5.5 Conclusion 97may start from a unique replication initiation locus [139]. This dissymmetry
implies that the error replication rates differ on each strand, with different proof
reading systems. Many proofreading processes exist, including those, such as the
ATP‐powered RecBCD nanomachine that takes care of double‐strand breaks in
E. coli [140].
Transcription operates with constraints similar to those of leading strand rep
lication. Following transcription, the protein biosynthetic machinery brings
together complexes composed of ribosomes, chaperones, and localization fac
tors into similar actions (begin, elongate, and end). It also interacts directly with
factors dedicated to disposal of protein fragments (generated during mistransla
tion, translation interruption, or premature termination) and more generally to
protein degradation [141]. The genetic code accommodates 20 amino acids plus
two variable ones, selenocysteine (coded for by UGA) and pyrrolysine (coded for
by UAG). Remarkably it seems that in some organisms, the genetic code can be
modulated via specific growth conditions [142] and that the UGA codon can be
reassigned to a particular amino acid, differing from tryptophan or selenocyst
eine [143]. This implies that the genome could be read at levels of information
much more elaborate than those understood until now. Nothing is known about
the corresponding gene organization in the genome, but this opens up consider
ably the possibilities of information management in SynBio constructs.
Many other functions must be considered in the making of macromolecules
and eventually implemented in SynBio constructs. Most deal with the fact that
the threadwire machinery that makes macromolecules cannot fold them readily
into their final proper three‐dimensional shape (discussed in [27] to account for
the hard time witnessed to succeed in genome transplantation) as well as in
maintenance of the designed shape.
Finally, regulation is another key informational process. It is the main subject
of most present SynBio experiments, many “BioBricks” being DNA segments
used to construct regulatory logical gates, with strong emphasis on similarity
with electronic circuits [144]. Some regulatory functions linked to sensing are
regulated by the widely spread sensor‐regulator two‐component systems [145],
where the channeling of information (separating channels is a challenge) has not
yet been explored. Mechanical sensing is also important during cell growth, as
well as when gases witness pressure changes [146]. Among the functions of
information transfer, the control of metabolic and development processes is
essential. Indeed, regulation lies at the core of the SynBio activities centered on
the genetic program, and the bulk of the work dealing with BioBricks and the like
aim at constructing sophisticated regulatory devices [147, 148]. This will not be
explored further here as regulation is the focus of the vast majority of SynBio‐
devoted work [149].
5.5 Conclusion
SynBio rests on the description of living organisms as separating a genetic
program from the machine that runs it. In general it is implicitly assumed that
it is possible to use extant organisms as reference chassis into which on may