On Recursive Production and Evolvability of Cells: Catalytic Reaction Network Approach

Abstract

To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control mechanism. A cell consists of a huge number of chemical species that catalyze each other. Often the number of each molecule species is not so large, and accordingly the number fluctuations in each molecule species can be large. In the amidst of such diversity and large fluctuations, how can a cell make recursive production? On the other hand, a cell can change its state to evolve to a different type over a longer time span. How are reproduction and evolution compatible? We address these questions, based on several model studies with catalytic reaction network.In the present survey paper, we first formulate basic questions on the recursiveness and evolvability of a cell, and then state the standpoint of our research to answer the questions, that is termed as 'constructive biology'. Based on this standpoint, we present general strategy of modeling a cell as a chemical reaction network.At the first part we investigate of the origin of heredity in a cell, by noting that the molecules carrying heredity must be preserved well and control the behavior of a cell. We take a simpled model consisting of two mutually catalyzing molecule species, each of which has catalytically active and inactive types. One of the molecule species is synthesized slowly, and thus is a minority in population. Through the growth and division of this cell, it is shown to reach and remain in a state in which a active, minority molecules are preserved over generations, and control the cell behavior. This minority controlled state is achieved by preserving rare number fluctuations of molecules. The state gives rise to a selection pressure for mechanisms that ensure the transmission of the minority molecule. The minority molecule, thus, carries heredity, and is a candidate for "genetic information". Experimental confirmation of this minority control is also presented.Next, a protocell model consisting of a large number mutually catalyzing molecule species is studied, in order to investigate how chemical compositions are transferred recursively under replication errors. Depending on the numbers of molecules and species in a cell, and the path rate in the reaction network, three phases are found: fast switching state without recursive production, recursive production, and itinerancy between the above two states. At a recursive production state chemicals are found to form intermingled hypercycle network that consists of core hypercycle and peripheral network that influence each other. How this intermingled network supports the recursive production, and how minority in the core hypercycle gives rise to a switch to other recursive states at the itinerancy phase are elucidated. Evolution of this hypercycle network is also studied, to show the approach to recursive production of cells and switch to more efficient reproduction states. Finally, statistic...

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