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Article

Synthetic Biology Articles

 
 

8. Influential Papers

8.1 Ten important Synthetic Biology papers

8.1.1 Paper no 1 - "Creation of a bacterial cell controlled by a chemically synthesized genome."  

Abstract:

"We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication."

Science. 2010 Jul 2;329(5987):52-6. Epub 2010 May 20.

Gibson DG  , Glass JI  , Lartigue C  , Noskov VN  , Chuang RY  , Algire MA  , Benders GA  , Montague MG  , Ma L  , Moodie MM  , Merryman C  , Vashee S  , Krishnakumar R  , Assad-Garcia N  , Andrews-Pfannkoch C  , Denisova EA  , Young L  , Qi ZQ  , Segall-Shapiro TH  , Calvey CH  , Parmar PP  , Hutchison CA 3rd  , Smith HO  , Venter JC  .

The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.

Comment in: Science. 2010 Jul 2;329(5987):38-9. 

 

8.1.2 Paper no 2 - "A synthetic oscillatory network of transcriptional regulators."  

Abstract:

"Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks."

Nature. 2000 Jan 20;403(6767):335-8.

Elowitz MB  , Leibler S  .

Department of Molecular Biology and Physics, Princeton University, New Jersey 08544, USA.  

 

8.1.3 Paper no 3 - "Construction of a genetic toggle switch in Escherichia coli."  

Abstract:

"It has been proposed' that gene-regulatory circuits with virtually any desired property can be constructed from networks of simple regulatory elements. These properties, which include multistability and oscillations, have been found in specialized gene circuits such as the bacteriophage lambda switch and the Cyanobacteria circadian oscillator. However, these behaviours have not been demonstrated in networks of non-specialized regulatory components. Here we present the construction of a genetic toggle switch-a synthetic, bistable gene-regulatory network-in Escherichia coli and provide a simple theory that predicts the conditions necessary for bistability. The toggle is constructed from any two repressible promoters arranged in a mutually inhibitory network. It is flipped between stable states using transient chemical or thermal induction and exhibits a nearly ideal switching threshold. As a practical device, the toggle switch forms a synthetic, addressable cellular memory unit and has implications forbiotechnology, biocomputing and gene therapy."

Nature. 2000 Jan 20;403(6767):339-42.

Gardner TS  , Cantor CR  , Collins JJ  .

Department of Biomedical Engineering, Center for BioDynamics, Boston University, Massachusetts 02215, USA.

 

8.1.4 Paper no 4 - "Foundations for engineering biology."  

Abstract:

"Engineered biological systems have been used to manipulate information, construct materials, process chemicals, produce energy, provide food, and help maintain or enhance human health and our environment. Unfortunately, our ability to quickly and reliably engineer biological systems that behave as expected remains quite limited. Foundational technologies that make routine the engineering of biology are needed. Vibrant, open research communities and strategic leadership are necessary to ensure that the development and application of biological technologies remains overwhelmingly constructive."

Nature. 2005 Nov 24;438(7067):449-53.

Endy D  .

Division of Biological Engineering, Massachusetts Institute of Technology, Room 68-580, Koch Biology Building, 31 Ames Street, Cambridge, Massachusetts 02139, USA.  

 

8.1.5 Paper no 5 - "A synthetic multicellular system for programmed pattern formation."  

Abstract:

"Pattern formation is a hallmark of coordinated cell behaviour in both single and multicellular organisms. It typically involves cell-cell communication and intracellular signal processing. Here we show a synthetic multicellular system in which genetically engineered 'receiver' cells are programmed to form ring-like patterns of differentiation based on chemical gradients of an acyl-homoserine lactone (AHL) signal that is synthesized by 'sender' cells. In receiver cells, 'band-detect' gene networks respond to user-defined ranges of AHL concentrations. By fusing different fluorescent proteins as outputs of network variants, an initially undifferentiated 'lawn' of receivers is engineered to form a bullseye pattern around a sender colony. Other patterns, such as ellipses and clovers, are achieved by placing senders in different configurations. Experimental and theoretical analyses reveal which kinetic parameters most significantly affect ring development over time. Construction and study of such synthetic multicellular systems can improve our quantitative understanding of naturally occurring developmental processes and may foster applications in tissue engineering, biomaterial fabrication and biosensing."

Nature. 2005 Apr 28;434(7037):1130-4.

