Extended Data Fig. 9: Activation of y-genes in biofilm.
From: Spatial transcriptome uncovers rich coordination of metabolism in E. coli K12 biofilm
Activation of y-genes in biofilm. (a) Ratio of y-genes in four spatial patterns as shown in Fig. 2j. Y-genes are labeled as dark grey while others kept light grey; pattern 1: 162 y-genes out of 962 genes; pattern 2: 586 y-genes out of 1,702 genes; pattern 3: 61 y-genes out of 184 genes; pattern 4: 304 y-genes out of 823 genes. (b) The spatial expression profiles of 10 representative y-genes with ascending spatial patterns (n = 5; red line and shaded area indicate mean ± std); blue dot is the expression level at the stationary phase of planktonic culture (n = 2, error bar: mean ± std). (c) Activation of sociality protein domains carried by y-genes in biofilm; the fold of activation of the associated y-genes in biofilm relative to planktonic culture are presented as circles; The colors encode cellular locations; Genes previously shown to be related to biofilm formation are highlighted as squares. (d) Occurrence of the activated sociality Pfam-A domains of (c) in prokaryotic genomes. Occurrence are counted based on the distribution of these Pfam-A domains in relevant phyla of bacteria and archaea. Red color indicates that a given domain is present in at least one genome of the relevant class. (e) and (f) Genomic neighborhoods between representative y-genes activated in biofilm and genes of known sociality functions, aligned with the phylogenetic tree of relevant bacteria. For (e), 1: Betaproteobacteria, 2: Alphaproteobacteria, 3: Gammaproteobacteria, 3.1: Aeromonadales, 3.2: Pseudomonadales, 3.3: Enterobacterales, 3.3.1: Enterobacteriaceae; For (f), 1: Firmicutes, 1.1: Clostridia, 1.2: Bacilli, 1.3: Lactobacillales, 2: Proteobacteria, 2.1: Alphaproteobacteria, 2.2: Gammaproteobacteria. Genomic neighborhoods are identified from STRING database according to gene interaction scores. The homologues of y-genes are shown in red and neighborhood genes with known sociality functions are shown in blue; The color bars indicate the degree of identity between homologues in relevant bacteria and in E. coli K-12 MG1655, as calculated by BLASTP. Note that the dgcN homologue in S. flexneri is a pseudogene due to a premature stop codon; and yfcC’ in (f) indicates a paralog of yfcC in (e) encoded by E. coli K12 BW25113.
