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Noise and robustness in the evolution of novel protein phenotypes

Periodic Reporting for period 2 - NoiseRobustEvo (Noise and robustness in the evolution of novel protein phenotypes)

Reporting period: 2019-04-01 to 2020-09-30

Living cells are constantly barraged by perturbations that originate within themselves. Especially abundant – far more than DNA mutations – are two kinds of such perturbations. The first is gene expression noise, pervasive stochastic variation of transcript and protein levels. The second is mistranslation noise, the misincorporation of amino acids by ribosomes during protein synthesis. Organisms and protein molecules can evolve robustness – the persistence of well-adapted phenotypes – to both kinds of noise. Theory predicts that noise and robustness can affect the adaptive evolution of new proteins, but we do not know whether they help or hinder adaptive evolution.
We hypothesize that noise and robustness can accelerate protein evolution both separately and jointly. To validate this hypothesis, we are evolving light-emitting fluorescent proteins towards new color phenotypes via directed laboratory evolution in E.coli. During evolution, we anipulate expression noise by driving FP expression from noisy or quiet promoters, and we manipulate mistranslation via host strains with low and high mistranslation rates. We manipulate protein robustness in three biologically important ways, chaperone overexpression, gene duplication, and stabilizing selection. We study how rapidly FPs evolve new colors, and analyze protein evolutionary dynamics through a combination of high-throughput sequencing, engineering of selected adaptive mutations, and data-driven modeling.

In our ongoing work, we discovered that stabilizing selection substantially accelerates adaptive evolution of a novel color phenotype and we could explain why it does so. During stabilizing selection, a large reservoir of cryptic genetic variants accumulate that have little effect on the old phenotype but that greatly accelerate evolution of the new phenotype. By reconstructing dozens of mutant genotypes and measuring their properties, we showed that these cryptic variants render otherwise inaccessible parts of an adaptive landscape accessible. Our discovery resolves a decades-old question in evolutionary genetics: Is cryptic variation important for successful Darwinian evolution, and if so, why?
Our project will show how a ubiquitous but poorly understood source of phenotypic variation affects protein innovation. It will also help engineers discover new protein functions. Moreover, our work will help establish FPs as a major platform to study protein evolutionary dynamics. By revealing noise as a new and crucial factor in protein evolution, our observations have the potential to revolutionize molecular evolution research, much like earlier studies of noise have revolutionized cell biology.