The Origins of Synthetic Life
A brief story of the Minimal Synthetic Cell Project
Synthetic biology is an up and coming domain of biology whose main objective is to create fully operational biological systems from the smallest constituent parts possible, including DNA, proteins, and other organic molecules. It involves the design or construction of new biological so and so and even manipulation of existing systems to optimise them to our needs.
This article focuses on the development of the first synthetic organism — its major goals and methodology.
JCVI SYN Project
The first self-replicating synthetic cell was engineered in the year 2008 in the laboratory of J. Craig Venter at San Diego’s J. Craig Venter Institute(JCVI). This self-replicating synthetic cell was called Mycoplasma mycoides JCVI-syn1 (SYN1.0). Further research led to the development of the improved version, i.e. SYN 3.0.
Goals of the project
A major goal in synthetic biology is to have the capacity to predictably design and build DNA that produces a cell with new and improved biological functions that do not already exist in nature. Significant advances have been made in DNA design at the gene and pathway level and in engineering bacteriophage genomes. But, even with all the advances that have been made in genomics and synthetic biology, there is still not a single self-replicating cell in which we understand the function of every one of its genes. Toward this goal, the JCVI team, along with Venter’s company, Synthetic Genomics Inc(SGI). has been working to understand the gene content of a minimal cell — a cell that has only the machinery necessary for independent life.
All about the Research
In, 2010 Venter’s team had isolated the sole chromosome of Mycoplasma mycoides — a bacterium with a relatively small genome — and transplanted it into a different species of mycoplasma(term used for a unique class of bacteria) called M. capricolum, from which they had already removed the DNA. After several false starts, they showed that the synthetic microbe prepared and synthesized proteins normally made by M. mycoides rather than M. capricolum. Still, other than adding a bit of watermark DNA, the researchers left the genetic material in their initial synthetic organism, SYN 1.0, unchanged from that of the donor bacterial species.
In next part, Venter, along with project leader Clyde Hutchison at JCVI, set out to determine the minimal set of genes needed for life by stripping off nonessential genes from SYN 1.0. Each of them led a team of scientists, who had the same task: using all available genomic knowledge to design a bacterial chromosome with the hypothetical minimum genome. Proposed genomes from both teams were then synthesised and transplanted into M. Capricolum to see whether either would produce a viable organism.
It was Venter and his colleagues who had better success in this exercise which involved extensive trial and error. Venter and his team divided SYN 1.0’s genome, with its 901 genes, into eight sections. To the beginning and end of each section they added identical DNA tags that made the pieces easy to reassemble. That allowed them to treat the sections as independent modules, removing each one in turn, deleting chunks of DNA, then reassembling the full genome and re-inserting it into M. capricolum to see whether it produced a living cell. If the altered genome wasn’t viable, they knew they had cut out an essential gene that had to be restored. The researchers also assessed the necessity of numerous genes in the microbe by inserting foreign genetic material, called transposons, to disrupt their function.
All this enabled them to systematically whittle away genes that either had nonessential functions or duplicated the function of another gene. In this way, they ended up building, designing and testing “multiple hundreds” of constructs before zeroing in on Syn 3.0, with a genome about half the size of Syn 1.0’s. ( Syn 2.0 was an intermediate stage in this process, the first microbe with a genome smaller than that of M. genitalium, which with 525 genes has the fewest of any free-living natural organism.). The functions of the genes of Syn 3.0 are mentioned in the above figure.
Once the composition of the genome was decided on, the genes were reordered aligning the ones that work in the same pathways. The procedure tidied up the genome much as a computer compresses and reorganizes files on its hard drive to save disk space.
Conclusion
The project to build the new synthetic cell has evolved considerably since its inception. Initially the goal was to identify a minimal set of genes that are required to sustain life from the genome of Mycoplasma genitalium, and rebuild these genes synthetically to create a “new” organism. Mycoplasma genitalium was originally chosen as the basis for this project because at the time it had the smallest number of genes of all organisms analyzed. Later, the focus switched to Mycoplasma mycoides and took a more trial-and-error approach.
In 2010, the complete genome of M. mycoides was successfully synthesized from a computer record and transplanted into an existing cell of Mycoplasma capricolum that had had its DNA removed. It is estimated that the synthetic genome used for this project cost US$40 million and 200 man-years to produce. The new bacterium was able to grow and was named JCVI-syn1.0, or Synthia. After additional experimentation to identify a smaller set of genes that could produce a functional organism, JCVI-syn3.0 was produced, containing 473 genes.149 of these genes are of unknown function. Since the genome of JCVI-syn1.0 is novel, it is considered the first truly synthetic organism.