Basu S  , Gerchman Y  , Collins CH  , Arnold FH  , Weiss R  .

Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA.

 

8.1.6 Paper no 6 - "Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitaliumgenome."  

Abstract:

"We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments."

Science. 2008 Feb 29;319(5867):1215-20. Epub 2008 Jan 24.

Gibson DG  , Benders GA  , Andrews-Pfannkoch C  , Denisova EA  , Baden-Tillson H  , Zaveri J  , Stockwell TB  , Brownley A  , Thomas DW  , Algire MA  , Merryman C  , Young L  , Noskov VN  , Glass JI  , Venter JC  , Hutchison CA 3rd  , Smith HO  .

J. Craig Venter Institute, Rockville, MD 20850, USA.

Comment in: Science. 2008 Feb 29;319(5867):1196-7. 

 

8.1.7 Paper no 7 - "Reconstruction of genetic circuits."  

Abstract:

"The complex genetic circuits found in cells are ordinarily studied by analysis of genetic and biochemical perturbations. The inherent modularity of biological components like genes and proteins enables a complementary approach: one can construct and analyse synthetic genetic circuits based on their natural counterparts. Such synthetic circuits can be used as simple in vivo models to explore the relation between the structure and function of a genetic circuit. Here we describe recent progress in this area of synthetic biology, highlighting newly developed genetic components and biological lessons learned from this approach."

Nature. 2005 Nov 24;438(7067):443-8.

Sprinzak D  , Elowitz MB  .

California Institute of Technology, Division of Biology and Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA.

 

8.1.8 Paper no 8 - "Engineered gene circuits."  

Abstract:

"A central focus of postgenomic research will be to understand how cellular phenomena arise from the connectivity of genes and proteins. This connectivity generates molecular network diagrams that resemble complex electrical circuits, and a systematic understanding will require the development of a mathematical framework for describing the circuitry. From an engineering perspective, the natural path towards such a framework is the construction and analysis of the underlying submodules that constitute the network. Recent experimental advances in both sequencing and genetic engineering have made this approach feasible through the design and implementation of synthetic gene networks amenable to mathematical modelling and quantitative analysis. These developments have signalled the emergence of a gene circuit discipline, which provides a framework for predicting and evaluating the dynamics of cellular processes. Synthetic gene networks will also lead to new logical forms of cellular control, which could have important applications in functional genomics, nanotechnology, and gene and cell therapy."

Nature. 2002 Nov 14;420(6912):224-30.

Hasty J  , McMillen D  , Collins JJ  .

Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA.  

 

8.1.9 Paper no 9 - "Production of the antimalarial drug precursor artemisinic acid in engineered yeast." 

Abstract:

"Malaria is a global health problem that threatens 300-500 million people and kills more than one million people annually. Disease control is hampered by the occurrence of multi-drug-resistant strains of the malaria parasite Plasmodium falciparum. Synthetic antimalarial drugs and malarial vaccines are currently being developed, but their efficacy against malaria awaits rigorous clinical testing. Artemisinin, a sesquiterpene lactone endoperoxide extracted from Artemisia annua L (family Asteraceae; commonly known as sweet wormwood), is highly effective against multi-drug-resistant Plasmodium spp., but is in short supply and unaffordable to most malaria sufferers. Although total synthesis of artemisinin is difficult and costly, the semi-synthesis of artemisinin or any derivative from microbially sourced artemisinic acid, its immediate precursor, could be a cost-effective, environmentally friendly, high-quality and reliable source of artemisinin. Here we report the engineering of Saccharomyces cerevisiae to produce high titres (up to 100 mg l-1) of artemisinic acid using an engineered mevalonate pathway, amorphadiene synthase, and a novel cytochrome P450 monooxygenase (CYP71AV1) from A. annua that performs a three-step oxidation of amorpha-4,11-diene to artemisinic acid. The synthesized artemisinic acid is transported out and retained on the outside of the engineered yeast, meaning that a simple and inexpensive purification process can be used to obtain the desired product. Although the engineered yeast is already capable of producing artemisinic acid at a significantly higher specific productivity than A. annua, yield optimization and industrial scale-up will be required to raise artemisinic acid production to a level high enough to reduce artemisinin combination therapies to significantly below their current prices."

Nature. 2006 Apr 13;440(7086):940-3.

