E-GEOD-50870 - A Serine Sensor for Multicellularity in a Bacterium

Released on 22 October 2013, last updated on 25 November 2013
Bacillus subtilis subsp. subtilis str. NCIB 3610
Samples (6)
Protocols (4)
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 UCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these UCN codons with AGC or AGU impaired biofilm formation and gene expression. Conversely, switching AGC or AGU to UCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosomes paused longer at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome pausing and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, ribosome pausing at serine codons may be exploited by other microbes in adapting to stationary phase. 4 samples for ribosome profiling and 2 samples for total mRNA profiling
Experiment types
RNA-seq of coding RNA, RNA-seq of non coding RNA 
Arvind R Subramaniam <asubram@fas.harvard.edu>, Aaron DeLoughery, Erin O'Shea, Niels Bradshaw, Richard Losick, Yun Chen, Yunrong Chai
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-50870.idf.txt
Sample and data relationshipE-GEOD-50870.sdrf.txt
Processed data (1)E-GEOD-50870.processed.1.zip