Synthetic Biology Resources

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== 4. Tools and Web-resources of SybBio ==
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== Tools and Web-resources of SybBio ==
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== 5. Implications of Synthetic Biology ==
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== Implications of Synthetic Biology ==

Revision as of 03:41, 16 September 2008

Contents

Definition of Synthetic Biology

Synthetic biology (also known as Synbio, Synthetic Genomics, Constructive Biology, Extreme Genetic Engineering or Systems Biology) – the design and construction of new biological parts, devices and systems that do not exist in the natural world and also the redesign of existing biological systems to perform specific tasks. Advances in nanoscale technologies – manipulation of matter at the level of atoms and molecules – are contributing to advances in synthetic biology.

Basics of SynBio

At the core of synthetic biology is a belief that all the parts of life can be made synthetically (that is, by chemistry), engineered and assembled to produce working organisms. DNA code is regarded as the software that instructs life, while the cell membrane and all the biological machinery inside the cell are regarded as the hardware (or wetware as it is sometimes known) that need to be snapped together to make a living organism.

DNA synthesis reduces the time it takes genetic engineers to isolate and transfer DNA in order to build genetically modified organisms.

“We’re going to build you exactly what you are looking for: Whole plasmids, whole genes, gene fragments . . . and in one to two years, possibly a whole genome.” – John Mulligan CEO of Blue Heron Biotechnology, Washington (USA)

There is no technical barrier to synthesizing plants and animals, it will happen as soon as anyone pays for it.” — Drew Endy, MIT

Drew Endy of MIT speculates that within 20 years human genomes will be synthesised from scratch.

At present Craig Venter holds the world’s gene-speed record for synthetically producing a 5,386 bp genome (of the virus phiX 174) in under 14 days (although there were errors in his copy).

Synthetic biologists want to work below the level of the gene, at the level of the codon – to identify codons and rearrange them to build new sets of biological instructions. Because there are 64 possible codons (four bases linked together in sets of three, or 4*4*4) but only 20 different amino acids they translate into, synthetic biologists can choose among different options for codons when they want to express a specific amino acid (known as codon optimization). It may be that one codon works better in bacteria and another in plants even though both produce the same amino acid.

Some synthetic biologists take the approach of combing through the genetic code of existing organisms and removing or reducing unnecessary codons to get a sleeker version of the genetic code. Others, by combining codons into stand-alone programming instructions, are developing “standard parts” analogous to the standard parts of electronic circuitry or the standard commands of a computer language. They keep an inventory of these standard parts, and are making them available for others to assemble into more complex genetic systems. Others are designing entirely new artificial amino acids that result from codon combinations not found in nature.

In the US and Europe some synthetic biologists hope to build an artificial “protocell” that will contain and express synthetic DNA as flexibly as a computer stores document files and runs computer programmes.

Unfortunately for would be life builders, genetic code is not as linear as computer code. While the popular view of genetics links units of DNA (genes) to specific traits, the reality is messier. In real life, genes and parts of genes co-operate in subtle and complex networks, each producing proteins that promote or suppress the behaviour of other genes. The result is a system of cellular regulation that controls the amount or timing by which a substance or trait is produced – a bit like electronic circuits that regulate electrical current.

Geneticists interested in manipulating genomes have begun mapping the interactions between genes to try to determine the full set of interactions necessary to produce a desired protein. They can represent these networks with circuit diagrams similar to those used in electronics. The set of interactions that involve a network of DNA molecules acting together to produce a protein can be referred to as a “genetic pathway” and synthetic biologists are now trying to rebuild or alter these genetic pathways as discreet sections of the genome. This involves designing not just one coding region of DNA, but several different areas of code, and then putting them together as a synthetic chromosome. By altering these networks and pathways, synthetic biologists can increase the production of a protein or stimulate the production of an entirely different substance, such as a plastic or a drug.

