Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-Seq of bacteriophage S-PM2d infecting Synechococcus spp. WH7803 at high light and low light treatments

ABSTRACT: The aim of this experiment is to identify genes in the bacteriophage S-PM2d that are deferentially expressed in response to light intensity during infection. We were interested in light since the host (Synechococcus) obtains all energy and carbon for growth from light, through photosynthesis. The amount of light entering the cell is therefore approximately proportional to the amount of energy that can be generated. Therefore we wanted to increase the amount of energy available for an infecting virus (S-PM2) and observe the physiological and transcriptional response of the virus. This is particularly interesting because the virus itself encodes genes involved in harvesting this light into energy.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Synechococcus phage S-PM2

SUBMITTER: David Scanlan

PROVIDER: E-MTAB-5840 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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

Dataset Information

RNA-Seq of bacteriophage S-PM2d infecting Synechococcus spp. WH7803 at high light and low light treatments

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