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World’s first synthetic organism with fully recoded DNA is created at MRC LMB in Cambridge

A new lifeform has entered the world: one that plays by different biological rules to any other before it.

Jason Chin at the MRC Laboratory of Molecular Biology in Cambridge. Picture: Keith Heppell
Jason Chin at the MRC Laboratory of Molecular Biology in Cambridge. Picture: Keith Heppell

It is synthetic – that is, artificial, man-made – yet is very much alive.

And its creation could unlock the doors to a new world of materials for humankind, the scale of which we can scarcely comprehend yet.

The lead creator of this unique and intriguing lifeform, Jason Chin, at the MRC Laboratory of Molecular Biology in Cambridge, hopes it will lead to a “paradigm shift” in biochemistry.

His team’s achievement, five years in the making, is the synthesis of the entire genome of the bacterium Escherichia coli (E. coli) – and they have done it while recoding its DNA completely.

Only once before has a full genome been synthesised. That was in 2010, when US geneticist Craig Venter announced that after a decade of work by a team of 20 scientists, the Mycoplasma bacterial genome had been synthesised.

Dr Venter’s achievement led to accusations in some quarters of ‘playing God’ and concerns that rogue organisms could escape the lab and play havoc – four watermarks were written into the DNA of the synthesised single-cell organism to identify it, and its descendants, as synthetic.

Mycoplasma’s genome consists of about one million ‘bases’ – the fundamental units of DNA,

But E. coli can trump that: it has four million of them, so new technology was developed to take on the challenge.

“We were interested in being able to make the genome of E. coli, which is a commonly-used laboratory bacterium, and we wanted to make a version with particular changes in its DNA sequence,” Dr Chin explains to the Cambridge Independent.

For E. coli – and all known life on Earth – 64 is an important number.

It is derived from the fact that DNA is made of four bases – represented by the letters G, A, T and C. The code they create is ‘read’ by the biological machinery inside cells in sets of three in order to create amino acids, the building blocks of proteins.

There are 64 possible combinations of these sets of three, also known as codons.

From humans to fish, elephants to mosquitoes, all life uses 64 codons – and 61 of them provide the instructions for the 20 different amino acids used to build proteins. The other three function as full-stops, terminating the production of a protein.

“This means that there is redundancy in the code – there are ‘synonymous codons’ that encode the same amino acids,” explains Dr Chin.

The MRC Laboratory of Molecular Biology in Cambridge has recoded the genome of the bacterium Escherichia coli (E. coli). Picture: MRC LMB
The MRC Laboratory of Molecular Biology in Cambridge has recoded the genome of the bacterium Escherichia coli (E. coli). Picture: MRC LMB

“A long-standing question in biology is why are 20 amino acids encoded by 64 codons? Is there any function to having more than one codon to encode each amino acid?

“What would happen if you made an organism that used a reduced set of codons?”

In their experiment, the researchers designed an E. coli genome in which all instances of two codons for the amino acid serine (TCG and TCA) were replaced with synonymous codons (AGC and AGT), and every instance of the stop codon TAG was replaced by another, TAA.

Using these rules, 18,214 codons were recoded – and if the full genome code was printed out on A4, it would stretch to a dizzying 970 pages.

“It’s like taking the sequence of a genome written down in a text file and doing a ‘find and replace’ at 18,000 positions,” says Dr Chin.

Having designed the recoded genome, the researchers had to assemble it – a task that took two years.

Julius Fredens, Kaihang Wang, Daniel de la Torre, Louise Funke, and Wesley Robertson, researchers from Dr Chin’s group, deployed a technique that another colleague, Kaihang Wang, had developed.

“We wanted methods to replace the E. coli genome in sections piece by piece with synthetic DNA, with the changes in codons,” says Dr Chin. “We developed an approach that allowed us to replace, in a single step, 100,000 base pairs of DNA in the E. coli genome with the corresponding recoded piece of synthetic DNA that we had made in the laboratory.

