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Expression of intergenic regions of Synechococcus WH 7803 under environmentally relevant stresses

ABSTRACT: We constructed a tiling microarray, covering nearly all of the intergenic regions larger than 50 bp on both strands of the genome of the marine picocyanobacterium Synechococcus WH7803. We analyzed transcript levels from cultures grown under ecologically relevant stress conditions. The investigated stress conditions were cold stress, high light stress, phosphate depletion and iron depletion. We identified several previously unknown small RNAs, partially differentially expressed. The detected RNAs provide a starting point for further investigations on the acclimatisation to different stresses for Synechococcus WH7803.

ORGANISM(S): Synechococcus sp. WH 7803

PROVIDER: GSE28263 | GEO | 2012/03/31

SECONDARY ACCESSION(S): PRJNA139275

REPOSITORIES: GEO

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Expression of intergenic regions of Synechococcus WH 7803 under environmentally relevant stresses

Project description:We constructed a tiling microarray, covering nearly all of the intergenic regions larger than 50 bp on both strands of the genome of the marine picocyanobacterium Synechococcus WH7803. We analyzed transcript levels from cultures grown under ecologically relevant stress conditions. The investigated stress conditions were cold stress, high light stress, phosphate depletion and iron depletion. We identified several previously unknown small RNAs, partially differentially expressed. The detected RNAs provide a starting point for further investigations on the acclimatisation to different stresses for Synechococcus WH7803. For every applied growth condition the cultures were grown in triplicates as were the respective controls. Respective controls were treated the same as the stressed bacterial cultures in terms of centrifugation and / or dilution. Bacteria were harvested by rapid filtering and directly freezed by liquid nitrogen.

2012-03-30 | E-GEOD-28263 | biostudies-arrayexpress

Transcriptiome dynamics of cyanopodovirus S-SBP1 and its host Synechococcus sp. WH7803

Project description:Whole-genome expression dynamics of cyanopodovirus P-SSP7 and its host Prochlorococcus strain MED4 have been reported. To investigate whether cyanopodoviruses infecting Prochlorococcus and Synechococcus have similar transcription strategy and host response to phage infection, genomic and transcriptomic analyses were conducted on cyanopodovirus S-SBP1 that infects Synechococcus strain WH7803. S-SBP1 has a latent period of 8 h and a burst size of 30 progeny phages per cell. S-SBP1 was most similar to cyanopodovirus S-RIP2 that also infects Synechococcus WH7803, in terms of whole genome phylogenetic relationship and average nucleotide identity (ANI). Three hypervariable genomic islands were found when comparing the genomes of S-SBP1 and S-RIP2, and single nucleotide variants (SNV) were observed on three genes of S-SBP1, which are located within the island regions. Based on RNA-seq analysis, genes of S-SBP1 were clustered into three temporal express classes, with gene content within each class similar to that of P-SSP7. Thirty-two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome component and stress response. These upregulated genes were also similar to those of Prochlorococcus MED4 in response to infection by P-SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection.

2020-12-07 | GSE150732 | GEO

Transcription profiling of cyanophage S-PM2 as it infects Synechococcus WH7803 over a 9 hr time series

Project description:To monitor the expression of cyanophage S-PM2 genes as it infects Synechococcus WH7803 over a 9 hr time course. Samples were take from 3 independent cultures. A reference design was used with dye swaps (technical replicates) for each time point.

2009-10-01 | E-MAXD-26 | biostudies-arrayexpress

Copper toxicity response influences mesotrophic Synechococcus community structure

Project description:Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, “species” also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbor stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.

2016-10-28 | GSE89262 | GEO

Marine Synechococcus sp. strain WH7803 shows specific adaptative responses to assimilate nanomolar concentrations of nitrate

Project description:Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrients availability or temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to ammonium or nitrogen starvation. We found that Synechococcus has a specific response to nanomolar nitrate concentration that differs to the response showed under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentration of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural field.

2022-07-11 | PXD031142 | Pride

Synechococcus sp.

Project description:a community consisted of 4 Synechococcus species, including HK10, WH7803, WH5701 and MW01 Targeted loci cultured

| PRJNA624241 | ENA

Synergic effects of temperature and irradiance on the physiology of the marine Synechococcus strain WH7803

Project description:Understanding how microorganisms adjust their metabolism to maintain their ability to survive to short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here WH7803, the best physiologically characterized marine Synechococcus strain was submitted to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem II (PSII) quantum yield, PSII repair rate, pigment and lipid content as well as whole transcriptomes. This notably revealed that cells previously acclimated to HL seem to be better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of this key component of marine ecosystems. Our data also highlighted important specificities of the stress responses compared to model freshwater cyanobacteria.

2020-06-17 | GSE146246 | GEO

Exoproteomes of marine cyanobacteria grown under different regimes to detect their pili production; analysed by LC-MS/MS

Project description:Exoproteome and cellular proteome generated from Synechococcus sp. WH7803 and its pili mutant.

2021-02-24 | PXD019315 | Pride

Response of Synechococcus sp. WH7803 LL- and and HL- acclimated cells to oxidative stress (HP and MV)

Project description:To identify the respective roles of light and ROS in the photoinhibition process and detect a possible light-driven tolerance to oxidative stress, we compared the transcriptomic responses of Synechococcus sp. WH7803 acclimated to low (LL) or high light (HL) to oxidative stress, induced by hydrogen peroxide (H202) or methylviologen (MV). Cultures were acclimated during many generations to continuous low light (LL, 18 ?mol photons m-2 s-1, hereafter LL cells) and high light (HL, 250 ?mol photons m-2 s-1, hereafter HL cells) provided by Sylvania Daylight 58W/154 fluorescent bulbs. For all stress experiments performed in this study, exponentially growing cultures (1 to 3 x 107 cells mL-1), were split into subcultures and submitted to oxidative stress by addition of H2O2 or MV and harvested when PSII quantum yield fell to half of the initial value. For H2O2 experiments, this level of PSII photoinactivation was reached 2 h after submitting LL and HL cultures to 750 M and 25 M respectively. Because of the large divergence in dose and kinetics responses to MV between LL- and HL cells, it was not possible to find MV concentrations leading to 50 % decrease of quantum yield at the same time for both light acclimations. Thus, array analyses for MV were performed on HL and LL cultures incubated at the same MV concentration (50 M) but harvested once PSII quantum yield was halved, i.e. after 1 and 3.5 h of stress respectively. All hybridizations were performed on 4 independent biological replicates and using as reference sample a pool of RNA from all samples investigated in this study. Pairwise comparison were performed to analyze the stress induced by either H2O2 or MV on both LL- and HL cultures (i.e. LL-Ct vs. LL+MV, LL-Ct vs. LL+H2O2, HL-Ct vs. HL+MV, HL-Ct vs. HL+H2O2) as well as to compare the steady state acclimation to different light conditions (i.e. LL-Ct vs. HL-Ct).

2011-08-18 | E-MTAB-681 | biostudies-arrayexpress

Gene expression response to copper toxicity between coastal and open ocean strains of marine Synechococcus

Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner.

2009-07-01 | GSE13910 | GEO

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