92 5 Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology
Novel features of electron transfers are related to the way protons and elec
trons can be transported within and between cells. A considerable effort has yet
to be devoted to the production of hydrogen as an energy store [74–76]. Research
on microbial fuel cells is expected to develop dramatically [77–79]. It has now
been recognized that cells can make wires that conduct electricity, creating an
entirely new field for management and extraction of energy via living systems
[80–82]. Some cells make large syncytia, which requires management of the
genome DNA and energy sources (polyphosphate in particular) in a way that is
not yet understood [71]. The role of membranes is essential in building up and
maintaining the electrochemical potential of the cell via vectorial transport. In
the same way energy is stored in a variety of polymer compounds such as lipid
droplets, carbohydrate polymers, polyphosphates, and so on. This introduces a
specific link between energy and space, the role of which we now discuss.5.4.3 Managing Space
In the cell, the three dimensions of space play together in a concerted fashion.
The genetic program is stored by a molecule of DNA that can be considered as
linear in the way it maintains its coding capacity; membranes organize space in
two dimensions; finally the interior of the cell is three‐dimensional. In terms of
biosyntheses this has consequences that are seldom taken into account. Filling
up the cytoplasm with proteins as the cell grows requires an increase as the cube
of the cell’s size (if the cell is spherical, less when it is of another shape) while
placing proteins in the membrane would go as the square of the cell’s size. This
discrepancy introduces a considerable constraint on the length of the genome. It
cannot be too short, which implies that despite a selective tendency to stream
line the genome sequence because of the cost to maintain functional genes, there
is an opposite tendency to fill it in with extra DNA sequences. Amplification of
insertion sequences or similar structures and horizontal gene transfer can com
pensate for deletions. Overall insertions and deletions create an equilibrium that
results in an optimum length, where the DNA length is considerably longer than
that of the cell. Indeed, 4′,6‐diamidino‐2‐phenylindole (DAPI) staining shows
that the genome in itself occupies a significant proportion of the cell’s volume
[83], shaping it more like a three‐dimensional structure, via folding into a Peano
curve‐like space‐filling setup [84]. This constraint is likely to be important in the
gene flow that maintains a particular genome length [85].
Chromosome DNA folds can be classified into three categories [86]: short
range, of up to 16 kb (fitting with the local bias in codon usage [87]); medium
range, over 100–125 kb (fitting with old observations of supercoiled DNA loops
upon mild cell lysis [88]); and long range, over 600–800 kb (fitting with the size
of the shortest bacterial chromosomes and associated with macrodomains [89,
90]). In Eukarya, the problem of the various space scales has been solved by the
preservation of a nucleus accommodating the genome in a space much smaller in
general than the size of the cell and multiplying membranes (in particular the
endoplasmic reticulum) to couple protein synthesis with occupation of the cyto
plasmic space. Chromosome folding requirements appear to impose sequence
constraints that create ubiquitous 11 bp periodic patterns, the “class A flexible