Supplementary Materials

A bacterial global regulator forms a prion

Andy H. Yuan, Ann Hochschild

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S9
  • Captions for tables S1 and S2
  • Table S3
  • References
Table S1
Candidate bacterial prion proteins. All sequenced bacterial genomes available as of January 2013 were mined by PLAAC (10, 11) for proteins with prion-like amino acid composition. Proteins exhibiting an LLK score < 0 were discarded. All other proteins are binned by phylum (arranged alphabetically). Within each phylum, proteins are sorted by LLK score (descending). Additional information concerning PLAAC data analysis and output has been described in detail previously (10).
Table S2
RNA-seq analyses. The Expression Ratio (Blue:Pale) represents the Rockhoppernormalized RNA-seq counts of transcripts in "blue" reporter strain cells divided by the Rockhopper-normalized RNA-seq counts of transcripts in "pale" reporter strain cells. The Expression Ratio (+BCM:-BCM) represents the Rockhopper-normalized RNA-seq counts of transcripts in wild-type E. coli cells treated with the Rho-inhibitor bicyclomycin divided by the Rockhopper-normalized RNA-seq counts of transcripts in untreated wild-type E. coli cells. qValues reflect the statistical significance of observed changes in gene expression as determined by Rockhopper. Raw data from Peters et al., 2012 (16) corresponding to untreated (GSM1027911, GSM1027912) and bicyclomycintreated (GSM1027913, GSM1027914) wild-type E. coli cells were obtained from the Gene Expression Omnibus and analyzed by Rockhopper as two experiments each consisting of two biological replicates.