Subramaniam et al. 2013 (PRJNA219205)

General Details

Title A Serine Sensor for Multicellularity in a Bacterium
Organism
Number of Samples 4
Release Date 2013/09/13 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP029937
ENA SRP029937
GEO
BioProject PRJNA219205

Publication

Title
Authors Subramaniam AR,Deloughery A,Bradshaw N,Chen Y,O'Shea E,Losick R,Chai Y
Journal eLife
Publication Date 2013 Dec 17
Abstract We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four TCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these TCN codons with AGC or AGT impaired biofilm formation and gene expression. Conversely, switching AGC or AGT to TCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosome density was higher at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome occupancy and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, reduced translation speed at serine codons may be exploited by other microbes in adapting to stationary phase. DOI: http://dx.doi.org/10.7554/eLife.01501.001.
PMC PMC3862929
PMID 24347549
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR987018 PRJNA219205 Bacillus subtilis Ribo-Seq
SRR987020 PRJNA219205 Bacillus subtilis Ribo-Seq
SRR987022 PRJNA219205 Bacillus subtilis Ribo-Seq
SRR987023 PRJNA219205 Bacillus subtilis Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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