Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1224187 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32358100_1.fastq.gz | Fastqsanger.gz | |||
| SRR32358100_2.fastq.gz | Fastqsanger.gz | |||
| SRR32358101_1.fastq.gz | Fastqsanger.gz | |||
| SRR32358101_2.fastq.gz | Fastqsanger.gz | |||
| SRR32358102_1.fastq.gz | Fastqsanger.gz |
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Project description:Genome streamlining in bacteria evolving under high predation pressure
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Project description:In this study, we performed a global quantitative proteomic analysis under extreme temperatures, pH, hydrostatic pressure (HP) and salinity on an archaeal strain, Thermococcus eurythermalis A501. Here is the result of pressure adaptation: HP (40 MPa) tested under 85°C and 95°C, and the optimal culture condition (85°C, pH 7, 2.3% NaCl, 10 MPa) was used as the control.
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Project description:Molecular adaptation of Pseudomonas aeruginosa to protozoan predation
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Project description:Growth and transcriptional profiles of the barophilic methanarchaeon Methanocaldococcus jannaschii were studied at temperatures up to 98C and pressures up to 500 atm. Application of 500 atm of hyperbaric pressure shifted the optimal growth temperature upwards, and heat shock from 88C to 98C at 500 atm resulted in termination of growth. Pressure shock of M. jannaschii from 7.8 to 500 atm over 15-min, the first pressure upshift reported for a barophile, did not accelerate growth. Transcriptional profiles indicated a similar pressure response under growth and heat shock at 500 atm and pressure shock to 500 atm suggesting that the commonly affected genes are important for high-pressure adaptation. Factorial microarray design allowed de-convolution of the interacting effect of elevated pressure and heat shock on expression profiles, thus suggesting genes that may contribute to the organism’s survival in the turbulent in situ conditions of deep-sea hydrothermal vents. Keywords: stress response, time course, high pressure, heat shock, pressure shock
2007-04-05 | GSE4620 | GEO
Project description:Low temperature is the most wide-spread “hostile” environmental factor on earth while at the same time the most common condition for marine organisms. However, the unique adaptive mechanisms that enable the survival of marine microorganisms under low temperature are unclear. Since low temperature is always accompanied by high pressure and other adverse conditions in marine environment, here we studied the metabolic adaptation of a marine strain to prolonged low temperature under high pressure. The strain studied is a psychrotolerant Microbacterium sediminis isolated from deep sea sediment. By using 1H nuclear magnetic resonance (NMR)-based metabolomics approach, we detected the spectral data of polar extracts of the strain M. sediminis, and applied multivariate statistical analysis methods together with univariate analysis to analyze metabolic profiles associated to different conditions. The metabolic profiles of the M. sediminis strain cultivated under high pressure at low temperature were distinctly different from those cultivated under high pressure at normal temperature. We identified the differential metabolites which were responsible for distinguishing the metabolic profiles and compared their relative intensities between groups. We also compared the different adaptive responses of the strain at different growth stages to the prolonged low temperature under high pressure. We proposed that the low-temperature adapting process of the M. sediminis strain involves, 1) the regulation of osmotic pressure using amino acids as possible alternative osmolytes, and, 2) the strengthen of glycolysis and the maintenance of TCA cycle via amino acids anaplerotic reaction. We put forward that the main difference of adaptation to low temperature for the strain at different growth stages was related to energy metabolism. Our findings improved the understanding of the low-temperature adaptive mechanisms for marine microorganisms under high pressure on the metabolic level.
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Project description:Microbially influenced corrosion (MIC) poses a major threat to metal structures across various industries, resulting in substantial economic losses and environmental risks. As deep-sea exploration expands, understanding MIC under high hydrostatic pressure becomes increasingly critical. Microorganisms in these extreme environments undergo distinct structural and metabolic adaptations to survive and thrive. In this study, we employed a proteomic approach to examine the lifestyle and corrosive potential of two sulfate-reducing bacteria (SRB) species with different pressure optima under simulated depths ranging from the sea surface to 3000 meters. Species-specific corrosion mechanisms and unique proteomic signatures associated with pressure adaptation were identified, correlating with opposing trends in corrosion rates. Our findings emphasize the need to characterize microbial physiology in relation to environmental conditions to better predict corrosion risks in extreme deep-sea settings.
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Project description:Purpose: Protozoan predators affect the structure of bacterial communities, but investigations into how predation influences bacterial evolution and antagonistic behaviours are scarce. We performed a 20-day predator-prey evolution experiment on solid media to investigate the adaptive traits that arise in bacterial prey under continuous protozoan predation. Methods: Pseudomonas fluorescens SBW25 and a wild Acanthamoeba sp. isolate as a predator prey pair co-evolved for 20 days yielded both previously described (Wrinkly Spreader; WS) and novel colony morphotype (Wrinkly Fried Egg; WFE) isolates with conferred grazing resistance. These isolates were subjected to RNAseq profiling with and without predation to determine transcriptional changes contributing to grazing resistance. Results: For differential gene expression the WT SBW25 without predation was used as a baseline. For the WS condition, a total of 881 differentially expressed genes (DEGs) were identified, of which 424 were upregulated and 457 were downregulated. In the WFE condition, a total of 908 DEGs were identified, of which 475 were upregulated and 434 were downregulated. Among all DEGs, 335 upregulated and 313 downregulated genes were shared between the WS1 and WFE conditions Conclusions: Our findings suggest that protozoan predation can profoundly influence the course of genetic and phenotypic evolution in a short period of time. Together, the differential expression results suggest expression of features that would be expected to increase biofilm formation in WFE according to previous studies. However, increased expression of these traits may not lead to a stronger biofilm, but may still provide predation resistance. For example, fibrils may increase the effective profile size of a bacterial cell. Increased Fap-mediated biofilm formation also induces increased alginate synthesis in P. aeruginosa PA01, an exopolysaccharide that protects mucoid P. aeruginosa against macrophage killing. Interestingly, we found increased expression of alginate biosynthesis genes in both WFE and WS1 (algA, algF), suggesting alternate mechanisms leading to increased alginate production in these two strains.
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Project description:DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements (TEs) in eukaryotes. Numerous examples of cis-elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans-regulators of mCG leading to adaptation. Here, using genome-wide association studies, we identify CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 ALPHA (CDCA7α) as a trans-regulator of mCG in natural populations of Arabidopsis thaliana. CDCA7α and its paralog, CDCA7β, directly bind to the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. CDCA7α/β selectively regulates mCG and minimally impacts other DDM1-dependent processes such as non-CG methylation and histone variant deposition. We identify the cis-regulatory sequence modulating CDCA7α expression in natural populations and determining the degree of mCG and TE silencing. The geographic distribution of CDCA7α alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Altogether, our findings provide new insight into how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation.
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