Synthetic biology of minimal living cells: primitive cell models and semi-synthetic cells

Abstract

This article summarizes a contribution presented at the ESF 2009 Synthetic Biology focused on the concept of the minimal requirement for life and on the issue of constructive (synthetic) approaches in biological research. The attempts to define minimal life within the framework of autopoietic theory are firstly described, and a short report on the development of autopoietic chemical systems based on fatty acid vesicles, which are relevant as primitive cell models is given. These studies can be used as a starting point for the construction of more complex systems, firstly being inspired by possible origins of life scenarioes (and therefore by considering primitive functions), then by considering an approach based on modern biomacromolecular-encoded functions. At this aim, semi-synthetic minimal cells are defined as those man-made vesicle-based systems that are composed of the minimal number of genes, proteins, biomolecules and which can be defined as living. Recent achievements on minimal sized semi-synthetic cells are then discussed, and the kind of information obtained is recognized as being distinctively derived by a constructive approach. Synthetic biology is therefore a fundamental tool for gaining basic knowledge about biosystems, and it should not be confined at all to the engineering side.

Keywords: Autopoiesis; Cell-free protein synthesis; Minimal cell size; Self-reproduction; Semi-synthetic minimal cells.

Fig. 1

Schematic drawing of an autopoietic cell. The autopoietic unit (in gray) is composed of a boundary formed by self-assembly of S, the boundary-forming compound. S, in turn, is formed from A, which is available to the autopoietic cell since it is present in the environment. A permeates in the cell, and it is transformed—by means of a metabolic network M, into S. S also decay to a waste product (Y), which does not take part in the autopoietic organization, and it is released into the environment. In order to be fully self-producing, the autopoietic cell must also produce (self-produce) the network M, at the expenses of precursors B and so producing the by products W. Overall, the autopoietic cell uses “nutrients” A and B, release waste products Y and W, and keeps its dynamic continuously out of equilibrium, conserving the organization of the “whole” despite the fact that parts are continuously synthesized and destroyed

Fig. 2

General schemes for the self-reproduction of supramolecular structures. The uptake of a suitable precursor P by the preformed self-assembled structure brings about the formation of two (or more) self-assembled structures (not necessarily of the same size). This mechanism has been studied for micelles (bottom, left), reverse micelles (bottom, centre), and vesicles (bottom, right; not drawn to scale)

Fig. 3

Semi-synthetic minimal cells are formed by entrapping cell-free kits inside liposomes (e.g., all molecular parts required to perform a certain function as protein expression, such as a gene, RNA polymerase, ribosomes, tRNA, aminoacyl-tRNA-synthase, energy recycling enzymes, and low molecular weight compounds such as amino acids, nucleotides triphosphates, cofactors, etc.). Different methods of liposome formation have been used, and a standard procedure is not yet available