Tag Archives: Semi-synthetic life

DNA.

DNA just got a major update, with readable synthetic nucleotides

Earlier this year, scientists were unveiling the first, stable semi-synthetic life form. In a paper published today, another research group reports enabling their spawn to read and use the synthetic genetic data, creating compounds entirely new to biological systems.

DNA.

Image credits Colin Behrens.

This year started off with a bang for everyone even remotely interested in the fields of genetics and genetic engineering when researchers from the Scripps Research Institute, California, announced the creation of a stable organism carrying semi-synthetic DNA. While it might not sound like much, the result was a breakthrough. Virtually all life on Earth shares DNA made from four different elements called nuclear bases. These are adenine (A), cytosine (C), guanine (G), and thymine (T). All the complexity of life ever to spring up on this fair planet was borne out of different re-arrangements of these four. Not only can we re-arrange the letters that tell life how to be alive, but now, we can introduce our own symbols in there.

Today, another team from the same institution published a paper that could create a paradigm shift in how we interact with life’s fundamental building blocks. They report that life understands the synthetic nucleotides embedded in DNA.

CTAG-XY

The team first snuck the two additional ‘letters’, X and Y,  into the genome of an E. coli bacterium strain back in 2014. However, the organism was highly unstable. It could maintain X and Y in its genome while going about its daily business, not so much during cell division. Which is a problem when you’re gene-shaping.

“Your genome isn’t just stable for a day,” senior researcher Floyd Romesberg explained earlier in the year. “Your genome has to be stable for the scale of your lifetime. If the semisynthetic organism is going to really be an organism, it has to be able to stably maintain that information.”

Subsequent refining of the organism, including switching to a new nucleotide transporter that would enable more stable DNA replication, a re-design of the Y base, and better delivery through the use of CRISPR-Cas9, allowed it to remain stable even through division.

Now, a paper describing further improvements brought to the organism’s stability comes to expand on that work. Romesberg and his colleagues started by embedding their unnatural bases in genes that also contained A, C, G and T. They found that within the semi-synthetic organism, these genes could be successfully transcribed into RNA molecules also containing the unnatural bases. The cells could then use these RNA molecules at their ribosomes (protein manufacturing plants) to direct the incorporation of unnatural amino acids into proteins.

Fluorescent E. coli.

The fluorescent protein in these bacteria is encoded by artificial DNA bases.
Image credits Yorke Zhang et al., 2017, Nature.

Scientists demonstrated this new transcription process in the E. coli strain, successfully transcribing its artificial X and Y nucleotides into biochemical compounds with the same efficiency it would for natural A, C, G, or T bases. This means that the bacterium could synthesize products containing non-canonical amino acids (ncAAs), compounds encoded by stretches of DNA containing Y and X. Its the first organism to both contain unnatural bases in its DNA and use the bases to instruct cells to make a new protein.

The synthesis process also hints at a new way of replicating molecules that rely to a lesser extent on hydrogen bonds (the type of electrochemical interactions which form the ‘rungs’ in DNA).

“Remarkably, this reveals that for every step of information storage and retrieval, hydrogen bonds, so obviously central to the natural base pairs, may at least in part be replaced with complementary packing and hydrophobic forces,” the team explains in the paper. “Despite their novel mechanism of decoding, the unnatural codons can be decoded as efficiently as their fully natural counterparts.”

The result of this process is a new class of semi-synthetical proteins — compounds we’ve never before seen in natural systems. What sets them apart is their incorporation of the unnatural base pair (UBP), the team writes, while retaining high stability. The four natural DNA bases code 20 amino acids. With the addition of X and Y, an organism could code for up to 152 new amino acids. The researchers hope these amino acids could become building blocks for new medicines.

“We have examined the decoding of only two unnatural codons, but the UBP is unlikely to be limited to these,” the researchers explain. “Thus, the reported SSI is likely to be just the first of a new form of semi-synthetic life that is able to access a broad range of forms and functions not available to natural organisms.”

It’s still unknown where this breakthrough will lead — what’s sure for now is that DNA on Earth just got a major update to its complexity.

The paper “A semi-synthetic organism that stores and retrieves increased genetic information” has been published in the journal Nature.

For the first time, researchers create “semi-synthetic” life form with man-made DNA

Researchers have created the first stable semi-synthetic life, a strain of E. coli bacteria with two extra artificial nucleotides in its genetic code.

