Synechococcus sp. JA-3-3Ab strain:A-Prime
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ABSTRACT:
PROVIDER: PRJNA16251 | ENA |
REPOSITORIES: ENA
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Project description:Hot spring microbial mat cyanobacterial strain
| PRJNA16252 | ENA
Project description:Cyanobacteria are valuable organisms for studying the physiology of photosynthesis and carbon fixation as well as metabolic engineering for the production of fuels and chemicals. This work describes a novel counter selection method for the cyanobacterium Synechococcus sp. PCC 7002 based on organic acid toxicity. The organic acids acrylate, 3-hydroxypropionate, and propionate were shown to be inhibitory towards PCC 7002 and other cyanobacteria at low concentrations. Inhibition was overcome by a loss of function mutation in the gene acsA. Loss of AcsA function was used as a basis for an acrylate counter selection method. DNA fragments of interest were inserted into the acsA locus and strains harboring the insertion were isolated on selective medium containing acrylate. This methodology was also used to introduce DNA fragments into a pseudogene, glpK. Application of this method will allow for more advanced genetics and engineering studies in PCC 7002 including the construction of markerless gene deletions and insertions. The acrylate counter-selection could be applied to other cyanobacterial species where AcsA activity confers acrylate sensitivity (e.g. Synechocystis sp. PCC 6803).
2013-07-19 | GSE48981 | GEO
Project description:Cyanobacteria are valuable organisms for studying the physiology of photosynthesis and carbon fixation as well as metabolic engineering for the production of fuels and chemicals. This work describes a novel counter selection method for the cyanobacterium Synechococcus sp. PCC 7002 based on organic acid toxicity. The organic acids acrylate, 3-hydroxypropionate, and propionate were shown to be inhibitory towards PCC 7002 and other cyanobacteria at low concentrations. Inhibition was overcome by a loss of function mutation in the gene acsA. Loss of AcsA function was used as a basis for an acrylate counter selection method. DNA fragments of interest were inserted into the acsA locus and strains harboring the insertion were isolated on selective medium containing acrylate. This methodology was also used to introduce DNA fragments into a pseudogene, glpK. Application of this method will allow for more advanced genetics and engineering studies in PCC 7002 including the construction of markerless gene deletions and insertions. The acrylate counter-selection could be applied to other cyanobacterial species where AcsA activity confers acrylate sensitivity (e.g. Synechocystis sp. PCC 6803). Cultures were grown in medium modified with 5mM acrylic acid at pH 8 and compared to cultures grown in unmodified medium. Samples were processed in duplicate.
2013-07-19 | E-GEOD-48981 | biostudies-arrayexpress
Project description:Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity overtime. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in HotLake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gamma proteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities.
2014-06-24 | MTBLS75 | MetaboLights
Project description:Chloroflexus-dominated microbial mat metagenome from hot spring
| PRJNA679676 | ENA
Project description:Cyanobacteria fix atmospheric CO2 to biomass and through metabolic engineering can also act as photosynthetic cell factories for sustainable productions of fuels and chemicals. The Calvin cycle is the primary pathway for CO2 fixation in cyanobacteria, algae and C3 plants, and several studies have shown that overexpression of a cyanobacterial Calvin cycle enzyme, bifunctional sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (hereafter BiBPase), enhances CO2 fixation in both plants and algae, although its impact on cyanobacteria has not yet been rigorously studied. Here, we show that overexpression of BiBPase enhanced growth, cell size, and photosynthetic O2 evolution of the cyanobacterium Synechococcus sp. PCC 7002 in an environment with elevated CO2 concentration. Biochemical analysis, immunodetection, and proteomic analysis revealed that overexpression of BiBPase considerably elevated the cellular activities of two rate-limiting enzymes in the Calvin cycle, namely ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and aldolase, while it repressed several enzymes involved in the respiratory carbon metabolism (e.g. glycolysis and the oxidative pentose phosphate pathway) including glucose-6-phosphate dehydrogenase. Concomitantly, the content of glycogen was significantly reduced while the extracellular carbohydrate content increased. These results indicate that overexpression of BiBPase leads to global reprogramming of carbon metabolism in Synechococcus sp. PCC 7002, promoting photosynthetic carbon fixation and repressing the respiratory carbon catabolism, while altering carbohydrate partitioning.
2019-01-17 | PXD007963 | Pride
Project description:Cyanobacterial metagenome-assembled genomes from hot spring phototrophic microbial mats Metagenomic assembly
| PRJNA635751 | ENA
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
Project description:Primary productivity of open ocean environments, such as those inhabited by marine picocyanobacteria Synechococcus sp.WH8102, are often limited by low inorganic phosphate (P). To observe how this organism copes with P starvation, we constructed a full genome microarray and examined differences in gene expression under P-limited and P-replete growth conditions. To determine the temporal nature of the responses, comparisons were made for cells newly entered into P-stress (at a time point corresponding to the induction of extracellular alkaline phosphatase activity) and a later time point (late log phase). In almost all instances the P starvation response was transitory, with 36 genes showing significant upregulation (>log2 fold) while 23 genes were highly downregulated at the early time point; however, these changes in expression were maintained for only five of the upregulated genes. Knockout mutants were constructed for genes SYNW0947 or SYNW0948, comprising a two component regulator hypothesized to play a key role in regulating the response to P-limitation. A high degree of overlap in the sets of genes affected by P-limited conditions and in the knockout mutants supports this hypothesis; however there is some indication that other regulators may play a role in this response in Synechococcus sp. WH8102. Consistent with what has been observed in many other cyanobacteria, the Pho regulon of this strain is comprised largely of genes for alkaline phosphatases, P transport or P metabolism. Interestingly, however, the exact composition and arrangement of the Pho regulon appears highly variable in marine cyanobacteria.
2009-06-15 | GSE13170 | GEO