An Introduction to Five Major Areas of Research in Synthetic Biology

1. Making Minimal Microbes – Post-modern Genomics


In 1995 Venter announced that he was first to sequence the entire genome of a living organism (the bacterium known as Hemophilus influenzae). In 2003 Venter made headlines when his team created the first synthetic virus from scratch – and it took them only 14 days to do it. Venter is notorious for pushing the boundaries on the commercial exploitation of life. His newest commercial venture, Synthetic Genomics, Inc., founded in 2005 with $30 million in venture capital, aims to commercialise a range of synthetic biology applications, starting with energy production. He was also demostrated in Minimal Genome Project (1990) in Mycoplasma genitalium that the bacterium might be able to survive with almost half its genes removed. Others are now trying to minimise the genome of organisms such as E. coli.

Venter calls Mycoplasma laboratorium a “synthetic chromosome” and his intention is to use it as a flexible biofactory into which custom-designed synthetic “gene-cassettes” of four to seven genes can be inserted, genetically programming the organism to carry out specific functions. As a first application, Venter hopes to develop a microbe that would help in the production of either ethanol or hydrogen for fuel production (See the New Synthetic Energy Agenda ). He is also looking to harness the mechanisms of photosynthesis to more effectively sequester carbon dioxide, ostensibly as a means of slowing climate change. Venter talks big. In 2004 he predicted that “engineered cells and lifeforms [will be] relatively common within a decade.”


2. Assembly-Line DNA – “Lego” Life-forms to Order

Drew Endy (MIT), an engineer by training, is also a computer programmer and he and those around him use computer and electronics metaphors to describe synthetic biology: A living organism is a ‘computer’ or ‘machine’ made up of genetic ‘circuits’ in which DNA is the ‘software’ that can be ‘hacked.’ He points out that, Biological engineers of the future will start with their laptops, not in the laboratory. Let’s build new biological systems – systems that are easier to understand because we made them that way.” Endy longs for a logical and predictable biotechnology, what he and others refer to as “intentional biology.” “We would like to be able to routinely assemble systems from pieces that are well described and well behaved,” Endy explains.

The BioBrick Foundation - To do this he and his colleague at MIT, artificial intelligence pioneer Tom Knight, have invented several hundred discrete DNA modules that behave a little like electronic components. They include sequences that turn genes off and on, transmit signals between cells or change colours between red, green, yellow and blue. Knight and Endy then encourage others to combine those modules into more complex genetic circuits. They call these modules Biobricks or “standard parts” and their non-profit BioBricks Foundation maintains over 2000 BioBricks in its registry of standard parts that can be freely used by other synthetic biology researchers. Each of these BioBricks is a strand of DNA designed to reliably perform one function and to be easily compatible with other BioBricks in making longer circuits. The completed circuits are then dropped into E. coli, yeast or another microbial host to see if they function.

Every year Endy, Knight and their fellow synthetic biologists at MIT convene an International Genetically Engineered Machine Competition (known as iGEM).iGEM, now in its fifth year, mostly produces eye-catching gimmicks – bacteria that blink different colours and biological films that can be programmed to take simple photographs and display images. In 2006 the iGEM team from MIT designed E. coli bacteria that smell of bananas and wintergreen. Biological films that take photographs could be the basis of new forms of lithography for assembling computer circuits, while sweet smelling bacteria could interest the fragrance and flavouring industries.

Endy talks about building circuits into human body cells that count how many times they divide in order to prevent run-away cell growth. “I could hook it up to a suicide mechanism,” he speculates, “and any cell that divides more than 200 times, it would say, ‘Kill it, it’s forming a tumour’…” One of Endy’s long term ambitions is to re-design the seeds of a tree such that the tree is programmed to grow into a house.


3. Building Artificial Cells (Proto-Cell) from the Bottom Up – Ersatz Evolution


Steen Rasmussen & his research team believes their “protocell” will require three elements to sustain life – a metabolism that harvests and generates energy, an information-storing molecule (like DNA) and a membrane to hold it all together. to build a living cell entirely from scratch. While most synbio projects are top-down – re-arranging existing life or reverse-engineering.

