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SRX4347149: GSM3258875: R. lacicola strain Ta8, grown in constant dark. Replicate 4; Rhodoluna lacicola; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 15.6M spots, 793.4M bases, 588.8Mb downloads

Submitted by: NCBI (GEO)
Study: Light enhances growth in non-phototropic Actinobacteria (Rhodoluna lacicola strain Ta8)
show Abstracthide Abstract
Light is a source of energy and an environmental cue that is available in excess in most surface environments. In prokaryotic systems, conversion of light to energy by photoautotrophs and photoheterotrophs is well understood, but the conversion of light to information and the cellular response to that information has been characterized in only a few species. Our goal was to explore the response of freshwater Actinobacteria, which are ubiquitous in illuminated aquatic environments, to light. We found that Actinobacteria without functional photosystems grow faster in the light, likely because sugar transport and metabolism are upregulated in the light, while protein synthesis is upregulated in the dark. Based on the action spectrum of the growth effect, and comparisons of the genomes of three Actinobacteria with this growth rate phenotype, we propose that the photosensor in these strains is a putative CryB-type cryptochrome. The ability to sense light and upregulate carbohydrate transport during the day could allow these cells to coordinate their time of maximum organic carbon uptake with the time of maximum organic carbon release by primary producers. Overall design: Two bacterial strains (Rhodoluna lacicola and Aurantimicrobium sp. strain MWH-Mo1) grown in constant light or constant darkness until late exponential phase; 4 replicates each
Sample: R. lacicola strain Ta8, grown in constant dark. Replicate 4
SAMN09622493 • SRS3507001 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNA was extracted using protocols modified from the Qiagen RNAprotect Bacteria Reagent Handbook. The ethanol-precipitated, rRNA-depleted RNA pellet was resuspended in 18 µL of the Fragment, Prime, Finish Mix from Illumina's TruSeq Stranded mRNA LT product (RS-122-2101). RNA was fragmented for 1 min. at 94°C. Subsequently, cDNA copies of the RNA were synthesized using SuperScript II Reverse Trancriptase (Invitrogen 18064022) and double-stranded cDNA was purified with Agencourt AMPure XP beads (Beckman Coulter A63880) following Illumina's TruSeq protocol (RS-122-9004DOC). The 3' ends of the cDNA were adenylated, indexing adapters were ligated onto the ends, then the cDNA was amplified by PCR using primers that anneal to the ends of the adapters. The Pippin Blue DNA size selection system was used to select for fragments <500 bp.
Experiment attributes:
GEO Accession: GSM3258875
Links:
Runs: 1 run, 15.6M spots, 793.4M bases, 588.8Mb
Run# of Spots# of BasesSizePublished
SRR747766615,556,853793.4M588.8Mb2018-07-08

ID:
5902897

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