Constructive Approaches for Understanding the Origin of Self-Replication and Evolution

Abstract

The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is the origin of life-specific functions such as the replication of genetic information, the reproduction of cellular structures, metabolism, and evolution. These functions require the coordination of many different kinds of biological molecules. A direct strategy to approach the second part of the mystery is the constructive approach, in which life-specific functions are recreated in a test tube from specific biological molecules. Using this approach, we are able to employ design principles to reproduce life-specific functions, and the knowledge gained through the reproduction process provides clues as to their origins. In this mini-review, we introduce recent insights gained using this approach, and propose important future directions for advancing our understanding of the origins of life.

Keywords: constructive approach; evolution; in vitro system; self-replication system.

Figure 1

Self-replication schemes. RNA and DNA are colored red and blue, respectively. A schematic of Spiegelman’s RNA system is shown in (A). The complimentary strand RNA (RNA (−)) is synthesized from the template RNA (RNA (+)) by an RNA replicase. The template RNA is then resynthesized from the complimentary strand by the replicase. (B) The ribozyme-based self-sustained sequence replication (3SR) system is shown. First, the template RNA (a ribozyme) catalyzes its own ligation to a DNA containing promoter sequence (1). Then, a DNA primer hybridizes to the 3′ terminus, and the complementary RNA is synthesized by a reverse transcriptase (2). Finally, the original template RNA is transcribed from the RNA/DNA hybrid by a DNA-dependent RNA polymerase (3). (C) A schematic of the strand displacement amplification (SDA) system is shown. Primer 1 first binds to the single-stranded template DNA. DNA polymerase then elongates both strands (1). Next, an endonuclease introduces a nick in one of the strands (2). DNA polymerase synthesizes a DNA strand from the nick, and displaces one of the strands, which then binds to Primer 2 (3). DNA polymerase then generates double-stranded DNA using Primer 2 and this DNA strand (4). Next, another endonuclease introduces a nick in the resulting double-stranded DNA (5). Finally, DNA polymerase reproduces the original single-stranded template DNA by synthesizing a strand starting from the nick (6). (D) The translation-coupled RNA replication (TcRR) system is shown. This system is composed of a template RNA that encodes an RNA replicase, along with all translation factors, tRNAs, ribosomes, NTPs, amino acids, and so on. The RNA replicase is translated internally, and it then replicates the original template RNA as in Spiegelman’s system (A).

Figure 2

The effect of compartmentalization on replication in the TcRR System. We measured the template RNA concentration for each round of the transfer experiments. Under bulk conditions without compartmentalization, the template RNA was not detected after 17 rounds of a transfer experiment (red line). Conversely, under compartmentalized conditions, RNA replication continued and then increased due to evolution (blue line). Only part of the result is shown here. Reproduced with permission from Nature Publishing Group [45].

Figure 3

Schematic drawing of the TcRR system under bulk or compartmentalized conditions. (A) Under bulk conditions, the replicases are shared among all the template RNA, and thus even a mutant template RNA that encodes inactive replicase can replicate using an active replicase translated from another template RNA. (B) Under compartmentalized conditions, each template RNA can use only the replicase translated from itself, and thus a mutant template RNA that encodes an inactive RNA replicase cannot replicate.

Figure 4

The evolutionary process of the template RNA in the TcRR system. (A) The template RNA sequences were analyzed over 32 rounds (R1 to R32) of a transfer experiment using the TcRR system. The Hamming distances of 91 major genotypes were calculated and projected on a two-dimensional landscape. The genotypes were classified into four major clusters (Clusters 1 to 4) and colored accordingly. The fitness of each genotype was estimated from the rate of change in its frequency and plotted on the z-axis. (B) Only the genotypes that constituted more than 1% of the population at each round were shown. The RNA population first diverged within Cluster 1 (R0 to R5). Three RNA genotypes that had higher fitness then appeared within Cluster 2 (arrowheads in R8). The RNA population then continued to diverge within Cluster 2 (R8 to R11). Subsequently, two genotypes that had much higher fitness appeared in Cluster 3 (R14, arrowheads). The RNA population again diverged within Cluster 3 (R14 to R20), and three new genotypes appeared in Cluster 4 (R23, arrowheads). Finally, the population diverged within Cluster 4 (R23 to R32). Reproduced with permission from Oxford Journals [52].