Rasmussen is tweaking nature’s cell design for his “Los Alamos Bug.” Rather than an oily membrane keeping water inside, his cell is basically a droplet of oil, which keeps water on the outside. Furthermore, it uses a different double helix molecule to carry instructions: Rather than DNA, the Los Alamos Bug uses human-made PNA – peptide nucleic acid. PNA has the same structure and is made from the same chemical bases as DNA – G, C, A and T – but the molecule’s backbone is made of peptides, the build- ing blocks of proteins – instead of DNA’s sugar-phosphate backbone. Howard Packer, Rasmussen’s collaborator as well as a pioneer of chaos theory, says that using PNA rather than DNA is a good idea for biosafety reasons. Because PNA doesn’t exist in nature, he says, the Bug may be easier to control so it doesn’t “escape and cause problems. he argues that the protocell approach will lead to a better understanding of living and non-living systems.

PACE – Programmable Artificial Cell Evolution – is a project involving 14 European and US universities and companies and is funded by the European Commission.


4. Pathway Engineering – Bug Sweatshops

“Really, we are designing the cell to be a chemical factory. We’re building the modern chemical factories of the future.” – Jay Keasling, Professor of Chemical Engineering, University of California at Berkeley.

Jay Keasling is engineering the genetic pathways of cells to produce valuable drugs and industrial chemicals. Keasling’s team has synthesised about a dozen genes that work together to make the chemical processes (or ‘pathways’) behind a class of compounds known as isoprenoids – high-value compounds important in drugs and industrial chemicals. Isoprenoids are natural substances produced primarily by plants. Because of their structural complexity, chemical synthesis of most isoprenoids has not been commercially feasible, and isolation from natural sources yields only very small quantities. Synthetic biologists at Berkeley hope to overcome these limitations by designing new metabolic pathways in microbes, turning them into “living chemical factories” that produce novel or rare isoprenoids. Most notably, they are focusing on a powerful anti-malarial compound known as artemisinin. Backed by a $42.5 million grant from the Bill and Melinda Gates Foundation, the Berkeley team believes that synthetic biology is the tool that will allow unlimited and cheap production of a previously scarce drug to treat malaria in the developing world. In 2003 Keasling and colleagues founded a synbio start-up called Amyris Biotechnologies to bring the project to fruition. Keasling says “We’ve essentially created a platform that will allow you to produce many drugs cheaper. Down the road, we will be able to modify enzymes to produce a number of different molecules, even some that don’t exist in nature.” Amyris plans to use synthetic biology to produce commercial drugs, plastics, colourants, fragrances and biofuels.

Keasling’s lab is also attempting to re-engineer the metabolic pathways that produce natural rubber (also an isoprenoid).101 These pathways will then be incorporated into bacteria, or in sunflowers or desert plants, to boost rubber production.

Other researchers exploring commercial uses for pathway engineering, include:

Chris Voigt, a synthetic biologist at the University of California at San Francisco announced in May 2006 that he had re-engineered a strain of salmonella to produce the precursor to spider silk – a substance as strong as Kevlar with 10 times the elasticity.

California-based Genencor has been working with chemical giant DuPont to add synthetic genetic networks to the cellular machinery of E. coli. When mixed with corn syrup in fermentation tanks, their modified bacterium produces a key component in Sorona, a spandex like fibre. DuPont hopes that its new bio-based textile will cause as much fuss as the introduction of nylon back in the 1930s.


5. Expanding Earth’s Genetic System – Alien Genetics


“We’re trying to expand the genetic code.” — Dr. Floyd E. Romesburg, Scripps Research Institute.

Steven Benner, a biochemist and founder of the Westheimer Institute for Science and Technology (Benner was formerly based at the University of Florida) is a pioneer of synthetic biology. He builds models of how life might function using unnatural genetic systems. His argument is simple: There is no reason the limited set of molecules in DNA should be the only form of life that has arisen in the universe and we need models of what other kind of life could be out there. “We can’t think of any transparent reason that these four bases [A, G, C and T] are used on earth,” explains Benner.

Benner has demonstrated that a number of novel biological molecules can be chemically synthesised so that they reproduce and pass on their genetic inheritance in the same way that DNA does. He sees artificial genetics as a way to explore basic questions, such as how life got started on earth, how it evolves and even what forms it may take elsewhere in the universe.

