Ontology highlight
ABSTRACT:
PROVIDER: PRJNA919028 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22999326_1.fastq.gz | Fastqsanger.gz | |||
| SRR22999326_2.fastq.gz | Fastqsanger.gz | |||
| SRR22999327_1.fastq.gz | Fastqsanger.gz | |||
| SRR22999327_2.fastq.gz | Fastqsanger.gz | |||
| SRR22999328_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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
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.
2010-12-03 | GSE25579 | 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. 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:Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia
| PRJEB12152 | ENA
Project description:Marine bacterium capable of aerobic anoxygenic photosynthesis
| PRJNA16425 | ENA
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:The Gram-negative photoheterotrophic bacterium Dinoroseobacter shibae is a member of the high abundant marine Roseobacter group. In the ocean, OMVs have about the same abundance as bacteria, a distinct depth distribution, and contain DNA from a variety of marine bacterial taxa. In the present study, we determined the abundance, size, and ultrastructure of membrane vesicles of D. shibae and analysed the protein inventory of the soluble and membrane fractions of cells and vesicles in order to study the origin of OMV membranes and content. The proteomic analyses were complemented by fatty acid analyses.
2020-12-16 | PXD014351 | Pride
Project description:In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.
2024-02-01 | GSE253351 | GEO