Synthetic Biological Life

ORIGINAL: HPlusMagazine

By: Laura E. Bratton, MD, Rodney Shackelford, DO, Ph.D.

May 3, 2012

The idea of producing artificial or synthetic life has long fascinated mankind and from ancient times many human and animal-imitating “automata” or self-operating machines have been created for entertainment, instructional, and sometimes religious purposes. The creation of actual synthetic biological life only became possible with the discovery of the structure of DNA, the genetic code, and the development of the basic tools of molecular biology, such as the ability to isolate, sequence, and join different DNA sequences. Especially important has been the recently developed ability to artificially synthesize relatively long DNA molecules with designed sequences. Although the creation of completely synthetic biological life was first accomplished in 2010, the field is already yielding significant information concerning the core gene groups or genetic “chassis” indispensible for life and how these gene products (proteins, RNAs, and lipids) function as an integrated unit. With the identification of these chassis, exogenous natural or synthetic gene sequences can be integrated into organisms designed for specific purposes and applications.

The first genetically engineered organism was created in 1973 when a naturally occurring DNA sequence was transferred into and expressed in a bacterium, conferring antibiotic resistance. The first organism to actually have a synthetic (or man-made “added”) biochemical pathway was created in 2003, when an E. coli was artificially created with a new genetic code and amino acid synthesizing enzymes. The engineered bacterium could synthesize and incorporate an amino acid (O-methyl-L-tyrosine) that does not normally occur in nature into proteins, increasing the number of amino acids used in virtually all life forms from twenty to twenty-one amino acids. Thus a new, human-designed functioning genetic chassis and genetic code was placed into a microorganism.

In 2010, after some fifteen years of intense research effort, the first entirely synthetic organism was created with a genome entirely synthesized “out of four bottles” i.e., chemically synthesized from the four DNA bases; thymine, cytosine, guanine, and adenine. The organism was partially based on M. mycoides, a genetically simple microorganism containing roughly 480 protein-encoding genes and a genome size of 1.08 million DNA base pairs – in comparison the human genome has roughly 20,500 genes over three billion DNA base pairs. The synthetic genome was chemically synthesized in 80-90 base units and slowly assembled into “DNA cassettes”, verified by sequencing, and assembled into a circular genome. To insure that no natural DNA contaminated the synthetic DNA “watermark” sequences were inserted into synthetic genome to differentiate it from the natural M. mycoides genome. Additionally, antibiotic resistance genes were added and a disease-inducing gene was removed from the synthetic genome. The resulting genome was place in an empty M. capricolum cell (i.e., without a nucleus) and the resulting synthetic life from was able to grow in culture indefinitely. Since 2010 this synthetic organism has been useful in identifying the “minimal genome” required for life – about 380 of the 480 protein-encoding genes. Additionally, comparison of the synthetic organism to similar naturally occurring organisms (Mycoplasmas), allowed the identification of gene groups involved in cellular processes such as 

• information storage, 
• metabolism, 
• energy production and conversion, and 
• cell membrane biogenesis. 

Identification of these gene sets is an important first step designing synthetic life that can perform specific functions.

Although a significant first step in the creation of synthetic biological life, this initial work met with extensive criticism. The researchers who made synthetic life were accused of “playing God” and possibly opening up a new technology that would allow the creation of “biological super weapons”. The later objection has some validity, as existing DNA synthesis and end-joining technology could allow the synthesis of fully infective polio or smallpox viruses. Other researchers pointed out that the new synthetic organism was a nearly one-to-one copy of a naturally occurring organism and for it to grow the synthetic genome had to be placed into a naturally occurring Mycoplasma that had its nucleus removed. Thus, other than the DNA being artificially synthesized, there was relatively little that was actually new about the organism. The creators of the new organism pointed out that this is a first step of many and “creating life from scratch” will come later.

Currently the immediate focus in synthetic biological life research is to use simple synthetic organisms to define the “minimal genome”, or the smallest set of genes required to support life and identify the components and functions of “biological gene-chassis” and find ways to modify these chassis. Specific applications include the creation of synthetic organisms that can: 

1. efficiently produce pharmaceuticals and vaccines that are otherwise difficult and expensive to produce, 
2. efficiently produce hydrocarbon biofuels (replacing oil, coal, etc.), and 
3. be useful as plant feedstock in agriculture, lowering the need for increasingly expensive petroleum-based fertilizers. 

An example of such an application has been inserting the enzymes for artemisinic acid synthesis into baker’s yeast. Artemisinic acid is the chemical precursor anti-malarial drug artmisinin, a drug that is currently extracted from the sweet wormwood plant at high cost, reducing the drugs availability in poorer countries. Once the enzymatic pathway is in place and efficiently working, the drug could be produced cheaply in large amounts through a process resembling brewing beer. Several of these projects are being researched at Synthetic Genomics, a new biotechnology company specializing in the creation of synthetic life for specific applications.

Not surprisingly the creation of synthetic animal life is more complex and difficult than for simpler microorganisms. However, a round worm (C. elegans) was created that carried an extensively expanded genetic code and protein synthesis pathways, allowing the incorporation of multiple novel (or “unnatural”) amino acids into the animal’s proteins. These protein modifications would facilitate the study of protein localization and interactions within a living animal. Additionally, modified proteins could be designed for specific purposes, such as protein-based drugs with very long half-lives due to novel amino acids that inhibit normal cellular protein degradation.

Although difficult, our present molecular biology technology could allow the creation of more complex organisms, including fungi and even animals. The present challenges in creating synthetic life include the following:

1. Create synthetic life “from scratch” without the need to largely copy existing life forms.
2. Improve on our ability to design and integrate molecular pathways within synthetic life.
3. Create a strategy or “algorithm” to for the efficient creation of synthetic life forms.
4. Create policies and rules to prevent the creation of synthetic life forms that may be harmful, such as human pathogens (smallpox, virulent influenza viral types, etc.).

With time these goals could be achieved and the technology to accomplish these goals is largely in place.

In the more distant future synthetic biology could allow the extensive modification of existing genomes and even the creation of entirely new genomes and species. While this is the goal of many Transhumanists, one hopes that if and when such technology exists, the human race has the intelligence to apply such technology with wisdom.

Dr. Shackelford is an Assistant Professor of Clinical Pathology at Tulane Medical Center. He has a DO degree from Des Moines University of Osteopathic Medicine and a Ph.D. in molecular pathology from Duke University. His areas of research include DNA repair, molecular mechanisms of carcinogenesis, and cell division.