Synthetic Biology Parts, Devices and Applications

86 5 Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology

worn‐out components. The relationship between the machine and the program

is central to this essential interaction. This situation is also common in contem­

porary computers, which remember our past actions and do not behave today as

they did some time ago, improving their adaptation to our wishes as time elapses.

In cells, this corresponds to exploiting an information that is not directly present

in the genes, but, rather, to a contextual information present in the way genes are

placed (and sometimes tagged by specific biochemical processes) in the genome

and its disposition within the cell as well as in the ultimate matter making the

genome. We note in passing that the transplantation founding experiments tells

us something more in terms of functions. It uncovers the first hidden functional

constraint on the genome structure: the chromosome needs to be compacted to

fit a small volume, and this is why (Figure 5.2) the transplantation experiment

requires as a first step the making of a syncytium to accommodate a decondensed

DNA molecule [27].

5.4 Helper Functions

For life to keep going and to develop into a descent, a chore of helper functions

is needed. These functions operate at different levels. They are organized along

hierarchies that are segmented (like organs in an animal body) or branched

Mycoplasma capricolum Mycoplasma mycoides

Final chassis = donor’s

Receiving chassis

Chassis of the donor

Replication

Reproduction

Chromosome of the host Chromosome of the donor

Tr ansplant

ation

PEG fusion

Transplanted DNA

condensation

Host DNA

degradation

DNA decondensation

Tr ansplanted DNA-

directed growth

Cell lysis

Chassis of the host

Figure 5.2 Replication of the program, reproduction of the chassis. The sequence of the

ycoplasma mycoides DNA transplanted into ycoplasma capricolum is identical to that at the

end of the experiment. Transplantation has triggered degradation of the. capricolum

DNA, while the DNA of. mycoides replicates and dilutes out the component of the initial

host. At the end of the experiment, the components of the cells are identical to those of

. mycoides, not to those of the recipient. capricolum.