What can we learn from the construction of in vitro replication systems?

Abstract

Replication is a central function of living organisms. Several types of replication systems have been constructed in vitro from various molecules, including peptides, DNA, RNA, and proteins. In this review, I summarize the progress in the construction of replication systems over the past few decades and discuss what we can learn from their construction. I introduce various types of replication systems, supporting the feasibility of the spontaneous appearance of replication early in Earth's history. In the latter part of the review, I focus on parasitic replicators, one of the largest obstacles for sustainable replication. Compartmentalization is discussed as a possible solution.

Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology

“…Replication and propagation of genetic material is a key feature of life and is distributed among all living systems, and a robust in vitro implementation is crucial in particular for efforts in bottom-up construction of synthetic cells. While self-replicating systems including autocatalytic peptides, ribozyme replication, or RNA replicators have been established in the past (Ichihashi, 2019), it is crucial to develop a DNA replication system with regard to a transcription-translation based synthetic cell. Here we will focus on efforts to reconstitute DNA replication processes using cell-free TX-TL.…”

“…This parasitic DNA may eventually out-compete the original DNA template, if no selection pressure is applied. Compartmentalization, as discussed above in section 3.3, may be a method to address this challenge, as discussed in Ichihashi (2019). Furthermore, implementation of a stable, continuous platform for in vitro DNA replication would enable the study of the evolutionary dynamics of molecular replicators, as the system is well-defined, simple, tunable, and does not rely on life-sustaining processes.…”

Hydrophobic-cationic peptides enhance RNA polymerase ribozyme activity by accretion

“…Indeed, compartmentalization or spatial confinement are seen as particularly important for the emergence of genetic self-replication and Darwinian evolution, as otherwise genetic kin selection cannot occur and a replication system becomes vulnerable to be overrun by replication parasites. 1,2 In all modern organisms, cell membranes made of phospholipids and, to some extent, polypeptide scaffolds and demixing phases maintain the spatial organization and integration of the complex macromolecular systems. However, how in what form such organizing principles emerged on the prebiotic earth and what molecules/structures achieved accumulation of functional biopolymers has remained elusive.…”

Structural transition of replicable RNAs during in vitro evolution with Qβ replicase

“…Single-stranded RNA (ssRNA), one of the possible genetic information carriers, is used as a genomic molecule in some viruses and also experimental models of primitive life-forms in the hypothetical RNA or RNA-protein world (Higgs and Lehman 2015;Joyce and Szostak 2018). The synthesis and evolution of such experimental models provide important insights into the early evolution of life (Szostak et al 2001;Ichihashi 2019).…”