Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions
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ABSTRACT:
ORGANISM(S): Synechococcus elongatus PCC 7942 = FACHB-805
PROVIDER: GSE104204 | GEO | 2017/12/16
SECONDARY ACCESSION(S): PRJNA412026
REPOSITORIES: GEO
Similar Datasets
Project description:We used RNA sequencing to measure genome-wide gene expression in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the variation in light intensity seen on a Clear Day in nature, or the rapid changes in light intensity that accompany changes in shading We compare these gene expression dynamics to those of a culture grown under a Low Light condition that mimics the standard laboratory conditions used for study of cyanobacteria. Our analysis reveals that naturally relevant light conditions drastically modify gene expression dynamics in cyanobacteria Notably, the expression of circadian clock-controlled genes is responsive to changes in light intensity, showing modulated dynamics that can allow cyanobacteria to adapt their metabolism to changing environmental conditions
2017-12-16 | GSE104203 | GEO
Project description:We used ChIP sequencing to measure genome-wide binding of transcription factors in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the rapid changes in light intensity that accompany changes in shading. Our analysis reveals that rapid changes in light intensity modulate the binding of RNA polymerase (RNAP) upstream of genes in a way that correlates with changes in downstream gene expression, suggesting that changes in transcriptional regulation control light-responsive gene expression changes. Also, binding of the circadian clock-controlled transcription factor RpaA and the light-responsive transcription factor RpaB change upstream of genes in a manner correlating with RNAP enrichment and downstream gene expression. This suggests that changes in RpaA and RpaB binding upstream of genes regulate the light-responsive expression of genes in cyanobacteria.
2017-12-16 | GSE104202 | GEO
Project description:Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions
| PRJNA412026 | ENA
Project description:Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions [RNA-Seq]
| PRJNA412032 | ENA
Project description:Measurement of transcription factor binding in cyanobacteria grown under simluated natural light conditions [ChIP-Seq]
| PRJNA412031 | ENA
Project description:The whole-genome sequence of the endosymbiotic bacterium Azorhizobium caulinodans ORS571, which forms nitrogen-fixing nodules on the stems and roots of Sesbania rostrata, was recently determined. The sizes of the genome and symbiosis island are 5.4 Mb and 86.7 kb, respectively, and these sizes are the smallest among the sequenced rhizobia. In the present study, a whole-genome microarray of A. caulinodans was constructed, and transcriptomic analyses were performed on free-living cells grown in rich and minimal media and in bacteroids isolated from stem nodules. Transcriptional profiling showed that the genes involved in sulfur uptake and metabolism, acetone metabolism, and the biosynthesis of exopolysaccharide were highly expressed in bacteroids compared to the expression levels in free-living cells. Some mutants having Tn5 transposons within these genes with increased expression were obtained as nodule-deficient mutants in our previous study. A transcriptomic analysis was also performed on free-living cells grown in minimal medium supplemented with a flavonoid, naringenin, which is one of the most efficient inducers of A. caulinodans nod genes. Only 18 genes exhibited increased expression by the addition of naringenin, suggesting that the regulatory mechanism responding to the flavonoid could be simple in A. caulinodans. The combination of our genome-wide transcriptional profiling and our previous genome-wide mutagenesis study has revealed new aspects of nodule formation and maintenance.
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Project description:Foraging on flowers in low light at dusk and dawn comes at an additional cost for insect pollinators with diurnal vision. Nevertheless, some species are known to be frequently active at these times. To explore how early and under which light levels colonies of bumblebees, Bombus terrestris, initiate their foraging activity, we tracked foragers of different body sizes using RFID over 5 consecutive days during warm periods of the flowering season. Bees that left the colony at lower light levels and earlier in the day were larger in size. This result extends the evidence for alloethism in bumblebees and shows that foragers differ in their task specialization depending on body size. By leaving the colony earlier to find and exploit flowers in low light, larger-sized foragers are aided by their more sensitive eyes and can effectively increase their contributions to the colony's food influx. The decision to leave the colony early seems to be further facilitated by knowledge about profitable food resources in specific locations. We observed that experience accrued over many foraging flights determined whether a bee started foraging under lower light levels and earlier in the morning. Larger-sized bees were not more experienced than smaller-sized bees, confirming earlier observations of wide size ranges among active foragers. Overall, we found that most foragers left at higher light levels when they could see well and fly faster. Nevertheless, a small proportion of foragers left the colony shortly after the onset of dawn when light levels were below 10 lux. Our observations suggest that bumblebee colonies have the potential to balance the benefits of deploying large-sized or experienced foragers during dawn against the risks and costs of foraging under low light by regulating the onset of their activity at different stages of the colony's life cycle and in changing environmental conditions.
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