Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature

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

By comparing J among OmpF + and OmpFλ, Meyer et al. (2012) suggested that the OmpF + innovation required four mutations: one at residue 1012, two in the codon for residue 1107, and a fourth mutation somewhere between residues 990 to 1000, but these criteria were not directly tested. Here, our first step was to test this prediction by determining which combinations of J mutations facilitate the gain-of-function. Our second step was to determine whether the identified sites also evolve similarly in nature. For our final step, we tested whether the identified sites affect the evolutionary trajectory of the virus by examining whether they are associated with diversification. This last step was motivated by an observation in our alignment of J homologs: indels at residues 1012 and 1107 change the amino acid sequence of J and seem to define distinct J lineages. Since a signature of adaptive diversification is the birth of new clades (Herron and Doebeli 2013) , we reasoned that if indels at residues 1012 and 1107 cause adaptive diversification through host-shifts, then they should trigger the birth of the clades observed in the J alignment. If true, then the indels should occur on long, diverging branches on the J phylogeny (Rozen et al. 2005) . Indeed, this prediction was borne out in a phylogenetic analysis of the J homologs.