Marine Synechococcus genome assemblies
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PROVIDER: PRJEB26976 | ENA |
REPOSITORIES: ENA
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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
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. In this series four conditions have been analyzed. These are moderate copper shock for Synechococcus sp. WH8102 and CC9311 (pCu 11.1 and pCu 10.1, respectively), and high copper shock for WH8102 and CC9311 (pCu 10.1 and pCu 9.1, respectively). For each slide, an experimental RNA sample was labeled with Cy3 or Cy5 and was hybridized with a reference RNA from a non-copper-shocked sample labeled with the other Cy dye. There are six or eight slides per condition, each with two biological replicates. There are three or four technical replicates for each biological replicate including at least one flip-dye comparison. Each slide contains six replicate spots per gene.
2010-05-17 | E-GEOD-13910 | biostudies-arrayexpress
Project description:In this study, we explored the use of BONCAT in Synechococcus sp. – a globally important cyanobacteria. We characterized the growth and microscopically quantified HPG uptake under a range of HPG concentrations in marine Synechococcus sp. Further, we examined changes in protein expression of Synechococcus sp. grown under normal and nitrate-stressed conditions relative to a non-HPG control.
2021-04-01 | PXD023371 | Pride
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
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
Project description:Proteins secreted by marine cyanobacterium Synechococcus under phosphorus stress is largely uncharacterized. This dataset characterizes the exoproteins for both an open ocean (WH8102) and coastal (WH5701) Synechococcus strain and were collected as part of the study "Dissolved organic phosphorus bond-class utilization by Synechococcus". Study Abstract: Dissolved organic phosphorus (DOP) contains compounds with phosphoester (P-O-C), phosphoanhydride (P-O-P), and phosphorus-carbon (P-C) bonds. Despite DOP’s importance as a nutritional source for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by cultures of an open ocean and a coastal ocean Synechococcus strain. Both strains exhibited comparable growth rates when provided phosphate, short-chain and long-chain polyphosphate (P-O-P), adenosine 5’-triphosphate (P-O-C and P-O-P), and glucose-6-phosphate (P-O-C) as the phosphorus source. However, growth rates on phosphomonoester adenosine 5’-monophosphate (P-O-C) and phosphodiester bis(4-methylumbelliferyl) phosphate (C-O-P-O-C) varied between strains, and neither strain grew on selected phosphonates. Consistent with the growth measurements, both strains preferentially hydrolyzed 3-polyphosphate, followed by adenosine 5’-triphosphate, and then adenosine 5’-monophosphate. The strains’ exoproteome contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5’-triphosphate under phosphate deficiency, suggests active mineralization of short-chain polyphosphate by Synechococcus’ exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity towards short-chain polyphosphate, with varying affinities between the two strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition, thereby expanding our understanding of microbially-mediated DOP cycling in marine ecosystems.
2024-07-15 | PXD051991 | Pride
Project description:In this study we inactivated SYNW2176 and characterized the stress response and outer membrane protein composition of the mutant in order to better understand the overlap between envelope stress and copper stress in marine Synechococcus.
2019-12-17 | PXD000989 | Pride
Project description:The genome of the marine Synechococcus sp. WH8102 displays a minimal regulatory network yet physiological and molecular responses of this organism are tuned to episodic limitation for nitrogen and phosphorus. Microarray analyses have demonstrated a key role for the two-component regulatory system, PhoBR, in the regulation of P transport and metabolism in this strain. However, there is some evidence that another regulator, SYNW1019 (designated as ptrA), probably under the control of PhoB, is involved in the wider response to P-depletion. PtrA is one of only two genome encoded DNA binding proteins of the CRP family in Synechococcus sp. WH8102, and a potential transcriptional regulator with homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the precise role of this regulator we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-deplete growth conditions. During P-depletion the ptrA mutant failed to up-regulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is directly controlled by PtrA, including two phosphatase genes (SYNW0196, SYNW2390), a predicted phytase (SYNW0762) and a gene of unknown function (SYNW0165) all of which are highly up regulated during P-limitation. This result was confirmed by electrophoretic mobility shift assays which demonstrated binding of over expressed PtrA to promoter sequences upstream of the induced phosphatases (SYNW0165, SYNW0196 and SYNW2390). This work suggests a two-tiered response to P-depletion in this strain, the first being PhoB-dependent induction of high affinity PO4 transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly controlled by PtrA, including those involved in cell surface modification, metal uptake, photosynthesis, stress responses and other metabolic process, which may indicate a wider role for PtrA in cellular organisation. In an environmental context ptrA is found in a number of picocyanobateria isolated from a range of oceanic provinces, including strains that lack a functional phoBR..These results give broader insight into the regulation of physiological responses that may dictate niche adaptation in genetically diverse lineages of marine Synechococcus, and suggest that signalling networks and coordinated responses to nutrient availability are important, even in oligotrophic ocean environments.
2010-04-08 | GSE18511 | GEO
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.
2012-03-31 | GSE28263 | GEO
Project description:The genome of the marine Synechococcus sp. WH8102 displays a minimal regulatory network yet physiological and molecular responses of this organism are tuned to episodic limitation for nitrogen and phosphorus. Microarray analyses have demonstrated a key role for the two-component regulatory system, PhoBR, in the regulation of P transport and metabolism in this strain. However, there is some evidence that another regulator, SYNW1019 (designated as ptrA), probably under the control of PhoB, is involved in the wider response to P-depletion. PtrA is one of only two genome encoded DNA binding proteins of the CRP family in Synechococcus sp. WH8102, and a potential transcriptional regulator with homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the precise role of this regulator we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-deplete growth conditions. During P-depletion the ptrA mutant failed to up-regulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is directly controlled by PtrA, including two phosphatase genes (SYNW0196, SYNW2390), a predicted phytase (SYNW0762) and a gene of unknown function (SYNW0165) all of which are highly up regulated during P-limitation. This result was confirmed by electrophoretic mobility shift assays which demonstrated binding of over expressed PtrA to promoter sequences upstream of the induced phosphatases (SYNW0165, SYNW0196 and SYNW2390). This work suggests a two-tiered response to P-depletion in this strain, the first being PhoB-dependent induction of high affinity PO4 transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly controlled by PtrA, including those involved in cell surface modification, metal uptake, photosynthesis, stress responses and other metabolic process, which may indicate a wider role for PtrA in cellular organisation. In an environmental context ptrA is found in a number of picocyanobateria isolated from a range of oceanic provinces, including strains that lack a functional phoBR..These results give broader insight into the regulation of physiological responses that may dictate niche adaptation in genetically diverse lineages of marine Synechococcus, and suggest that signalling networks and coordinated responses to nutrient availability are important, even in oligotrophic ocean environments. In this series gene expression of a ptrA mutant has been analyzed under phosphorus deplete conditions just after the onset of induction of phosphatase activity in wild type. There are six duel-channel slides upon which both ptrA mutant and wild type samples were hybridized. There are three technical replicates for each of two biological replicates including one flip-dye comparison. Each slide contains six replicate spots per gene.
2010-04-08 | E-GEOD-18511 | biostudies-arrayexpress