Research

How did life originate from non-living matter? It is widely believed that simple biological molecules evolved into complex living systems about four billion years ago on the early Earth. To understand key processes during the origins and early evolution of life, we demonstrate how molecules could give rise to the development of biological systems in test tubes. For example, we find or construct self-replicating molecular systems, such as those based on RNA, and evolve them to uncover possible evolutionary transitions toward the emergence of life. In another approach, we combine molecular components to create and characterize protocell models. These attempts also contribute to technological developments in synthetic biology, evolutionary engineering, and artificial cells.

There are three ongoing projects:

Prebiotically accessible self-reproducing RNA

According to the RNA World hypothesis, the first genetic system before the emergence of life may have been based on RNA. To understand how such a system could form, we investigate the emergence, development, and evolution of simple, prebiotically accessible self-reproducing RNA molecules.

[Related publications]

1. Mizuuchi, R.*, Ichihashi, N. (2023). Minimal RNA self-reproduction discovered from a random pool of oligomers. Chemical Science, 14, 7656–7664.
2. Mizuuchi, R.*, Blokhuis, A., Vincent, L., Nghe, P., Lehman. N., and Baum, D. (2019). Mineral surfaces select for longer RNA molecules. Chemical Communications, 55, 2090–2093.
3. Mizuuchi, R.*, Lehman, N. (2019). Limited Sequence Diversity Within a Population Supports Prebiotic RNA Reproduction. Life, 9 (1), 20.
4. Smail, B.A., Clifton, B.E., Mizuuchi, R.*, Lehman, N. (2019). Spontaneous advent of genetic diversity in RNA populations through multiple recombination mechanisms. RNA, 25, 453–464.

Protocell models and artificial cells

We combine biological molecules to construct and characterize artificial cell models, for understanding the properties of primitive cells and using them in various applications such as evolution experiments (see below). These systems often contain an RNA genome and a cell-free translation system, which enable translation-coupled RNA genome replication inside the cell models. One example is a membrane-free cell model generated by liquid–liquid phase separation, in which RNA and proteins are enriched and function.

[Related publications]

1. Mizuuchi, R.*, Ichihashi, N. (2020). Translation-coupled RNA replication and parasitic replicators in membrane-free compartments. Chemical Communications, 56, 13453–13456.
2. Mizuuchi, R.*, Ichihashi, N.* (2021). Primitive compartmentalization for the sustainable replication of genetic molecules. Life, 11 (3), 191.

Darwinian evolution of a life-like (RNA-protein) replication system

How a simple molecular replication system could develop complexity by continuously expanding information and functions is a central issue in prebiotic evolution. To delineate a possible evolutionary pathway, we have developed an artificial RNA replication system and subjected it to evolution experiments. In the system, an RNA replicates using its encoded RNA replicase, during which mutations are introduced. So far, we have observed diversification, cooperation, parasitism, complexification (establishment of replication networks), and information integration. The simplicity of the replication system, compared with biological organisms, also allows us to examine evolutionary events with unprecedented resolution.。

[Related publications]

1. Ueda, K., Mizuuchi, R.*, Ichihashi, N.* (2023). Emergence of linkage between cooperative RNA replicators encoding replication and metabolic enzymes through experimental evolution. PLOS Genetics, 19 (8), e1010471.
2. Mizuuchi, R.*, Furubayashi, T., Ichihashi N.* (2022). Evolutionary transition from a single RNA replicator to a multiple replicator network. Nature Communications, 13, 1460.
3. Mizuuchi, R., Usui, K., Ichihashi, N. (2020). Structural transition of replicable RNAs during in vitro evolution with Qβ replicase. RNA, 26, 83–89.
4. Mizuuchi, R., Ichihashi, N. (2018). Sustainable replication and coevolution of cooperative RNAs in an artificial cell-like system. Nature Ecology & Evolution, 2, 1654–1660.
5. Mizuuchi, R., Ichihashi, N., Yomo, T. (2016). Adaptation and diversification of an RNA replication system under initiation- or termination-impaired translational conditions. ChemBioChem, 17 (13), 1229–1232.
6. Mizuuchi, R., Ichihashi, N., Usui, K., Kazuta, Y., Yomo, T. (2015). Adaptive Evolution of an Artificial RNA Genome to a Reduced Ribosome Environment. ACS Synthetic Biology, 4 (3), 292–298.