In the 19th century, Bavarian King Ludwig II - whose most famous legacy is Neuschwanstein castle - had artificial marble made for another one of his castles that cost far more than the real thing.
In the Jan. 24, 2008, issue of Sciencexpress, researchers from the J. Craig Venter Institute have pulled off a parallel feat. They chemically synthesized the genome of a real bacterium, Mycoplasma genitalium.
So far, researchers have not yet inserted the artificial chromosome into a cellular cytoplasm to see whether it can take functional control of that cytoplasm and turn into a true living organism. But the same team published research last year showing that they managed to transplant an entire chromosome of of Mycoplasma mycoides into a close relative, Mycoplasma capricolum. (See BioWorld Today, June 29, 2007.)
The results suggested that such a transplantation will be possible for the artificial M. genitalium as well. Venter told reporters at a press briefing that "I will be . . . disappointed if we can't do it in 2008."
M. genitalium has roughly 500 genes in 600,000 base pairs, which makes it have the smallest known genome of any life form that can replicate independently. Many viruses have smaller genomes, but they cannot replicate without enlisting the support of their hosts. The work was done as part of the institute's synthetic biology program, which Hamilton Smith, who is the paper's senior author, directs. "The goal," Smith told Science in a podcast, "would be to get a cell in which every gene is absolutely essential."
Smith estimated that the number of essential M. genitalium genes will be about 400. More than a hundred genes have been knocked out of the bacterium's genome one at a time without killing it, but it is not clear how many can be knocked out simultaneously - let alone which ones in which combinations.
Hamilton's team says that knocking out complex combinations of genes can be achieved most easily by synthesizing genomes lacking the genes of interest.
Beyond such basic science questions, though, the team has high hopes for practical applications of making either whole artificial chromosomes or a combination of natural and artificial genes. The authors noted in their paper that "nothing in our methodology restricts its use to chemically synthesized DNA. It should be possible to assemble any combination of synthetic and natural DNA segments in any desired order."
The work reported in Sciencexpress was funded in large part by institute spinout Synthetic Genomics Inc., which according to its website, is "dedicated to developing and commercializing genomic-driven solutions to address global energy and environmental challenges." Venter and Smith are co-founders and share the position of chief scientific officer at Synthetic Genomics. Putting the synthetic genome back together from scratch was a "formidable technical challenge," the authors wrote in their paper. M. genitalium may have the smallest known genome, but that genome size is still an order of magnitude larger than the biggest bit of synthetic DNA that has been reported to date.
The researchers first used what Smith described as "standard techniques" to assemble 101 short synthetic genetic sequences that together made up the whole of the M. genitalium genome. They then combined shorter stretches in E. coli. That combination worked until they had four quarter-sections of the M. genitalium genome, but "when we tried to string those into halves, we were totally unsuccessful for several months," Smith said. So they switched to yeast, which has "an extraordinarily efficient recombination system" and will combine two overlapping strands of DNA into one longer strand. In fact, in yeast the scientists found that they could dispense with making genome halves altogether. The yeast was able to combine all four quarters into a single artificial genome.
"It really was a surprise to us that we could do it all in one step," Smith said, though he stressed that yeast would not have been able to combine all 100 pieces at once.
When asked at last year's press conference announcing the genome transplant about how synthetic organisms could contribute to solving practical problems, Venter was short on specifics, but he did name "designer fuels based on bacterial metabolism" as a way to produce energy.
There is certainly a market for that application, and if those hopes pan out, they might make artificial chromosomes similar to Bavarian castles in yet another sense. Ludwig's castles, although they nearly bankrupted Bavaria during his lifetime, have certainly proven to be a long-term economic boon. In 2005, the size of the Bavarian tourist economy was upward of €11 million.