Are Prosthetic Genes Next?

A section of DNA; the sequence of the plate-li...

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By Robert Holt

There is nothing particularly thought provoking about a Teflon frying pan, but it has enormous utility when frying eggs. Teflon (the DuPont brand name for polytetrafluuoroethylene) doesn’t exist in nature. It is a polymer, a chainlike assembly of simple, repeating, fluorinated carbon molecules that was first synthesized by DuPont scientist Roy Plunkett in 1938. It is the only know substance to which a gecko cannot stick.

DNA, or deoxyribonucleic acid, is a polymer. It is a natural polymer, comprised of a chainlike assembly of four different constituent deoxyribonucleotides, commonly referred to as DNA bases A, G, C and T. Each base has considerably more structural ornamentation than the pedestrian fluorinated carbons of Teflon, and when appropriately paired and polymerized as they are in the genome of every living thing, they form an elegant double helical structure. Genetic information, the instructions for cells to make gene products that form the structural and functional components of cells, is carried in the particular order of bases in the double helix. The order of bases in the sum total of DNA that encodes our biosphere has been laid down over evolutionary time. The order is not immutable but it is resilient, left on its own. We have become very good at reading the order of DNA bases (ie. DNA sequences) to the point where an individual human genome comprising billions of ordered bases can be read in about a week. A bacterial genome, typically containing a million or so nucleotides can be read about as fast as the DNA can be purified.

Like Teflon, the new bacteria, Mycoplasma mycoides JCVI-syn1.0, has its origins in polymer chemistry. The genome sequence of its forbearer, Mycolplasma mycoides LC has been known for some time. When we know the order of bases in a piece of DNA we can physically reconstruct it. The procedure involves chemically modifying a base to specify its reactivity, joining it to another base to create a sequence of two, then demodifying this product in readiness for addition of the next base. It is slow, expensive and error prone and can support only a few dozen additions. The approach hasn’t changed much since the first chemical synthesis of DNA molecule, a 77 base fragment of a yeast gene, was synthesized by Har Gobind Khorana and colleagues in 1965. This being the case, the synthesis of a plethora of short DNA precursors, each a carbon copy of a particular fragment of the 1.08 million base Mycoplasma mycoides LC genome, and the assembly of these chemical precursors into the complete, accurate and functional genome of JCVI-syn1.0 is a tour de force in both polymer chemistry and synthetic biology.

The Mycoplasma mycoides JCVI-syn1.0 genome is a prosthetic genome because like any other prosthesis, it is an artificial replacement of a missing body part, albeit an essential one in this particular case. Where will this remarkable new direction in chemical synthesis lead us? Unlike Teflon frying pans, JCVI-syn1.0 cells have zero utility. In fact, if anything they are more likely to have negative utility. It is well established that some types of mycoplasmas are infectious, and in the laboratory many a research project has been derailed by incidental mycoplasma contamination of cell cultures and considerable effort goes into making molecular biology labs mycoplasma free, to the point where an entire industry is dedicated to this problem. A google search for “Laboratory Mycoplasma Decontamination” returns 160,000 hits. Try it.

So why would anyone want to dedicate years of R&D and tens of millions of dollars to build a mycoplasma? Why create the synthetic genome of a parasitic pathogen? To digress a little, synthetic mycoplasma is a legacy project. Initial studies begun over a decade ago focused on Mycoplasma genitalium because it was known to have one of the smallest genomes of any cellular organism – only half a million bases. It was anticipated that the small genome size, plus lack of a fortified cell wall, would make genome reconstruction and activation of more tractable. The reason to try to reconstruct and activate a synthetic genome was simply to show that it could be done. However, when the genitalium genome was built it could not be activated by transfer into a recipient mycoplasma cell, probably because its genomic composition was just too different from that of the standard recipient, Mycoplasma capricolum. To digress further, since capricolum was already known to be able to support transfer of the natural, but larger, mycoides genome the synthetic genitalium operation was scrapped and replaced by the now successful synthetic mycoides project. Although there have been claims that, being engineerable, mycoplasmas could now have commercial applications, this is is highly debatable. The fragile cell membrane that positions mycoplasmas so well as experimental organisms for microbial genomics makes them, at the same time, completely unsuitable for the heavy lifting of industry. These tasks are better suited to their more robust bacterial cousins.

Although lacking any real world utility, Mycoplasma mycoides JCVI-syn1.0 is definitiely thought provoking. Why is this genome not just another synthetic polymer? What makes it more intriguing than polyester? At first glance it is probably clear to anyone that what sets this polymer apart is that unlike any former product of chemical synthesis it is supporting what is, undebatably, cellular life. Of course we don’t have a clue how to do the design of an organism from scratch, to pick a particular order of A, G, C an T’s that yields some startlingly new but entirely pre-designed outcome. But we are now able to copy organisms. Change them a bit. So where do things go from here? Could we create a more complex microbe? A yeast, perhaps, which is an organism with a cell structure more related to multicellular entities like ourselves than to bacteria. Various yeast strains have been sequenced, and a typical yeast genome is only about ten times larger than Mycoplasma mycoides JCVI-syn1.0. How about a fruit fly, ten times larger still, and with a well characterized genome sequence? Or, if we follow this train of thought about as far as anyone would care to, how about a person? This is the real impact of the JCVI-1. It is demonstration that once we know a genome sequence, we can rebuild the organism it encodes. Even, in principle, a person. From scratch. Using chemically synthesized DNA fragments. To be sure, the technology is nowhere near being up to the task of constructing or activating anything as large and complex as a human genome, but the point is just that. The hurdle would be a technical one. A problem of scale. For better or worse, contemplation of human existence need no longer be purely metaphysical. We should ask ourselves how we feel about that, and start to act accordingly.

[Ref: Cosmology Magazine]

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