Species-specific transcriptomic network inference of interspecies interactions
Ontology highlight
ABSTRACT:
ORGANISM(S): Thermosynechococcus vestitus BP-1 Meiothermus ruber
PROVIDER: GSE113134 | GEO | 2018/04/14
REPOSITORIES: GEO
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Project description:Cyanobacterium with co-occuring heterotroph Metagenomic assembly
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Project description:Previous molecular and mechanistic studies have identified several principles of prokaryotic transcription, but less is known about the global transcriptional architecture of bacterial genomes. Here we perform a comprehensive study of a cyanobacterial transcriptome, that of Synechococcus elongatus PCC 7942, generated by combining three high-resolution data sets: RNA sequencing, tiling expression microarrays, and RNA polymerase chromatin immunoprecipitation (ChIP) sequencing. We report absolute transcript levels, operon identification, and high-resolution mapping of 5' and 3' ends of transcripts. We identify several interesting features at promoters, within transcripts and in terminators relating to transcription initiation, elongation, and termination. Furthermore, we identify many putative non-coding transcripts. We provide a global analysis of a cyanobacterial transcriptome. Our results uncover insights that reinforce and extend the current views of bacterial transcription. RNA Sequencing of the cyanobacterium Synechococcus elongatus PCC 7942 RNA polymerase ChIP Sequencing of the cyanobacterium Synechococcus elongatus PCC 7942 Tiling Microarray of the cyanobacterium Synechococcus elongatus PCC 7942
2011-05-16 | E-GEOD-29264 | biostudies-arrayexpress
Project description:The advent of high-throughput 'omics approaches coupled with computational analyses to reconstruct individual genomes from metagenomes provides a basis for species-resolved functional studies. Here, a mutual information approach was applied to build a gene association network of a commensal consortium, in which a unicellular cyanobacterium Thermosynechococcus elongatus BP1 supported the heterotrophic growth of Meiothermus ruber strain A. Specifically, we used the context likelihood of relatedness (CLR) algorithm to generate a gene association network from 25 transcriptomic datasets representing distinct growth conditions. The resulting interspecies network revealed a number of linkages between genes in each species. While many of the linkages were supported by the existing knowledge of phototroph-heterotroph interactions and the metabolism of these two species several new interactions were inferred as well. These include linkages between amino acid synthesis and uptake genes, as well as carbohydrate and vitamin metabolism, terpenoid metabolism and cell adhesion genes. Further topological examination and functional analysis of specific gene associations suggested that the interactions are likely to center around the exchange of energetically costly metabolites between T. elongatus and M. ruber. Both the approach and conclusions derived from this work are widely applicable to microbial communities for identification of the interactions between species and characterization of community functioning as a whole.
| S-EPMC6052077 | biostudies-literature
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, most genes show rhythmic expression controlled by the Kai-based clock under continuous light conditions (LL). We found that rpoD6-null mutants impaired expression of clock-controlled genes peaking at hours 8-10 in LL, while sasA-null or rpaA-null mutants each arrested the expression profiles at subjective dawn. Time-course data (0-24 h) of wild type (WT), rpoD6-null, sasA-null and rpaA-null S. elongatus PCC 7942 strains analyzed under continuous light (LL) conditions after two 12h:12h light:dark (LD) cycles using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing 2,515 predicted protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also for the almost homologous strain, S. elongatus PCC 7942.
2012-03-01 | E-GEOD-28430 | biostudies-arrayexpress
Project description:Species-specific transcriptomic network inference of interspecies interactions
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Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression in kaiA-overexpressor (Ptrc::[GTG]kaiA) strains under LL. KaiC has been proposed to globally activate gene expression, our analysis revealed that dawn expressing genes were downregulated by kaiA-overexpression, such that the clock was arrested at subjective dawn. IPTG-inducible kaiA-overexpressor (oxA) S. elongatus PCC 7942 strains were analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: a single experiment in oxA under LL in the presence or absence of an inducer, IPTG, from hour 24 to 48 in LL timecourse data (24~48 hours under continuous light) from Synechococcus elongatus PCC 7942 (inducible kaiA-overexpressor) strains
2013-12-31 | E-GEOD-47015 | biostudies-arrayexpress
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression in the kaiCEE mutant strains in which the KaiC phosphorylation cycling is abolished under LL.. In the kaiCEE mutant strain more than 23% of transcripts significantly oscillated with a period of about 48 h. 409 cyclic genes were shared with the wild type strains. kaiCEE mutant strain was analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: a single experiment in kaiCEE mutant under LL from hour 8 to 96 in LL timecourse data (8~96 hours under continuous light) from Synechococcus elongatus PCC 7942 (kaiCEE mutant) strains
2013-11-28 | E-GEOD-48901 | biostudies-arrayexpress
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, most of genes are downregulated in the dark, while 10% of genes are upregulated. Here, we employed high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild type and kaiABC-null strains under continuous dark (DD) conditions. We found that expression profile of a subset of genes on the genome in DD was dramatically affected by kaiABC-nullification, and the magnitude of dark-induction was dependent on time when cells were transferred from light to DD Keywords: timecourse data (0-12 h) under continuous darkness after dark:light cycles from Synechococcus elongatus PCC 7942 wild type and kaiABC-null strains Wild type (WT) and kaiABC-null (DkaiABC) S. elongatus PCC 7942 strains were analyzed under continuous dark (DD) conditions after two 12h:12h light:dark (LD) cycles using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: Two independent experiments in WT and Dkai strains under DD (hours 0, 0.5, 1, 2, 4, 8 and 12).
2011-09-29 | E-GEOD-22468 | biostudies-arrayexpress
Project description:Here, we treated the model cyanobacterium Synechococcus elongatus PCC7942 with streptomycin, which selectively binds to bacterial ribosomes, at a concentration of 50 µg/mL and performed transcriptome analysis using RNA sequencing. In addition to antibiotic stress, we treated salt stress (0.4 M NaCl) and performed RNA sequencing analysis.
2023-05-17 | GSE225426 | GEO
Project description:In the unicellular cyanobacteriuIn the cyanobacterium, Synechococcus elongatus PCC 7942, most genes show rhythmic expression controlled by the Kai-based clock under continuous light conditions (LL). Overexpression of clpX led to a decrease in kaiBC promoter activity, disruption of circadian rhythm, and eventually cell death. We found that overexpression of clpX upregulated mRNA levels of ribosomal protein subunits, after which expression of other genes containing the clock genes was decreased. Wild type (WT) and inducible clpX-overexpressor (ox-clpX) S. elongatus PCC 7942 strains were analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: WT at hours 16 in LL (IPTG-free): WT under LL 20 in LL (addition of 100 µM IPTG for 4 hours): ox-clpX cells at hours 16 in LL (IPTG-free): ox-clpX cells at hours 20 in LL (addition of 100 µM IPTG for 4 hours)
2013-07-31 | E-GEOD-42542 | biostudies-arrayexpress