In 2004 Benner further showed that his six-letter DNA-like molecule (including letters ‘K’ and ‘X’) could support the molecular “photocopying” operation known as polymerase chain reaction, in which the molecule copies itself and then directs the synthesis of copies of copies. Since natural polymerase enzymes rejected his artificial base pairs, Benner was forced to design a new, compatible version of the enzyme polymerase.

“Considering how hard we had to work to get Earth polymerases to accept our artificial DNA, we doubt that our artificial DNA would survive for an instant outside of the laboratory on this planet,” explains Benner. “But a six-letter DNA might support life on other planets, where life started with six letters and is familiar with them. Or even DNA that contains up to 12 letters, which we have shown is possible.”

In 2005 Floyd Romesburg, a biochemist at the Scripps Institute in La Jolla, California, added an extra letter F (made from flourobenzene) to the existing four bases that occur naturally in DNA, and successfully created an enzyme that can make the modified biomolecules self-replicate.

Stanford University chemist Eric T. Kool has re-designed the existing base pair A and T to be larger – creating an expanded double helix that glows in the dark and is unusually stable at higher temperatures. Kool dubbed his new molecule xDNA (for expanded DNA): “We’ve designed a genetic system that’s completely new and unlike any living system on Earth,” announced Kool. Like Benner, Kool emphasises that expanded DNA will not pose new biosafety risks. “This new DNA couldn’t function in the natural system on Earth,” he asserts. “It’s too big. However, we like to think that one day it could be the genetic material for a new form of life, maybe here or on another planet.”

Benner and Kool haven’t built their artificial genetic systems into full organisms yet. “I suspect that, in five years or so, the artificial genetic systems that we have developed will be supporting an artificial lifeform that can reproduce, evolve, learn and respond to environmental change,” Benner predicted in 2004.

Although Benner and others are confident that artificial genetic systems will not survive outside the lab, research in this field raises profound biosafety questions. Dr. Jonathan King, a professor of molecular biology at MIT told the New York Times: “It’s a powerful technology, and like all powerful technologies it needs appropriate oversight and regulation.” One possible scenario he suggested is that proteins with artificial amino acids could elicit allergic reactions if used in drugs or in food.


Tools and Web-resources of SybBio

Implications of Synthetic Biology

1. Building a Better Bio-Weapon – What does synthetic biology mean for bioweapons?

“I expect that this technology will be misapplied, actively misapplied and it would be irresponsible to have a conversation about the technology without acknowledging that fact.” – Drew Endy, Synthetic Biologist, MIT.

Then there was the flu. The strain of avian influenza that jumped to humans early in the last century (H1N1), sometimes known as “The Spanish Flu,” killed somewhere between 20 and 50 million people worldwide in 1918-1919 – a higher death toll than all of World War I. Despite the lethal nature of the highly communicable virus, efforts to reconstruct it began in the 1950s. (By that time the H1N1 strain was eradicated from the earth – having disappeared with its last victims.) In 1997, Dr. Jeffrey Taubenberger of the US Armed Forces Institute of Pathology in Washington, DC succeeded in recovering and sequencing fragments of the viral RNA from preserved tissues of 1918 flu victims buried in the Alaskan permafrost. Eight years later, Taubenberger’s team and collaborating researchers at Mount Sinai School of Medicine in New York and the US Centers of Disease Control (CDC) in Atlanta adannounced that they had resurrected the lethal virus. They published details of the completed genome sequencing in Nature and details of the virus recreation in Science. About ten vials of the flu virus were produced with the possibility that more could be made to accommodate research needs, according to the CDC scientist who inserted the virus into a living cell, the last step in its reconstruction. Craig Venter later described the resurrection of the 1918 flu virus as “the first true Jurassic Park scenario.”

