Prochlorococcus
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ABSTRACT:
PROVIDER: PRJNA246696 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ultraviolet stress in light/dark synchronized cells of the marine cyanobacterium Prochlorococcus marinus PCC9511
2010-08-03 | E-TABM-1028 | biostudies-arrayexpress
Project description:Prochlorococcus is a cyanobacterium of abundance in open ocean environments and little is known of its iron requirements or iron metabolism. We used microarrays to measure the whole-genome expression response of Prochlorococcus MED4 and MIT9313 to iron stress and recovery from iron stress.
2011-01-11 | E-GEOD-26533 | biostudies-arrayexpress
Project description:RNA decay was measured in Prochlorococcus after inhibition of transcription by rifampicin using customized Affymetrix gene expression arrays. RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans. Using a combination of microarrays, quantitative RT-PCR and a new algorithm for determining RNA decay rates, we found a median half-life of 2.4 min and a median decay rate of 2.6 min for expressed genes â two-fold faster than that reported for any organism. The shortest transcript half-life (33 seconds) was for a gene of unknown function, while some of the longest (ca. 18 min) were for highly expressed genes. Genes organized in operons displayed intriguing mRNA decay patterns, such as increased stability, and delayed onset of decay with greater distance from the transcriptional start site. The same phenomenon was observed on a single probe resolution for genes greater than 2 kb. We hypothesize that the fast turnover relative to generation time in Prochlorococcus may enable a swift response to environmental changes through rapid recycling of nucleotides, which could be advantageous in nutrient poor oceans. Our growing understanding of RNA half-lives will inform on the modelling of cell processes and help interpret the growing bank of metatranscriptomic studies of wild populations of Prochlorococcus. The surprisingly complex decay patterns of large transcripts reported here, and the method developed to describe them, will open new avenues for the investigation and understanding of RNA decay for all organisms. Prochlorococcus cells were treated with rifampicin, which prevents initiation of new transcripts. Cells were harvested at 0 min (before rifampicin addition), 2.5 min, 5 min, 10 min, 20 min, 40 min and 60 min after rifampicin addition.
2010-05-16 | E-GEOD-17075 | biostudies-arrayexpress
Project description:RNA decay was measured in Prochlorococcus after inhibition of transcription by rifampicin using customized Affymetrix gene expression arrays. RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans. Using a combination of microarrays, quantitative RT-PCR and a new algorithm for determining RNA decay rates, we found a median half-life of 2.4 min and a median decay rate of 2.6 min for expressed genes – two-fold faster than that reported for any organism. The shortest transcript half-life (33 seconds) was for a gene of unknown function, while some of the longest (ca. 18 min) were for highly expressed genes. Genes organized in operons displayed intriguing mRNA decay patterns, such as increased stability, and delayed onset of decay with greater distance from the transcriptional start site. The same phenomenon was observed on a single probe resolution for genes greater than 2 kb. We hypothesize that the fast turnover relative to generation time in Prochlorococcus may enable a swift response to environmental changes through rapid recycling of nucleotides, which could be advantageous in nutrient poor oceans. Our growing understanding of RNA half-lives will inform on the modelling of cell processes and help interpret the growing bank of metatranscriptomic studies of wild populations of Prochlorococcus. The surprisingly complex decay patterns of large transcripts reported here, and the method developed to describe them, will open new avenues for the investigation and understanding of RNA decay for all organisms.
2009-12-31 | GSE17075 | GEO
Project description:Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy.
2015-04-15 | GSE65684 | GEO
Project description:Prochlorococcus genomes harbor a new type of mobile genetic elements named tycheposons. To study the effects on environmental stress on the gene expression and induction of tycheposons, we subjugated cultures of Prochlorococcus strain MIT0604 containing 7 such elements to treatments with mitomycin C and UV stress.
2021-04-04 | GSE171435 | GEO
Project description:Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy. Two biological replicates of timecourses under four conditions: medium bubbled with air (control) or three experimental gases (low CO2; low O2; or low CO2 and low O2)
2015-04-15 | E-GEOD-65684 | biostudies-arrayexpress
Project description:Prochlorococcus is an abundant, cosmopolitan, marine cyanobacterium with ecotypes that vary temporally and spatially across oligotrophic regions of the global ocean. This group of organisms can serve as a model system to understand the accumulation of organic compounds synthesized by primary producers in marine ecosystems. We applied targeted metabolomics to three axenic cultures of strains that span the Prochlorococcus phylogeny: a high-light adapted HLII-clade strain, a low-light adapted LLI-clade strain, and a low-light adapted LLIV-clade strain. Intracellular metabolites were extracted from cells captured in exponential growth and extracellular metabolites were adsorbed, from the same samples, to solid-phase extraction resin. Both pools were quantified using a triple quadrupole mass spectrometer. The resulting data reveal intraspecific differences in metabolites that provide clues about the selective pressures shaping the meta-metabolism of the Prochlorococcus collective, and its interactions with the surrounding microbes that depend on them.
2018-10-23 | MTBLS567 | MetaboLights
Project description:Prochlorococcus is an obligate marine microorganism which are dominant autotroph in tropical and subtropical central oceans. However, what is the low salinity boundary and how Prochlorococcus would response to low salinity exposure is still unknown. In this study, we first tested the growing salinity range of two Prochlorococcus strains, NATL1A and MED4, and then compared the global transcriptome of their low salinity acclimated cells and cells growing in normal seawater salinity. We found that MED4 could be acclimated in the lowest salinity of 25% and NATL1A could be acclimated in the lowest salinity of 28%. Measurement of the effective quantum yield of PSII photochemistry (Fv/Fm) indicated that both strains were stressed when growing in salinity lower than 34%. The transcriptomic response of NATL1A and MED4 were approximately different, with much more genes having changed transcript abundance in NATL1A than in MED4. To cope with low salinity, NATL1A downregulated the transcript of most genes involved in translation, ribosomal structure and biogenesis, while MED4 upregulated those genes. Moreover, low salinity acclimated NATL1A cells suppressed ATP-producing genes and induced the expression of photosynthesis related genes, while low salinity acclimated MED4 upregulated ATP-producing genes and downregulated photosynthesis related genes. These results indicate that the response to low salinity stress of different Prochlorococcus strains could be distinct. The study provided the first glimpse into the growing salinity range of Prochlorococcus cells and their global gene expression changes due to low salinity stress.
2022-02-02 | GSE195946 | GEO