The next evolutionary step

Human have always tried to improve on nature, from domestication of plants & animals through directed evolution in the test tube and GMO and up to Craig Venter’s synthetic bacteria and the expansion of the genetic code.
Today, another step was taken towards creating completely artificial life.

The natural genome is composed of four bases, which form two pairs: A-T and G-C. This pairing allows the double-helical DNA to maintain the information upon replication (the  semi-conservative replication).

The group of Floyd Romesberg from the Scripps institute now published a paper in Nature titled “A semi-synthetic organism with an expanded genetic alphabet”. I think that the title is a bit misleading, since its not really semi-synthetic, but is still awesome.

Roemsberg have previously published several papers on a synthetic deoxyribonucleotide pair: d5SICS and dNaM (I have failed to discover what these abbreviations stand for). These bases create an unnatural base-pair, yet it is still recognized, in vitro, by DNA and RNA polymerases and is maintained upon semiconservative replication (e.g. by PCR).

Now, they incorporated this pair into the bacteria E. coli to see if this pair can be maintained in vivo.

Chemical structures and the unnatural (d5SICS-dNaM) and natural Watson–Crick (dC-dG) base pairs. Source: Malyshev et al. (2012) PNAS vol 109:12005-12010.

The main problem going in vivo is how to get these bases into the bacteria, and how to get achieve the tri-phosphate (tri-P) form that can be incorporated by the DNA polymerase. They decided to use synthetic tri-P forms and screen to a transported that can import them into the cell. Having found a suitable nucleotide triphosphate transporters (NTT) from Phaeodactylum tricornutum and solved a problem of de-phosphorylation of the tri-P bases before they enter the cell, they set out to test if the bases-pair can be maintained in the E. coli cell.

To this end, they synthetically created a plasmid that harbors one d5SIC-dNaM base pair at a specific location. After transformation, they show that this base-pair is maintained at 95-97% of the plasmids for 15hr (24 generations). If they let the bacteria grow to stationary phase without supplementing them with fresh media (with fresh synthetic bases) then they slowly lose this pair to an A-T pair. but even after 6 days, ~10% of plasmids maintain this pair. This suggests that the replacement is not due to repair but due to the polymerase errors, and depletion of the bases in the media (though they don’t actually prove its not repair).

At this point, the paper ends. So, first of all, having one base pair is not semi-synthetic. I was disappointment 🙂

Second, I hope these experiments can be repeated by other labs, and we will not get another “arsenic life” scandal.  But by the looks of it, it seems more reliable.

Third, this could be a platform for real synthetic biology, with a 6-letter code, instead of the 4 we have now, (that’s 216 3-letter codons, instead of the 64 we naturally have.  If we go to 4-letter codons, that’s 1296 codons to use.)

These could be used to create synthetic, unnatural proteins to produce new products; ribozymes and other RNA structures; imagine gene therapy that can only be maintained by ingesting these synthetic bases and I’m sure there are many options I haven’t thought of. In terms of this blog – maybe fluorescent proteins or RNA aptamers with interesting or useful properties (e.g. fast folding, very bright, etc..).

And last, this is the first proof that a DNA molecule does not have to be composed by the bases we’re used to. Aliens from other planets could have DNA molecules with similar double-helix Watson-Crick structure, semiconservative replication, but made out of other ribo nucleotide bases.

At the very least, we can revive dinosaurs without fearing they will run off the island and get their Lysine contingency supplemented elsewhere.
Malyshev, D., Dhami, K., Lavergne, T., Chen, T., Dai, N., Foster, J., Corrêa, I., & Romesberg, F. (2014). A semi-synthetic organism with an expanded genetic alphabet Nature DOI: 10.1038/nature13314