Fig. 5 | Nature Communications

Fig. 5

From: Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance

Fig. 5

CRISPRi screening dissects the E. coli metabolic network. a Volcano plot of gene fitness in MOPS medium relative to −Log10P value from the two-tailed MWU test. Dashed lines represent the threshold (FDR = 0.05) for calling hits based on the screening score (see Methods). The size of the scatter is proportional to the 1/OD600 value of the relevant gene knockout reported with the Keio collection1. b GO enrichment analysis of auxotrophic genes identified by CRISPRi screening in MOPS medium. P values are derived from two-tailed Fisher exact test. c Comparison of gene fitness in MOPS medium with casamino acids (right) or a single carbon source (left) for E. coli. 78 genes responsible for amino acid biosynthesis are highlighted in green, whereas the five genes (trpABCDE) forming a branched pathway leading to tryptophan biosynthesis are in purple. The differences between fitness of amino acid biosynthesis genes and all other genes were quantified via the two-tailed MWU test (P, 10−10.0 with vs. 10−59.7 without casamino acid addition). d Schematic of E. coli amino acid biosynthetic network. Green and purple elements denote amino acid biosynthetic genes and tryptophan biosynthetic genes (trpABCDE), respectively, corresponding to those highlighted in (c)

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