperature in Synechocystis sp. PCC 6803. PSII acclimation is complete within 480 minutes of exposure to elevated temperature and is associated with a highly dynamic transcriptional response. 176 genes were identified and classified into seven distinct response profile groups. Response profiles suggest the existence of an early transient phase and a sustained phase to the acclimation response. The early phase was characterised by induction of general stress response genes, including heat shock proteins, which are likely to influence PSII thermal stability. The sustained phase consisted of acclimation-specific alterations that are involved in other cellular processes. Sustained responses included genes involved in phycobillisome structure and modification, photosynthesis, respiration, lipid metabolism and motility. Approximately 60% of genes with sustained altered expression levels have no known function. The potential role of differentially expressed genes in thermotolerance and acclimation is discussed. We have characterised the acclimation physiology of selected gene ‘knockouts’ to elucidate possible gene function in the response. All mutants show lower PSII rates under normal growth conditions. Basal PSII thermotolerance was affected by mutations in clpB1, cpcC2, hspA, htpG and slr1674. Final PSII thermotolerance was affected by mutations in cpcC2, hik34, hspA and hypA1, suggesting that these gene products play roles in long-term thermal acclimation of PSII. Gene expression levels were compared during a time-course (up to 8 hours) of thermal acclimation (from 25C to 38C) of a wild-type strain grown under continuous illumination and bubbled with CO2 -enriched air. Up to four independent biological replicates were generated and analysed. Each array: replicate matched time-point vs. 0hr control.

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Gene expression changes in group 2 sigma factor mutant, M-NM-^TsigCDE, in standard growth conditions and after high-light treatment

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