Ro DK  , Paradise EM  , Ouellet M  , Fisher KJ  , Newman KL  , Ndungu JM  , Ho KA  , Eachus RA  , Ham TS  , Kirby J  , Chang MC  , Withers ST  , Shiba Y  , Sarpong R  , Keasling JD  .

California Institute of Quantitative Biomedical Research, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA.

Comment in: Nature. 2006 Apr 13;440(7086):852-3.  

 

8.1.10 Paper no 10 - "Development of genetic circuitry exhibiting toggle switch or oscillatory behavior inEscherichia coli."  

Abstract:

"Analysis of the system design principles of signaling systems requires model systems where all components and regulatory interactions are known. Components of the Lac and Ntr systems were used to construct genetic circuits that display toggle switch or oscillatory behavior. Both devices contain an "activator module" consisting of a modified glnA promoter with lac operators, driving the expression of the activator, NRI. Since NRI activates the glnA promoter, this creates an autoactivated circuit repressible by LacI. The oscillator contains a "repressor module" consisting of the NRI-activated glnK promoter driving LacI expression. This circuitry produced synchronous damped oscillations in turbidostat cultures, with periods much longer than the cell cycle. For the toggle switch, LacI was provided constitutively; the level of active repressor was controlled by using a lacY mutant and varying the concentration of IPTG. This circuitry provided nearly discontinuous expression of activator."

Cell, 2003 May 30;113(5):597-607.

Atkinson MR  , Savageau MA  , Myers JT  , Ninfa AJ  .

Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.

8.2 Other papers of interest

(by subject)

 

Seminal papers in Synthetic Biology:

-"Total synthesis of a gene". Science 203 (4381): 614–25. doi  :10.1126/science.366749  . PMID   .

- The New Identity of Chemistry as Biomimetic and Nano-science  

 

- Biology by Design: From Top to Bottom and Back  

- Rewiring Cells: Synthetic biology as a tool to interrogate the organizational principles of living systems  

 

Multiplex genome engineering:

-Programming cells by multiplex genome engineering and accelerated evolution  

 

Synthetic chromosome:

-Synthetic chromosome arms function in yeast and generate phenotypic diversity by design  

 

Biological Gates:

- Environmental signal integration by a modular AND gate [1].

- Robust multicellular computing using genetically encoded NOR gates and chemical 'wires.' [2]

- Environmentally controlled invasion of cancer cells by engineered bacteria [3].

- Modular approaches to expanding the functions of living matter [4].

- Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion [5] .

 

Synthetic optogenetics:

- The promise of optogenetics in cell biology: interrogating molecular circuits in space and time [6].

- Multichromatic control of gene expression in Escherichia coli [7]

 

Other papers of potential interest:

- Rational design of memory in eukaryotic cells. [8]

- The New Identity of Chemistry as Biomimetic and Nano-science  

- Biology by Design: From Top to Bottom and Back  

- Rewiring Cells: Synthetic biology as a tool to interrogate the organizational principles of living systems  

 

 

 

 

References

  1. Environmental signal integration by a modular AND gate. Anderson, J.C., Voigt, C.A., Arkin, A.P. Mol. Syst. Biol. (2007) [Pubmed]
  2. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Tamsir, A., Tabor, J.J., Voigt, C.A. Nature. (2011) [Pubmed]
  3. Environmentally controlled invasion of cancer cells by engineered bacteria. Anderson, J.C., Clarke, E.J., Arkin, A.P., Voigt, C.A. J. Mol. Biol. (2006) [Pubmed]
  4. Modular approaches to expanding the functions of living matter. Chin, J.W. Nat. Chem. Biol. (2006) [Pubmed]
  5. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Wang, K., Neumann, H., Peak-Chew, S.Y., Chin, J.W. Nat. Biotechnol. (2007) [Pubmed]
  6. The promise of optogenetics in cell biology: interrogating molecular circuits in space and time. Toettcher, J.E., Voigt, C.A., Weiner, O.D., Lim, W.A. Nat. Methods. (2011) [Pubmed]
  7. Multichromatic control of gene expression in Escherichia coli. Tabor, J.J., Levskaya, A., Voigt, C.A. J. Mol. Biol. (2011) [Pubmed]
  8. Rational design of memory in eukaryotic cells. Ajo-Franklin, C.M., Drubin, D.A., Eskin, J.A., Gee, E.P., Landgraf, D., Phillips, I., Silver, P.A. Genes. Dev. (2007) [Pubmed]
 
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