Nucleotide chain at the “Miraikan” / The National Museum of Emerging Science and Innovation.
Image credits Miki Yoshihito / Flickr.

You, me, your pets, potatoes, coffee, basically all living things you can think of have one thing in common: the DNA that tells their cells what to do is encoded using only four bases. If you compare DNA to an instruction manual, nucleotides (or bases) would be the letters that make up words. In fact, we even represent them as letters — G, T, C, and A.

Pimp my DNA

You might have noticed that there’s only 4 of them. Which isn’t a lot. That’s why scientists have been toying around with the idea of adding extra letters to DNA for some time now.

It all started in 2014, when a team from the Scripps Research Institute in California successfully added synthetic nucelotides to a living organism’s DNA for the first time, creating so called semi-synthetic life. Their initial cultures were really bad at not dying, however. The team has spent two years refining the process, and has recently reported the creation of stable semi-synthetic organisms.

Their modified E. coli bacteria’s genetic code has two additional bases, X and Y, peppered throughout their DNA. The strain does not reject the X and Y bases and retains them in the genome for life. This achievement has incredible potential, as researchers can now tell cells what to do directly instead of rummaging around DNA strands for bits of code and being limited to natural processes.

“With the virtually unrestricted ability to maintain increased information, the optimised semi-synthetic organism now provides a suitable platform [to create] organisms with wholly unnatural attributes and traits not found elsewhere in nature,” the paper reads.

“This semi-synthetic organism constitutes a stable form of semi-synthetic life, and lays the foundation for efforts to impart life with new forms and functions.”

Bases for life

The team’s initial cultures weren’t viable as organisms. The main problems were that the cultures were weak and sickly compared to natural strains of E. coli, and that they couldn’t reliably replicate X and Y bases during division so their DNA often fractured during the process.

“If the semisynthetic organism is going to really be an organism, it has to be able to stably maintain [genetic] information,” said TSRI Professor and team leader Floyd Romsberg.

The team started by tweaking the nucelotide transport process, which inserts synthetic bases in the right spots of the bacterial genome. Their first transporter molecule was toxic to the bacteria, so it was altered until the cells showed no adverse reaction. Next, they changed the chemistry of the Y base so it was more easily recognized by the enzymes that power DNA replication during division. The last step was to use CRISPR-Cas9 to nudge  E. coli into considering the artificial bases as a natural part of their genome.

CRISPR-Cas9 is widely used as a genome-editing tool today, but it is originally a bacterial defensive mechanism. When encountering a new threat, such as a virus, bacteria take fragments of its genome and grafts it into their own DNA. Though foreign in nature, these pieces of code are treated as belonging to the bacteria. If the invader returns, these bits are used to create enzymes to attack them. The team programmed the semi-synthetic E. coli to treat genetic sequences without X and Y as a threat, meaning that any cells which lost them during replication were attacked.

Using the new methods, they were able to engineer stable E. coli cells. The bacteria are healthier and more autonomous than before. They also kept their artificial bases for 60 division cycles, so the team considers they an likely keep their genome make-up indefinitely.

Genetic gibberish

 

Each natural nucleotide pair encodes a different instruction. But cells don’t understand X and Y bases.
Image via Pixabay.

Right now, the X and Y bases don’t actually do anything. The pair they form doesn’t mean anything from the cell’s point of view — it doesn’t encode any information for the bacteria to use. Basically, they just take up space in the genome. In fact, they’re so foreign the bacteria don’t even know how to make more — the team has to supply X and Y for each division cycle.

As a proof of concept however, it shows that artificial bases can be grafted into a living organism and made to stick. The team will have to insert a gene that is actually readable for the bacteria to start using it.

Because X and Y are nothing like what nature has used up to now, Romsberg advises against panic that the semi-synthetic bug will evolve and wipe us out.

“Evolution works by starting with something close, and then changing what it can do in small steps,” Romesberg told Ian Sample at The Guardian.

“Our X and Y are unlike natural DNA, so nature has nothing close to start with. We have shown many times that when you do not provide X and Y, the cells die, every time.”

Having the ability to program cells to produce exotic proteins is the cornerstone in producing a huge range of new drugs. Alternatively, the E. coli can be used to produce novel materials, store information, and much more.

The full paper “A semi-synthetic organism with an expanded genetic alphabet” has been published in the journal PNAS.