Fig. 4. Mapping complex genotype–phenotype relationships.

a | A gene–antibiotic network for three antibiotics (based on refs^54,119). Each node (circle) depicts a gene, whereas each edge indicates a negative (solid grey line), neutral (dashed grey line) or positive (solid red line) effect on fitness between the genes in the presence of antibiotics as determined by transposon-insertion sequencing (TIS). All three antibiotics — penicillin G (PeniG), vancomycin (Vanco) and daptomycin (Dapto) — affect cell wall integrity but TIS uncovers a wide variety of genes involved, many of which are not direct targets of the antibiotic. In this case, the unknown gene Q is likely to be involved in peptidoglycan synthesis/membrane integrity on the basis of the function of other genes with similar fitness profiles. b | By mutation of gene Q and construction of a transposon library in this mutant background, genetic interactions can be identified (based on concepts from ref.³³). In this case, the genes uncovered in the mutant background, as depicted in the gene interaction map (GIM), further support a role in peptidoglycan synthesis, that it may function in the cell membrane and that it may be controlled by a particular regulator. Additionally, in vivo TIS data with the mutant library performed in healthy mice and mice depleted of neutrophils (neut−) indicate that gene Q is needed to establish lung infection but is dispensable in the absence of neutrophils. Adapted from ref.⁵⁴, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).