To construct a synthetic cell we need to understand the rules that permit life. A central idea in modern biology is that in addition to the four entities making reality, matter, energy, space and time, a fifth one, information, plays a central role. As a consequence of this central importance of the management of information, the bacterial cell is organised as a Turing machine, where the machine, with its compartments defining an inside and an outside and its metabolism, reads and (...) expresses the genetic program carried by the genome. This highly abstract organisation is implemented using concrete objects and dynamics, and this is at the cost of repeated incompatibilities (frustration), which need to be sorted out by appropriate «patches». After describing the organisation of the genome into the paleome (sustaining and propagating life) and the cenome (permitting life in context), we describe some chemical hurdles that the cell as to cope with, ending with the specific case of the methionine salvage pathway. (shrink)

The three processes needed to create life, compartmentalization, metabolism, and information transfer (memory stored in nucleic acids and manipulation operated by proteins) are embedded in organized genome features. The core of life puts together growth and maintenance (which drives survival), while life in context explores and exploits specific niches. Analysis of gene persistence in a large number of genomes shows that the former constitutes the paleome, which recapitulates the three phases of the origin of life: metabolism of small molecules on (...) surfaces, substitution of surfaces by an RNA-world where transfer RNA played a central role, and invention of template mediated information transfer. Colonization of each niche is performed using an almost unlimited set of genes, forming the cenome. The agreement of the paleome structure with a consistent scenario for the origin of life is such that we may consider extant genomes as providing us with an archive of the origin rather than as a palimpsest where most of our past would be irremediably hidden. (shrink)