Royal Road functions in Evolutionary Computations and modular organization of a gene: applications to directed and molecular evolution

Abstract

Modular organization of a gene, RNA and polypeptides attracts much attention in recent decades. Modularity in gene regulatory regions is crucial for our understanding of gene functioning and evolution. In the vast area of Evolutionary Computations, inspired by the ideas and concepts from evolutionary biology, a special attention was paid to the theoretical analysis of the evolutionary search efficacy. It was the Building block hypothesis, that laid the foundation for this area. On the way to further develop the theory, Royal Road functions (RRFs) were introduced and comprehensively studied.Here we are considering some case‐studies of the modular gene regulatory regions which could be treated as RRF implementations in directed (in vitro) molecular evolution. The essence is that we can treat the modules as the “building blocks”. The case examples are the bacterial promoter rrnP1 (ribosomal RNA operon promoter) and the hybrid synthetic yeast promoters with tandem copies of the upstream activation sequences (Hal Alper's lab).The theoretical considerations and our computational experiments (comparing with test‐tube evolution) demonstrate that the fitness trajectory for individual populations of the evolving macromolecules is not a smooth curve, but instead follows a step‐function (also known as “punctuated equilibria”). In the molecular evolution, the individuals in the molecular population spreads (via reproduction and mutation) over the neutral network of isofitness genotypes until one of them discovers a connection to a neutral network of higher fitness. The fraction of individuals on this network then grows rapidly, the new subset of individuals spreads again over the newly discovered neutral network, until one of them discovers a connection to a neutral network of even higher fitness, etc.Using analytical tools from statistical mechanics, dynamical systems theory, and mathematical population genetics, van Nimwegen and co‐authors developed a detailed and quantitative description of the search dynamics for the RRF class of problems that exhibit such stepwise (or epochal) evolution. Our aim is to bridge evolutionary computations from benchmark cases, such as RRF, which are well‐understood theoretically, to biological cases, which can serve as a basis for more efficient directed molecular evolution in the test tube and for understanding the mechanisms of biological evolution at the level of gene regulatory sequences. Namely, we will describe how the key results from RRFs area fit to the real problems of the theory of the directed evolution of the prokaryotic and yeast promoters. Particularly we will discuss the efficacy of some methods of directed evolution based on homologous recombination.Several approaches to improve and analyze bacterial and yeast promoters via directed evolution have been undertaken by experimentalists. While there is still some gap between the gene models in this presentation and real macromolecular evolution, we hope to have outlined the directions that can be taken for the computational work to provide a stronger theoretical basis for directing and analyzing experiments.Support or Funding InformationThe research was supported by RSF (project No. 17‐18‐01536).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.