A, T, C, G: Add X and Y (DNA bases)

[mfb]

All natural life uses the same four bases in its DNA: A paired with T and C paired with G. Scientists worked on adding more bases. Just putting them into DNA is not hard, the challenging part is to keep them there: They should not get removed/replaced during reproduction. This has now been achieved. They put a new set of base pairs (X/Y) in E. coli and added some other tools to make it stable in a cell line, including CRISPR-Cas9 that looks for sequences without the X/Y and kills those cells. The newly added bases were still there after 60 reproduction cycles.

A new base pair makes it easier to introduce completely new functions, as it doesn't encode anything in the original cell - every interpretation of it is more controlled.

Source: Press release

 

[Ygggdrasil]

Here's a link to the scientific publication: Zhang et al. 2017. A semisynthetic organism engineered for the stable expansion of the genetic alphabet. Proc Natl Acad Sci USA. Published online before print January 23, 2017, doi:10.1073/pnas.1616443114

Abstract:
All natural organisms store genetic information in a four-letter, two-base-pair genetic alphabet. The expansion of the genetic alphabet with two synthetic unnatural nucleotides that selectively pair to form an unnatural base pair (UBP) would increase the information storage potential of DNA, and semisynthetic organisms (SSOs) that stably harbor this expanded alphabet would thereby have the potential to store and retrieve increased information. Toward this goal, we previously reported that Escherichia coli grown in the presence of the unnatural nucleoside triphosphates dNaMTP and d5SICSTP, and provided with the means to import them via expression of a plasmid-borne nucleoside triphosphate transporter, replicates DNA containing a single dNaM-d5SICS UBP. Although this represented an important proof-of-concept, the nascent SSO grew poorly and, more problematically, required growth under controlled conditions and even then was unable to indefinitely store the unnatural information, which is clearly a prerequisite for true semisynthetic life. Here, to fortify and vivify the nascent SSO, we engineered the transporter, used a more chemically optimized UBP, and harnessed the power of the bacterial immune response by using Cas9 to eliminate DNA that had lost the UBP. The optimized SSO grows robustly, constitutively imports the unnatural triphosphates, and is able to indefinitely retain multiple UBPs in virtually any sequence context. This SSO is thus a form of life that can stably store genetic information using a six-letter, three-base-pair alphabet.

This work follows from efforts published in 2014, in which the same team of researchers first found a way to get the bacterium to uptake and use the unnatural base pair: https://www.physicsforums.com/threads/a-t-c-g-x-and-y-an-new-organism-with-unnatural-dna.752640/

It will be interesting to see what applications could come from organisms with unnatural base pairs. Of course, the organisms are reliant on unnatural bases supplied by the researchers and the protein synthesis machinery cannot recognize the new base pairs. An interesting, but very difficult, next step would be to engineer bacteria that not only contain the unnatural base pair, but actually make use of it.

 

[BillTre]

It sounds like this was only to show the maintenance of the sequence through a few generations of replication, but that it had no known function in the organism. (I could only read the abstract.)

How much sequence contained these bases?

An interesting, but very difficult, next step would be to engineer bacteria that not only contain the unnatural base pair, but actually make use of it.

Seems the next steps would involve something like:

• An expanded alphabet RNA monomers (same as for the DNA) and the enzymes to handle them,
or the encoded DNA information would revert from 6 (nucleotide)-speak to 4-speak RNA information.

• Enzymatic function might be created by making ribozymes (RNAs with enzymatic properties - they are important in some theories of life's origins). This could avoid the complexities of protein synthesis. An RNA molecule would assume some particular 3D shape, based upon its sequence and how it was made. Some of these shapes (encoded in some particular gene's 6-speak genetic code) would endow a ribomolecule with enzymatic properties, making it a ribozyme.

• Proteins might be made more diverse by using the new more complex sequence to encode additional amino acids. This has already been done with the 4-nucleotide code. However, its not clear the extra bases are advantageous for this. Perhaps the extra code cold be used as a fail-safe mechanism to prevent weird things from happening if it were to escape (as so many GMOs have).
Making proteins would additionally require an expanded set of tRNAs (already done), as well as the enzymes that load specific tRNAs with amino acids (coded for be genes for proteins). Plus enzymes to handle any additional metabolic tasks. (of the

 

[Ygggdrasil]

Enzymatic function might be created by making ribozymes (RNAs with enzymatic properties - they are important in some theories of life's origins). This could avoid the complexities of protein synthesis. An RNA molecule would assume some particular 3D shape, based upon its sequence and how it was made. Some of these shapes (encoded in some particular gene's 6-speak genetic code) would endow a ribomolecule with enzymatic properties, making it a ribozyme.

I suspect this might be the next big step. Look at the structure of the unnatural base pair (image taken from Fig 1 of the PNAS paper):

The thioketone and thioether in the dTPT3 nucleotide that the authors created might enable new types of chemistry in ribozymes.

 

[strangerep]

I used to believe: "If it's been the focus of an X-Files episode, then it's a load of rubbish". I guess I must now make an exception (even though it's not extra-terrestrial DNA).