Ontology highlight
ABSTRACT:
PROVIDER: PRJNA673898 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere.
2015-03-03 | GSE66443 | GEO
Project description:Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere. Bacteria were grown in batch culture and sampled twice during the initial, rapid phase of exponential growth and twice during the phase of slower growth that followed.
2015-03-03 | E-GEOD-66443 | biostudies-arrayexpress
Project description:The marine teleost intestine plays a vital role in whole body salt and water homeostasis. Marine fish must drink seawater in order to rehydrate, and processing of that seawater throughout the gastrointestinal tract allows for the extraction of water from this highly hyperosmotic source. Although the molecular mechanisms of this process have been the subject of much investigation, numerous questions remain. Here, Gulf toadfish (Opsanus beta) were acclimated to normal seawater (35 ppt) of hypersaline seawater (60 ppt) and changes in the anterior intestine, posterior intestine, and intestinal fluid proteomes were investigated using a shotgun proteomics approach employing isobaric TMT tags.
2018-06-26 | PXD005923 | Pride
Project description:Marine phytoplankton produce ~109 tons of dimethylsulfoniopropionate (DMSP) per year, an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide (DMS). SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemoorganotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell’s unusual requirement for reduced sulfur. Here we report that Pelagibacter HTCC1062 produces the gas methanethiol (MeSH) and that simultaneously a second DMSP catabolic pathway, mediated by a DMSP lyase, shunts as much as 59% of DMSP uptake to DMS production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release DMS when the supply of DMSP exceeds cellular sulfur demands for biosynthesis. These findings suggest that DMSP supply and demand relationships can significantly control rates of oceanic DMS production.
2017-12-08 | PXD001717 | Pride
Project description:The soft coral Scleronephthya gracillimum is an azooxanthellate octocoral order Alcyonacea. In this study, stress responses to increased seawater temperature and marine acidification were investigated using a microarray. The S. gracillimum microarray was constructed. The S. gracillimum microarray was constructed after RNA-seq. Oligonucleotides were picked from UniGene of S. gracillimum and the clones were annotated using Blast.
2021-07-24 | GSE180633 | GEO
Project description:In this research we present a transcriptomics analysis of the physiological response of a marine calcifier, Strongylocentrotus purpuratus, to ocean acidification, a decline in ocean pH that results from the absorption of anthropogenic carbon dioxide (CO2). Larvae were raised from fertilization to prism stage in seawater with elevated CO2 conditions based upon IPCC emissions scenario B1 (540ppm CO2) and A1FI (1020ppm CO2).
2009-08-14 | GSE13777 | GEO
Project description:Low salinity is one of the main factors limiting the distribution and survival of marine species. As estuarine species, Crassostrea hongkongensis can live in relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 13550 up-regulation genes and 9914 down-regulation genes that may regulate osmotic stress in C. hongkongensis. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in structural molecule activity, intracellular,cytoplasm protein metabolism, biosynthesis,cell and transcription regulator activity according to GO annotation. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. hongkongensis transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates. Twelve oysters were exposed in low salinity (8‰) seawater and in optimal salinity (25‰) seawater,respectively. Gills from six oysters in each condition were balanced mixed respectively. The transcriptomes of two samples were generated by deep sequencing, using Illumina HiSeq2000
2014-10-01 | E-GEOD-51157 | biostudies-arrayexpress
Project description:Low salinity is one of the main factors limiting the distribution and survival of marine species. As estuarine species, Crassostrea hongkongensis can live in relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 13550 up-regulation genes and 9914 down-regulation genes that may regulate osmotic stress in C. hongkongensis. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in structural molecule activity, intracellular,cytoplasm protein metabolism, biosynthesis,cell and transcription regulator activity according to GO annotation. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. hongkongensis transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates.
2014-10-01 | GSE51157 | GEO
Project description:Strain N16961 was incubated with crab shell in artificial seawater media for 24 hours. cDNA from 1 ug RNA was labeled with Cy3 (planktonic bacteria) and Cy5 (crab attached bacteria).
2005-07-21 | E-SMDB-2238 | biostudies-arrayexpress