Viral gain-of-function experiments uncover residues under diversifying selection in nature

Rohan Maddamsetti; Daniel T. Johnson; Stephanie J. Spielman; Katherine L. Petrie; Debora S. Marks; Justin R. Meyer

Typical laboratory strains of l infect Escherichia coli by binding to the outer membrane protein LamB 14 , but the phage rapidly evolves in the laboratory to exploit a different membrane protein, OmpF 3 . Since OmpF is not the usual E. coli receptor for l, these experiments are a proxy for the ability of the phage to switch hosts. The evolved gain-of-function phenotype in l, OmpF + , involves multiple non-synonymous mutations in the host-recognition gene J. Each OmpF + isolate had between 4 and 10 single nucleotide substitutions in J, and none had insertions or deletions (indels). 97% of the substitutions in 24 independently evolved OmpF + l phage occurred in the J protein 3 between residues 960-1132, which we call the 'specificity region' of J ( Figure 1A ).