But concerns about synbio’s bioweaponry potential are not limited to the construction or reconstruction of virulent microorganisms. Work in the area of pathway engineering is allowing synthetic biologists to construct the genetic networks that code for particular proteins and these synthetic networks can then be inserted into microbial hosts such as E. coli or yeast. Microbes could function as “biofactories” to produce natural protein poisons such as snake, insect and spider venoms, plant toxins and bacterial toxins such as those that cause anthrax, botulism, cholera, diphtheria, staphylococcal food poisoning and tetanus. In addition, biowarfare experts are concerned that protein engineering could be used to create hybrids of protein toxins.

A 2003 declassified CIA document from the US, entitled “The Darker Bioweapons Future,” acknowledges that, “Growing understanding of the complex biochemical pathways that underlie life processes has the potential to enable a class of new, more virulent biological agents engineered to attack distinct biochemical pathways and elicit specific effects...The same science that may cure some of our worst diseases could be used to create the world’s most frightening weapons.”

Synbio’s rapidly changing nature will also affect the way that nations conduct war.

"The same science that may cure some of our worst diseases could be used to create the world’s most frightening weapons.” — CIA report, “The Darker Bioweapons Future”


2. The New Synthetic Energy Agenda – Rebooting Biofuels

3. Synthesizing New Monopolies from Scratch – Synthetic Biology and Intellectual Monopoly

4. Synthetic Conservation – What are the implications of gene synthesis and digital DNA for conserving genetic resources and the politics of biodiversity?

5. Synthetic Commodities – Implications For Trade

6. SynBioSafety


Case Study : Synthetic Biology's Poster Child - Microbial Production of Artemisinin to Treat Malaria

List of Recent Synthetic Biology Patents

Table: A Sample of Recent Synthetic Biology Patents
Inventor Patent / Application Number Publication Date Description
Steven Benner US 6,617,106 9 September 2003 Methods for preparing oligonucleotides containing non-standard nucleotides
Steven Benner US20050038609A1 17 Feb. 2005 Evolution-based functional genomics
Steven Benner US 5,432,272 11 July 1995 Method for incorporating into a DNA or RNA oligonucleotide using nucleotides bearing heterocyclic bases
Harry Rappaport (Assignee: Temple University) US 5,126,439 30 June 1992 Artificial DNA base pair analogues
George Church, Brian Baynes (Assignee: Codon Devices, Inc.) WO06076679A1 20 July 2006 Compositions and methods for protein design
George Church, Jingdong Tian (Assignee: Harvard) US20060127920A1 15 June 2006 Polynucleotide synthesis
Noubar Afeyan, et al. (Assignee: Codon Devices, Inc.) WO06044956A1 27 April 2006 Methods for assembly of high fidelity synthetic polynucleotides
Jay Keasling, et al. US20040005678A1 8 Jan 2004 Biosynthesis of amorpha-4,11-diene (in a host cell, useful as pharmaceuticals)
Jay Keasling, et al. US20030148479A1 7 August 2003 Biosynthesis of isopentenyl pyrophosphate (in a host microorganism, useful for pharmaceutical purposes)
Keith K. Reiling, et al. (Assignee: University of California) WO05033287A3 14 April 2005 Methods for identifying a biosynthetic pathway gene product
Ho Cho, et al. (Assignee: Ambrx, Inc.) WO06091231A2 31 August 2006 Biosynthetic polypeptides utilizing nonnaturally encoded amino acids
Robert D. Fleischmann, J. Craig Venter, et al. (Assignee: Human Genomes Sciences, Johns Hopkins Univ.) US20050131222A1 16 June 2005 Nucleotide sequence of the haemophilus influenzae Rd genome, fragments thereof, and uses thereof (genome recorded on computer readable medium - useful for identifying commercially important nucleic acid fragments by homology searching)
Frederick Blattner, et al. (Assignee: Univ. of Wisconsin) US 6,989,265 24 January 2006 New bacterium with a genome genetically engineered to be at least 5% smaller than the genome of its native parent strain, useful for producing a wide range of commercial products
Glen Evans (Assignee: Egea Biosciences; subsidiary of Johnson & Johnson) US 6,521,427 18 Feb. 2003 Method for the complete chemical synthesis

