Evolution of new nonantibody proteins via iterative somatic hypermutation

B lymphocytes use somatic hypermutation (SHM) to optimize immunoglobulins. Although SHIM can rescue single point mutations deliberately introduced into nonimmunoglobulin genes, such experiments do not show whether SHIM can efficiently evolve challenging novel phenotypes requiring multiple unforeseeable mutations in nonantibody proteins. We have now iterated SHIM over 23 rounds of fluorescence-activated cell sorting to create monomeric red fluorescent proteins with increased photostability and far-red emissions (e.g., 649 nm), surpassing the best efforts of structure-based design. SHIM offers a strategy to evolve nonantibody proteins with desirable properties for which a high-throughput selection or viable single-cell screen can be devised.