Ontology highlight
ABSTRACT:
PROVIDER: PRJNA876835 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21463110_1.fastq.gz | Fastqsanger.gz | |||
| SRR21463110_2.fastq.gz | Fastqsanger.gz | |||
| SRR21463111_1.fastq.gz | Fastqsanger.gz | |||
| SRR21463111_2.fastq.gz | Fastqsanger.gz | |||
| SRR21463112_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 160 |
Similar Datasets
Project description:Marine bacterium capable of aerobic anoxygenic photosynthesis
| PRJNA16425 | ENA
Project description:Aerobic anoxygenic phototrophic bacteria (AAPs) of the Roseobacter group are abundant in the photic zone of the marine environment. Dinoroseobacter shibae, a typical representative, converts light into additional energy that enhances its survival under nutrient-depletion. AAPs produce cytotoxic singlet oxygenunder light exposition, but D. shibae developed mechanisms to counteract the lethal effects of illumination. Recent studies documented a pivotal role of extrachromosomal elements (ECRs) for the ecological fitness of roseobacters, and here we investigated their significance for the adaptation to specific environmental stress. D. shibae possessing five ECRs, i.e. three chromids and two plasmids, was starved for four weeks in the dark and light/dark cycles and the survival strategy was evaluated using transcriptomics. Few genes on the chromosome showed differential expression between non-starved and starved cells, in particular those with a role in oxidative stress response and photosynthesis. Extrachromosomal genes in contrast showed a systematic loss of transcriptional activity, especially in the dark starved cells. The observed silencing of gene expression was not due to plasmid loss, because all five ECRs were stably maintained. Exceptionally, the smallest 72-kb replicon was the least downregulated, and one region with genes for singlet oxygen stress response was even strongly activated under light/dark cycle. A ?72-kb curing mutant completely lost the ability to benefit from AAP under starvation, and we could thus document the essential role of the 72-kb chromid to light-stress adaptation. . Our data moreover suggest that the four ECRs of D. shibae without a vital function are transcriptionally silenced under starvation. Loop-design, two biological replicates of D. shibae DFL12T cultivated in artificial salt water medium with succinate as carbon source and 12/12 light-dark cycles. After reaching stationary phase the cells were starved for 4 weeks in the dark or under light-dark cycle.
2015-01-01 | E-GEOD-62869 | biostudies-arrayexpress
Project description:Transcriptional response of the photoheterotrophic marine bacterium D. shibea to changing light regimes. Second part of the study analysing the transition from photoheterotrophic light to heterotrophic dark growth. Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy gain in aquatic habitats, accounting for up to 5% of the surface ocean’s photosynthetic electron transport. The dominant AAP bacteria in marine communities belong to the Roseobacter clade. For this reason we used Dinoroseobacter shibae as a model organism to study the transcriptional response of AAP bacteria to changing light regimes. We used continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis in order to identify gene regulatory patterns after a change in illumination. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to cope with the formation of harmful singlet oxygen during photophosphorylation, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of electron transport chain components and upregulation of the transcriptional and translational apparatus. Furthermore, our data indicate that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after the switch from light to dark demonstrates that only few genes are directly regulated in response to light and other signals such as singlet oxygen concentration, electron flow, redox status and energy charge of the cell must be involved in the regulation of the processes accompanying AAP. Based on the transcriptome data first hypothesis about transcriptional control of AAP could be formulated. This study provides the first analysis of AAP on the level of transcriptome dynamics. Our data allow the formulation of testable hypotheses about the mechanisms involved in the regulation of this important biological process. Samples from light grown cells were used as a reference, 6 timepoints in the dark, biological replicates: 2
2010-12-03 | E-GEOD-25581 | biostudies-arrayexpress