and assembly of genes and genomes

Jay Keasling, et al. US20060079476A1 13 April 2006 Method for enhancing production of isoprenoid compounds
James Kirby, et al. (Assignee: Univ. of California) WO06014837A1 9 Feb. 2006 Genetically modified host cells and use of same for producing isoprenoid compounds
Nigel Dunn-Coleman, et al. (Assignee: Dupont; Genencor) US 7,074,608 11 July 2006 Method for the production of 1,3-propanediol by recombinant Escherichia coli strain comprising genes for coenzyme B12 synthesis
Eric T. Kool (Assignee: University of Rochester) US 7,033,753 25 April 2006 Compositions and methods for nonenzymatic ligation of oligonucleotides and detection

of genetic polymorphisms

List of Companies with Synthetic Biology Activities

Table: Companies with Synthetic Biology Activities
Company Location SynBio business area Synthetic Biologists
Ambrx La Jolla, CA USA Develops biopharmaceuticals utilizing artificial amino acids Associated with Dr. Peter Schultz, Scripps Research Institute, San Diego, USA
Amyris Biotechnologies Emeryville, CA USA Developing synthetic microbes to produce pharmaceuticals, fine chemicals, nutraceuticals, vitamins, flavors and biofuels Founded by Prof. Jay Keasling of University of California, Berkeley; CEO John G. Melo was previously president of U.S. Fuels Operations for British Petroleum; Vice President of Research is Dr. Jack D. Newman
Egea Biosciences Centocor San Diego, CA USA Now wholly owned by Johnson & Johnson.

Develops innovative genes, proteins and biomaterials for J&J medical immunology subsidiary Centocor; Egea holds broad patent on genome synthesis

Founded by Dr. Glen Evans, formerly a leading investigator in the Human Genome Project
Codon Devices Cambridge, MA, USA Describes itself as a ‘Bio Fab’ able to design and construct engineered genetic

devices for partners in medicine, biofuels, agriculture, materials and other application areas

Founders include: Prof. Drew Endy (MIT), Prof. George Church (Harvard), Prof. Jay Keasling (Berkeley), Prof. Ron Weiss (Princeton) and others
Diversa San Diego, CA USA Diversa adds new codons to ‘optimise’ enzymes taken from natural bacteria to apply to industrial processes Eric Mather, Vice-President of Scientific Affairs
DuPont Wilmington, Delaware USA DuPont is partnering with Genencor, BP, Diversa and others to develop microbes that will produce fibers (Sorona) and biofuels John Pierce is Vice President, Du-Pont Bio-Based Technology
EngeneOS Waltham, MA USA Designs and builds programmable biomolecular devices from both natural and artificial building blocks Founders include Prof. George Church (Harvard); Joseph Jacobson (MIT)
EraGen Biosciences Madison, WI USA Develops genetic diagnostic tech-nologies based on expanded genetic alphabet Founded by Dr. Steven A. Benner
Firebird Biomolecular Sciences Gainesville, FL USA Supplies nucleic acid components, libraries, polymerases, and software to support synthetic biology Founded by Dr. Steven A. Benner
Genencor Palo Alto, CA USA Develops and sells biocatalysts and other biochemicals. Undertakes pathway engineering Owned by Danisco
Genomatica San Diego, CA USA Designs software that models genetic network for synthetic biology applications
LS9 San Francisco, CA, USA Designs microbial factories that produce biofuels and other energy related compounds Founders include Prof. George Church (Harvard)
Mascoma Cambridge, MA, USA Developing microbes to convert agricultural feedstock into cellulosic ethanol Founded by Dr. Lee R. Lynd (Dartmouth College)
Protolife Venice, Italy Developing artificial cells and synthetic living systems Founded by Dr. Norman Packard
Sangamo Biosciences Richmond, CA, USA Produce engineered ‘zinc finger’ proteins for controling gene regulation
Synthetic Genomics Rockville, MD USA Developing minimal genome as chassis for energy applications Founded by Dr. Craig Venter and Dr. Hamilton Smith; President is Dr. Ari Patrinos (formerly US Department of Energy)



See Also

BioBrick

iGEM

Synthetic biology

New Synthetic Energy Agenda