88 5 Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology
However, the local stability and relevance of retained pathways is not optimized
in terms of what would be a human engineering design. This implies that optimi
zation – in terms of sparing energy and matter – will be at the core of next‐decade
metabolic engineering. To describe this logic would ask for a whole textbook,
and we will just enumerate here some of the rules that are beginning to emerge.
As the material support of the genetic program, DNA synthesis from nucleotides
required for replication of the genome will be described in some details.
The atoms of life are not random: carbon, hydrogen, nitrogen, and oxygen
compose living organisms because they are prone to combine via chains of cova
lent bonds that are stable at the temperature of the Earth’s surface; heavier ele
ments would not retain this property in general. Sulfur (together with iron) is
added to the list because of constraints well understood in scenarios of the origin
of life [34]. This atom is also a remarkably versatile support for electron transfers.
It exists in biological compounds in redox states going from −2 to +6, and this
useful property made that it has been retained in the course of evolution [35].
Phosphorus is unique when combined to oxygen, as phosphate bonds are prone
to hydrolyze (hence easy to disrupt in water), yet metastable (hydrolysis gener
ally requires a large activation energy). This property, which allows phosphate
compounds to store energy, is the reason phosphorus belongs to the core atoms
of life on Earth [36]. This constraint is essential to remember when looking for
xenologous BioBricks meant to construct genetic programs for xenobiology. The
role of phosphates provides us with a strong argument in favor of the engineering
stance. Had the way engineers think be favored, arsenic would never have been
considered as a substitute for phosphorus [37].
Phosphorus is a core component of nucleic acids, enabling a specific metabolic
driving force associated with hydrolysis of pyrophosphate (polymerization of
nucleotides is reversible; therefore going forward requires an irreversible step).
Furthermore, the organization of phosphate metabolism drives the nucleotide
composition of the genome in a way that is not still completely understood.
Indeed, deoxyribonucleotides are essentially synthesized from the ribonucleo
side diphosphates, not triphosphates. This constraint is likely derived from the
selection pressure that uses a metabolism developed in the three‐dimensional
environment, for synthesis of a linear molecule. This has a remarkable conse
quence for pyrimidines, as their anabolic pathway produces uridine diphosphate
(UDP), but not cytidine diphosphate (CDP). This should lead to deoxyuridine
diphosphate (dUDP) and then deoxyuridine triphosphate (dUTP), while input of
U in DNA must be avoided at all costs via a complex set of pathways. Missing
CDP would require an indirect process to make deoxycytidine diphosphate
(dCDP) and then deoxycytidine triphosphate (dCTP) [38] (Figure 5.3). The con
sequence of this imbalance is that, in most cases, the genetic program tends to
be progressively enriched in A+T nucleotides [39, 40]. The degradosome (with
its exosome counterpart in Eukarya) is the machinery that resolves this hurdle.
It allows buffering and equilibration of nucleic acids composition via degrada
tion of RNAs by phosphorolysis (directly producing the much wanted nucleo
side diphosphates (NDPs), in particular CDP, that are the precursors required
for DNA replication) while coupling the fluxes of nucleotides with energy
resources [38, 39, 41]. Furthermore, the physical relationship between phosphate