Emergent and Convergent Features in the Laboratory Evolution of Polymerase Ribozymes

In modern biology, molecular heredity is established by polymerase proteins that copy genetic information encoded in the sequence of nucleic acids. Prior to the emergence of coded protein synthesis, this role may have been filled by RNA polymerase ribozymes. Although such enzymes can no longer be found in extant life, ribozymes first evolved from random sequence populations have been progressively engineered in the laboratory to function as general RNA-dependent RNA polymerases. Polymerase ribozymes discovered in the past ten years can catalyze hundreds of sequential RNA synthesis reactions, match the complexity and catalytic sophistication of biological RNA enzymes, and employ many of the same strategies used by polymerase proteins to copy nucleic acids. This review describes the approaches to directed in vitro evolution that have led to the discovery of RNA enzymes that copy RNA molecules processively and accurately, and surveys how laboratory evolution has shaped biochemical and structural adaptations in these enzymes. The review then considers the challenges and opportunities that remain in the effort to propagate and evolve RNA genes with RNA catalysts alone.