“We can now begin working on our ultimate objective of synthesizing a minimal cell containing only the genes necessary to sustain life in its simplest form. This will help us better understand how cells work.” — Dan Gibson
We’ve been following the efforts of the Venter Institute to develop a synthetic bacterial cell. The goal of this research has been to achieve the capability to “understand by building” as applied to the cell.
Last night we noted that TED.com was hosting a Craig Venter press conference where on May 20th he announced their success. The talk is a bit dry compared to the typical TED Talk, but we think you will find it exciting. Venter describes several of the unexpected roadblocks encountered in the project, commenting to the effect that “over 99% of our experiments were failures”.
You can read a summary in a Venter/Gibson WSJ op-ed which begins:
In 1995, we reported the DNA sequences for the first two cellular genomes. Nowadays genome sequences, which contain the genetic instructions for an organism, are routinely obtained and deposited in computer databases.
Last week, we reported that this process can be reversed. The digitized DNA information of Mycoplasma mycoides, a simple bacterium, can now be brought to life.
To make this happen, our group of 25 researchers had to decipher this bacterium’s set of instructions, synthesize them, and then express them in a recipient cell. Many technical hurdles had to be overcome. But 15 years and $40 million worth of research later, we are able to combine all of these steps and produce synthetic cells in the laboratory.
So what is new and unique about what we did? The process of synthesizing a cell began at a computer. We started with the more than one million letters of genetic instructions for Mycoplasma mycoides, and then made slight modifications to its DNA sequence. First, we deleted 4,000 letters, which removed the function of two genes. We then replaced 10 genes with four “watermark” sequences. These watermark sequences are each over 1,000 letters in length and can be decoded to reveal the names of people, famous quotations and a website address. The entire sequence of DNA letters was then partitioned into 1,100 pieces, and each was synthesized using four different bottles of chemicals that make up DNA. These DNA fragments were designed such that adjacent pieces contained an 80-letter overlap, which facilitated the assembly process by providing unique regions where the synthetic pieces could join.
For the in-depth results you can access at Science Express: Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome [full text available here as PDF]. And the Venter Institute press release.
What does this accomplishment mean? First, the pace of synthetic biology has been much slower than we hoped (and slower than advocates like Stanford’s Drew Endy forecast). Second, the technical feat of assembling a 1 million letter DNA sequence is still staggering. E.g., just consider the error-detection/correction challenge — this is the debugging method developed to isolate a synthesis error in the final stages:
The initial synthesis of the synthetic genome did not result in any viable cells so the JCVI team developed an error correction method to test that each cassette they constructed was biologically functional. They did this by using a combination of 100 kb natural and synthetic segments of DNA to produce semi-synthetic genomes. This approach allowed for the testing of each synthetic segment in combination with 10 natural segments for their capacity to be transplanted and form new cells. Ten out of 11 synthetic fragments resulted in viable cells; therefore the team narrowed the issue down to a single 100 kb cassette. DNA sequencing revealed that a single base pair deletion in an essential gene was responsible for the unsuccessful transplants. Once this one base pair error was corrected, the first viable synthetic cell was produced.
I feel confident in predicting that Venter will not be building a pilot plant for his synthetic biofuel next year. But I would definitely not bet against important breakthroughs in the next five or so years. At least I hope the promise is not always “just five years ahead”. Here’s Venter/Gibson from the WSJ op-ed on one of our priority wishes, that of rapid-response vaccine development:
(…) We are currently working on the design of new cells that can much more efficiently capture carbon dioxide and “fix” (or incorporate) the carbon into new fuel molecules, new food oils, and new biologically derived sources of plastic and chemicals. We already have funding from the National Institutes of Health to use our synthetic DNA tools to build synthetic segments of every known flu virus so that we can rapidly build new vaccine candidates in less than 24 hours. We are also being funded to see if we can take sets of genes out of bacteria to design new synthetic pathways to make antibiotic compounds that are currently too complex for chemists to make.
One (of many) things we don’t yet grasp is “why did Venter switch from the original goal of synthesizing the minimal organism?” Please comment if you know. Meanwhile, we have this from the useful FAQ:
Q: What are the next steps for this research at JCVI?
A: The work to create the first self-replicating, synthetic bacterial cell was an important proof of concept. The team at JCVI has learned a lot from the nearly 15 years it has taken to get to this successful stage. From this proof of concept experiment the team is now ready to build more complex organisms with useful properties. For example, many, including scientists at SGI, are already using available sequencing information to engineer cells that can produce energy, pharmaceuticals, and industrial compounds, and sequester carbon dioxide. The team at JCVI is already working on their ultimate objective, which has been to synthesize a minimal cell that has only the machinery necessary for independent life. Now that a cell can be synthesized from a synthetic genome in a simple near-minimal bacterial cell, it becomes possible for the team to test for the functionality of a genome. They can whittle away non-essential DNA regions from the synthetic genome and repeat transplantation experiments until no more genes can be disrupted and the genome is as small as possible. This minimal bacteria cell will enable a greater understanding of the function of every gene in a cell and a new vision of cells as understandable machines comprised of biological parts of known function.