12
| December 2010 | Realising European potential in synthetic biology
EASAC
characterisation of
Mycoplasma pneumoniae (footnote
10) as a potential chassis for importing novel biological
functions through synthetic biology may bring new
therapeutic applications within range.
There is a rapidly growing database of synthetic
building blocks (DNA sequences of defi ned structure
and function). Signifi cant impetus in this area has been
provided by the Massachusetts Institute of Technology
(MIT) initiative to develop a standard registry of biological
parts (BioBricks
12
) and to host an international student
competition (International Genetically Engineered
Machine Competition, iGEM), where participants design
new systems based on BioBricks.
The research area of minimal genomes may lead to many
new utilities. One application currently being pursued
is the design of novel microbes to produce hydrogen or
other biofuels
13
. Other, still limited, experimental data
discussed in the Berlin meeting (Appendix 1) show that
some reduced genomes are more productive in certain
respects (for example amino-acid synthesis), potentially
supporting various other applications in industrial
production.
5.2
Orthogonal biosystems: expanding the
genetic code
As an alternative approach, new properties of cells
might be engineered to expand information storage
by adding coding capacity—for example, by building a
parallel protein translation capability within the cell. The
strategy associated with orthogonality aims to modify
subsystems without causing signifi cant disturbance
elsewhere. Several routes have been proposed for
engineering the genetic code to incorporate artifi cial
amino acids. One approach, pioneered in the USA
and UK over the past decade, is to create ribosomes
(nucleic-acid-dependent amino-acid polymerases)
with expanded chemical scope to act as novel cellular
translation systems able to synthesise unnatural proteins.
Control over macromolecular interactions exerted by
this parallel modular synthesis requires orthogonal
ribosome/messenger RNA (mRNA) pairs (the latter
generated by the unique aminoacylation of transfer
RNA (tRNA) with unnatural monomers). The artifi cial
proteins can be synthesised with high effi ciency (Wang
et al. 2007), bringing various applications in vivo within
range. For example, it will be possible to incorporate
specifi c functionality in order to study the topology of
protein interactions in systems that have been hard to
characterise hitherto (within biological membranes)
and to encode specifi c post-translational modifi cations,
creating homogenous protein therapeutics (such as
polyethylene glycol-derivatised proteins to improve
pharmacokinetics)
14
.
An alternative and complementary approach is based
on propagating in vivo additional types of nucleic acids
(xeno-nucleic acids, XNA), whose chemical backbone
differs from deoxyribose and ribose (Herdewijn and
Marliere 2009; Marliere 2009). XNA building blocks
would not be found in nature but can be supplied
exogenously to cells that would also have to be equipped
with the additional, appropriate, enzyme machinery for
replicating and expressing XNA. This would result in the
establishment of a genetic enclave unable to exchange
genetic information with the natural nucleic acids.
First steps in this endeavour are being explored in the
Framework Programme 7 Orthosome project.
As discussed in the German Statement on synthetic
biology compiled by the academies together with the
major research funder, DFG (DFG, German Academy
of Sciences Leopoldina and Acatech 2009), orthogonal
biosystems offer a generalisable way of increasing
biological safety because an artifi cial genetic code can
only be translated in organisms with the respective
orthogonal translation system.
5.3 Regulatory
circuits
Novel cellular function is a matter not just of molecular
chemistry but also of circuitry. Synthetic gene circuits
that emulate the expression dynamics of living systems,
and are perceived as analogous to electronic circuits, are
beginning to provide new insight into complex control
networks. Although there is no clear boundary between
classical biotechnology and synthetic biology with respect
to the development of artifi cial circuits, recent work has
led to the regulation of post-transcriptional mechanisms
as well as transcriptional control.
Artifi cial gene networks can be designed from modular,
well-characterised and compatible genetic components,
such as molecular switches and biological memory,
implanted into natural systems. For example, the work
of Fussenegger and colleagues in Switzerland, part-
funded by Framework Programmes, produced a synthetic
mammalian oscillator based on an auto-regulated,
sense-antisense transcription control circuit, that enables
autonomous, self-sustained and tuneable oscillatory gene
expression (Tigges et al. 2009). Earlier work by this group
described a range of new tools for circuitry; including
gas-inducible transcription control in a heterologous
system (Weber at al. 2004) and a synthetic time-delay
circuit in mammalian cells (Weber et al. 2007b). Even
more ambitiously, a synthetic ecosystem (interconnection
12
http://parts.mit.edu.
13
International patent applications were fi led by the Craig Venter Institute in 2007.
14
www.ambrx.com.