Project description:Transcriptional response of the photoheterotrophic marine bacterium D. shibea to changing light regimes. First part of the study analysing the transition from heterotrophic dark to photoheterotrophic light growth. Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy gain in aquatic habitats, accounting for up to 5% of the surface ocean’s photosynthetic electron transport. The dominant AAP bacteria in marine communities belong to the Roseobacter clade. For this reason we used Dinoroseobacter shibae as a model organism to study the transcriptional response of AAP bacteria to changing light regimes. We used continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis in order to identify gene regulatory patterns after a change in illumination. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to cope with the formation of harmful singlet oxygen during photophosphorylation, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of electron transport chain components and upregulation of the transcriptional and translational apparatus. Furthermore, our data indicate that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after the switch from light to dark demonstrates that only few genes are directly regulated in response to light and other signals such as singlet oxygen concentration, electron flow, redox status and energy charge of the cell must be involved in the regulation of the processes accompanying AAP. Based on the transcriptome data first hypothesis about transcriptional control of AAP could be formulated. This study provides the first analysis of AAP on the level of transcriptome dynamics. Our data allow the formulation of testable hypotheses about the mechanisms involved in the regulation of this important biological process. Samples from dark grown cells were used as a reference, 6 timepoints in the light, biological replicates: 3 to 4
2010-12-03 | E-GEOD-25579 | biostudies-arrayexpress
Project description:Aerobic anoxygenic phototrophic bacteria (AAPs) of the Roseobacter group are abundant in the photic zone of the marine environment. Dinoroseobacter shibae, a typical representative, converts light into additional energy that enhances its survival under nutrient-depletion. AAPs produce cytotoxic singlet oxygenunder light exposition, but D. shibae developed mechanisms to counteract the lethal effects of illumination. Recent studies documented a pivotal role of extrachromosomal elements (ECRs) for the ecological fitness of roseobacters, and here we investigated their significance for the adaptation to specific environmental stress. D. shibae possessing five ECRs, i.e. three chromids and two plasmids, was starved for four weeks in the dark and light/dark cycles and the survival strategy was evaluated using transcriptomics. Few genes on the chromosome showed differential expression between non-starved and starved cells, in particular those with a role in oxidative stress response and photosynthesis. Extrachromosomal genes in contrast showed a systematic loss of transcriptional activity, especially in the dark starved cells. The observed silencing of gene expression was not due to plasmid loss, because all five ECRs were stably maintained. Exceptionally, the smallest 72-kb replicon was the least downregulated, and one region with genes for singlet oxygen stress response was even strongly activated under light/dark cycle. A ?72-kb curing mutant completely lost the ability to benefit from AAP under starvation, and we could thus document the essential role of the 72-kb chromid to light-stress adaptation. . Our data moreover suggest that the four ECRs of D. shibae without a vital function are transcriptionally silenced under starvation.
2015-01-01 | GSE62869 | GEO
Project description:Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge on the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark‑light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy null mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark‑light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light‑induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.
2023-10-12 | GSE245047 | GEO
Project description:Transcriptional response of the photoheterotrophic marine bacterium D. shibea to changing light regimes. Second part of the study analysing the transition from photoheterotrophic light to heterotrophic dark growth. Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy gain in aquatic habitats, accounting for up to 5% of the surface ocean’s photosynthetic electron transport. The dominant AAP bacteria in marine communities belong to the Roseobacter clade. For this reason we used Dinoroseobacter shibae as a model organism to study the transcriptional response of AAP bacteria to changing light regimes. We used continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis in order to identify gene regulatory patterns after a change in illumination. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to cope with the formation of harmful singlet oxygen during photophosphorylation, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of electron transport chain components and upregulation of the transcriptional and translational apparatus. Furthermore, our data indicate that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after the switch from light to dark demonstrates that only few genes are directly regulated in response to light and other signals such as singlet oxygen concentration, electron flow, redox status and energy charge of the cell must be involved in the regulation of the processes accompanying AAP. Based on the transcriptome data first hypothesis about transcriptional control of AAP could be formulated. This study provides the first analysis of AAP on the level of transcriptome dynamics. Our data allow the formulation of testable hypotheses about the mechanisms involved in the regulation of this important biological process.
2010-12-03 | GSE25581 | GEO