Building Blocks

twoeggfinnishBiotechnology

Dec 14, 2012 (4 years and 6 months ago)

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Synthetic Biology

b
y Jodie A. Symington

Transport

Plasmid

Motility

Logic & Communication

Environmental sensors

Protein & Chemical
Synthesis

Binding Specificity

Standard biological parts can be used in a model organism (chassis)
to produce novel biological organisms.


“A new area of biological research that combines science and engineering in
order to design and build ("synthesize“) novel biological functions and
systems.”


First described by a Polish geneticist Waclaw Szybalski in 1974;


‘The real challenge will start when we enter the synthetic biology phase of research in our field.
We will then devise new control elements and add these new modules to the existing genomes or
build up wholly new genomes. This would be a field with the unlimited expansion potential and
hardly any limitations to building "new better control circuits" and ..... finally other "synthetic"
organisms, like a "new better mouse". ... I am not concerned that we will run out exciting and
novel ideas, ... in the synthetic biology, in general. ‘


Waclaw Szybalski,
In Vivo and in Vitro Initiation of Transcription
, Page 405. In: A. Kohn and A. Shatkay (Eds.), Control of Gene
Expression, pp. 23
-
24, and Discussion pp. 404
-
405 (Szybalski's concept of Synthetic Biology), 411
-
412, 415
-

417. New York:
Plenum Press, 1974


He wrote a comment in the editorial for the journal Gene;


‘The work on restriction nucleases not only permits us easily to construct recombinant DNA
molecules and to analyze individual genes, but also has led us into the new era of synthetic
biology where not only existing genes are described and analyzed but also new gene
arrangements can be constructed and evaluated. ‘


Szybalski, W., Skalka, A., 1978. Nobel
-
prizes and restriction enzymes. Gene 4, 181
-
182.

Protein generator

Reporter

Inverters

Signalling

Measurement/Sensor

Composite device

DEVICES

Bacterium

Yeast

CHASSIS

Promoters

Protein coding???

Protein domains

Ribosome binding sites

PARTS

Terminators

DNA

Plasmid backbone

Enzymes/Proteins

Registry of Standard Biological Parts

Bacteriophage T7

Plasmids

VECTORS

Biological ‘parts’ become engineering tools. Pick and
choose which parts are to be combined to produce a
novel system.


Parts/Devices are actually Genes

Design of the model organism is based upon Systems Biology.

Systems Biology aims to understand existing biological systems, these
‘systems’ can then be taken to ‘synthesise’ organisms with unique functions
not known to exist in nature.

Transport

Logic & Communication

Environmental
sensor

Motility

Basal metabolism

Binding Specificity

System

Protein & Chemical Synthesis

Genetic Engineering = Genetic Modification = Recombinant DNA Technology


Biopharmaceuticals are the best examples of Genetic Modification. Genes are
inserted into bacteria plasmids/vectors.


Plasmids are responsible for the transfer of genetic information between
bacterial species e.g.
E.coli

to
S.aureus
. They are what cause antibiotic
resistance.


It only involves one or two genes and the ‘system’ is not geared to carry out
this function. If given a chance the plasmid, which is a metabolic burden on
the bacteria will be lost.


The first GMO was an
E.coli

strain which produced human.

Is this not just Genetic Engineering???

Widmaier, D., Tullman
-
Ercek, D., Mirsky, E., Hill, R., Govindarajan, S., Minshull, J., & Voigt, C.A. (2009)
Engineering the Salmonella type
III secretion system to export spider silk monomers
,
Molecular Systems Biology
,
5: 309
.

Silk Production

Salmonella

Type
-
III injection system aids bacterial entry into a host cell.
Reengineered to produce spider silk monomers.








How was it done?

Genes for silk inserted via a plasmid (x3 used). Transport proteins needed to
recognise the silk monomer. Transport proteins needed to deliver the growing
monomer to Type
-
III injection system. Type
-
III injection system needed to
recognise the monomer as something to eject.

Not just one or two genes inserted via a plasmid!

Spiders silk Glands producing silk

Type
-
III injection system

J. Craig Venter and his team have been working on developing a standard chassis. It has t
be
an autonomous, self
-
replicating entity capable of performing thermodynamic work
cycle
.


Smallest genome known in a bacterium comes from
Mycoplasm genitalium
it has 517
genes.


How many of those genes are essential for survival and replication?

Developing the Chassis

HUTCHISON, C. A., III, PETERSON, S. N., GILL, S. R., CLINE, R. T., WHITE, O., FRASER, C. M., SMITH, H. O. & CRAIG
VENTER, J. (1999) Global Transposon Mutagenesis and a Minimal Mycoplasma Genome.
Science, 286
, 2165
-
2169.

Deemed 265
-
350 of those genes were essential under laboratory conditions.

GIBSON, D. G., BENDERS, G. A., ANDREWS
-
PFANNKOCH, C., DENISOVA, E. A., BADEN
-
TILLSON, H., ZAVERI, J., STOCKWELL, T. B., BROWNLEY
,
A., THOMAS, D. W., ALGIRE, M. A., MERRYMAN, C., YOUNG, L., NOSKOV, V. N., GLASS, J. I., VENTER, J. C., HUTCHISON, C. A., III
& S
MITH, H.
O. (2008) Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome.
Science, 319
, 1215
-
1220.

Synthesising the Minimal Genome

Minimal genome is relatively small, so it is possible to reconstruct without resorting to
cloning whole sections.


DNA synthesiser produces stretches of DNA. These are then joined together in sections in
a sequential fashion.

C

A

B

GIBSON, D. G., BENDERS, G. A., ANDREWS
-
PFANNKOCH, C., DENISOVA, E. A., BADEN
-
TILLSON, H., ZAVERI, J., STOCKWELL, T. B., BROWNLEY
,
A., THOMAS, D. W., ALGIRE, M. A., MERRYMAN, C., YOUNG, L., NOSKOV, V. N., GLASS, J. I., VENTER, J. C., HUTCHISON, C. A., III
& S
MITH, H.
O. (2008) Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome.
Science, 319
, 1215
-
1220.

How Does the Synthesised Genome get into the Cell?

Inserting isn’t the problem excising the original genome is.


The inserted genome recombines with the original genome and makes a ‘super
genome.’ Not quite minimal genome/chassis anymore!


Winner of the Synthetic
Biology Competition
2004.


UT Austin/UCSF team
designed a biofilm that
could detect light
changes. Theory is each
cell o the lawn would
update its state in
response to light input
and, depending on the
state of neighbouring
cells, decide whether or
not to change colour.

http://partsregistry.org/cgi/htdocs/SBC04/austin.cgi

Examples

iGEM team at Newcastle are tackling environmental issues


http://2009.igem.org/Team:Newcastle



Future Applications

Medicinal



search and destroy pathogens/tumour cells


Protein design



improve catalysis


Fuel production



raw waste into fuel??? Hydrogen, Ethanol


Drug production



Higher quantities produced than current




biopharmaceutical genetic engineering (the cell is




now developed specifically for this purpose!!!)


Bioremediation



clean up of the atmosphere e.g. Organisms which feed




on an oil spill, refuse, toxic chemicals


Summary

Synthetic Biology is cross disciplinary bringing together biologists,
geneticists, systems biologists, computing science and
engineering.


Novel ideas for its use makes the applications limitless.