Oscillator

Expanding the Genetic Code

genetic code.jpgAlmost every living thing shares an identical genetic code, with three nucleic acids in an RNA sequence coding for a single amino acid in the translated protein sequence. While there are 64 three-letter RNA sequences, there are only 20 amino acids and degeneracy in the code allows some amino acids to be coded by multiple codons. Chemists and synthetic biologists in the past few years have been working to expand this genetic code, with unnatural nucleotides that can be incorporated into DNA and RNA sequences and unnatural amino acids that can expand the chemical functionality of proteins. These amino acids can add chemical groups that are not usually present in proteins to create new biochemical reactions, or to create more stable bonds inside the protein for enzymes that are more resistant to harsh environments. Because each three-letter RNA codon already is matched to a specific amino acid, it’s very difficult to incorporate these unnatural amino acids into proteins of live cells. Some researchers have mutated one of the “stop” tRNAs in E. coli (there are three codons that tell the ribosome to stop, each corresponding to a different tRNA molecule that will terminate the amino acid chain) so that instead of stopping translation it inserts the unnatural amino acid instead. A cell with each of the “real” stop signals in the genome mutated to one of the other two stop codons would be a perfect “chassis” for using one of these unnatural amino acids.

i-fd8d65656fd9a1e451caed21048cc486-quadrupleribosome-thumb-250x193-41264.pngBut what if instead of mutating individual tRNAs, you could make a whole parallel genetic code in a living cell? An awesome paper in this week’s Nature makes progress towards this goal, by using directed evolution to design a ribosome that reads four letter codons instead of the normal three. With a four letter code, you could potentially program 256 different amino acids, to create altered proteins or entirely different biological polymers. For a lot more detail on how the researchers went about “reprogramming the code of life” check out the webcast of a presentation by the senior author, Jason Chin.

Expanding the genetic code to include unnatural biological building blocks is an interesting problem for synthetic biology. Most synthetic biologists aim to recombine natural systems in unnatural ways, making new connections between existing or slightly modified proteins to create a new function. Using different chemical building blocks has the potential to create totally new chemistries with fascinating implications for how we understand and use living systems. An editorial in the most recent issue of New Scientist addresses some of the typical concerns that arise with any new synthetic biology technology:

This is a fundamental advance that could lead to new drugs, materials and energy sources. But tampering with life’s operating system will inevitably raise safety concerns – and it’s true that we have no way of predicting the fallout of this work. Synthetic biologists need to confront openly and honestly public fears that they are “playing God”. If such deeply felt concerns go unanswered, the huge potential of this breakthrough could come to naught.

Designing unnatural amino acids can seem, well, unnatural, but most research in synthetic biology is primarily about better understanding how natural living things work. Moreover, realistically, we can’t change all that much without wrecking proteins and killing the cell. It is very hard to predict how a protein will fold from just looking at the protein sequence (with today’s computer technology it’s impossible for more than a handful of amino acids), and when you throw in unnatural amino acids with different chemistry it gets even harder. Unnatural amino acids may become gradually incorporated into research of how proteins fold and how they function chemically.

In many ways, the use of unnatural nucleotides and amino acids in laboratory strains of bacteria has the potential to actually create safer synthetic systems. Unnatural amino acids have to be chemically synthesized and supplied to the cell in the growth medium, thus preventing the cells from being able to grow in the wild if they were to escape. More importantly, wild-type cells would be unable to “read” the synthetic genes in a cell with an expanded genetic code, so any gene transfer between engineered cells and natural cells would make protein “gibberish” (most random protein sequences don’t actually fold in the cell, and thus would not lead to any new function). Instead of simply relying on the hand wave-y argument of “lab strains are already probably unfit for survival in the wild”, these sorts of “failsafe” systems may soon be feasible to ensure environmental health and safety for all new biological designs.

(via New Scientist)

Comments

  1. #1 Boris Legradic
    February 19, 2010

    Fascinating stuff, nearly makes me regret that I chose to study physics and not biology!

  2. #2 Christina
    February 19, 2010

    Haha it’s not to late! Many great biologists started out as physicists :)

  3. #3 Lucas
    February 19, 2010

    Truly a great accomplishment! It’s no small feat to create a new molecular toolbox, and that’s certainly true for a toolbox that functions alongside the original machinery of the cell.
    For example, if you want to identify interaction partners of a protein, instead of unwieldy techniques like TAP-tagging which add entire new strings of amino acids to existing proteins, it’s maybe possible to introduce a single modified a-acid which can be purified.

    And not to be a pessimist (I don’t like the negative undertone of the new scientist piece), but no system is failsafe of course. Al it took for their o-ribosomes to recognize quadruplets where a couple of mutations right? In any case, this technique is definitely ‘safer’ than current gene manipulation methods. But I think it’s wise to prepare for unlikely events, especially when dealing with living stuff ;).

  4. #4 Mike Barnkob
    February 20, 2010

    Thanks for a great post!

  5. #5 Jonathan Vos Post
    February 20, 2010

    Fascinating stuff; makes me glad that I chose to study, teach, and publish both physics and biology!

  6. #6 gregorylent
    February 21, 2010

    the “genetic code” is the bumps on the skin of an orange .. and tells nothing about the fruit inside, or, my god, the seeds …

    yeah, it needs expanding ..lol

  7. #7 jb
    February 21, 2010

    This kind of thing makes me a little nervous. I can think of two different science fiction stories I’ve read where scientists tampering with the genetics of microorganisms do so in such a clever and original way that they inadvertently create microorganisms that can out-compete all natural life, resulting in the demise of the entire biosphere (a “gray goo” scenario achieved through genetic engineering rather than nanotechnology). I’m sure the odds of this are very low, but creating organisms with an expanded genetic code that could never have evolved naturally would seem like one of the better ways of making it happen.

    True, any such creatures would initially rely on an outside supply of “unnatural amino acids,” which would seem to rule out this possibility. But many bacteria can synthesize their own amino acids. If synthetic life were to turn out to be a home run economically, and were widely used to produce many new and useful products, can we be absolutely certain that nobody would every create synthetic organisms that could supply all their own needs, either maliciously, or simply to shave a few cents of the cost of some product?

  8. #8 Max
    February 23, 2010

    It’s quite likely that early life forms “experimented” with different genetic coding systems before an optimal (or at least satisfactory) one emerged through a combination of chance and natural selection. The 3-letter genetic code has sufficiently low complexity to be efficient, and yet has enough built in redundancy to insure that not every mutation is leads to a drastically different aa substitution.

    Perhaps this protobiotic selection process can be replicated in silico?

  9. #9 Rockpicker
    February 23, 2010

    Isn’t this type of ‘manipulation’ exactly what Clifford Carnicom is suggesting he’s found examples of in EVERY sample of human blood he’s tested?

    Please, some of you who understand and have the equipment to study what he’s talking about, please, do take a look at his research, for humanity’s sake, as government and academia ignore what may well be the ultimate crime against humanity.

    http://www.carnicom.com/morgobs8.htm

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