“We were able to iterate that process, replacing the adjacent region. We did that five times to replace 500 kilobases of the genome. We did that from eight different places in eight different strains of E. coli, so we ended up with eight strains each with one eighth of the genome replaced with synthetic DNA. Then we developed an approach that combined them into a single genome.”

A key advantage with the approach was that if any mutations occurred that prevented the genome from functioning, the research team could pinpoint precisely where the fault lay, down to a single base pair, and correct it – like finding a bad line of code in a computer programme.

“This approach allowed us to make only the second synthetic genome ever made, and the largest by a factor of four, and the most radically altered,” says Dr Chin.

The synthetic E. coli grows more slowly than the natural version, and is a little longer. But it is alive – and has answered a fundamental question in biology.

“What we know from our experiment is that 64 codons are not essential for life,” says Dr Chin.

It is thought that evolution has led to all life using 64 codons – like a common genetic language that everyone can understand.

“It is advantageous for all organisms to use the same genetic code because it allows them to share information and so evolution can progress,” says Dr Chin. “If everyone can read from the same script, they can learn from each other.”

But one of the reasons for seeking to make organisms with fewer codons is precisely to avoid this sharing of information.

“One of the challenges in biotechnology is that when you’re growing bacteria in a fermenter to produce a pharmaceutical, you can get an infection from a phage or virus in that culture that can destroy the whole production,” says Dr Chin. “That’s because viruses or other type of cells share the same genetic code with the cell you are interested in using in bacteria.

“Viruses inject the DNA into the cell and rely on the host cell to copy that DNA and make proteins from that DNA.”

DNA bases are represented by letters
DNA bases are represented by letters

Removing some of the codons, and the translational machinery – known as tRNA – that reads them from a cell throws up a ‘genetic firewall’ around it. Instructions from a virus infecting that cell will be impossible to carry out.

“The host cell won’t co-operate and won’t make the proteins the virus needs. It’s one tangible application of making recoded genomes,” says Dr Chin.

But there are other even greater advantages.

Like freeing up space on a hard drive, removing codons and the machinery that reads them also creates space for new programmes.

“You can introduce genes containing codons and new machinery that would read them in a different way,” explains Dr Chin.

“You can put in machinery that will build polymers composed of things beyond natural biology.

“It has been one of the long-term goals of my laboratory: to develop approaches that allow us to take the way cells build proteins and use them to encode the biosynthesis of non-natural polymers.

“Could we biosynthesise new materials or new therapeutic molecules?

“This could allow us to build entirely new types of materials. It will be a paradigm shift in how we make polymeric materials.”

The MRC Laboratory of Molecular Biology in Cambridge has recoded the genome of the bacterium Escherichia coli (E. coli). Picture: MRC LMB
The MRC Laboratory of Molecular Biology in Cambridge has recoded the genome of the bacterium Escherichia coli (E. coli). Picture: MRC LMB

From environmentally-friendly plastic alternatives built by cyanobacteria using the power of the sun, to synthetic organisms that provide nitrogen for plants, reducing the need for fertilisers, synthetic biology experts around the world are already working on projects that could reshape our use of materials.

The work of Dr Chin and his team has given them a whole new toolkit, and could open up opportunities for new drugs and enzymes.

“We think this will be a transformational platform for being able to discover new types of molecules that are inaccessible because they lie between what biology can do and what chemistry can do,” he suggests.

“Biology is incredibly powerful at making polymers of defined sequences encoded in genes, but it can only do that with the building blocks of biology – in the case of proteins, it is 20 amino acids.

“Chemistry is very good at making small molecules and short polymers.

“If you combine the abilities that chemists have to make chemically-synthesised monomers with the ability of biology to string together polymers of defined sequence and composition, that would really open up the ability to make a whole new class of molecules.

“The idea is not to make something that already exists as a known material better or faster, but unlock the potential to discover endless new types of material that we currently can’t synthesise or access.”

In addition to exploring such applications, Dr Chin’s group will try to find out if the number of codons can be further compressed.

And they will aim to speed up the creation of synthetic genomes.

“This project was several years of work. We’ve set ourselves a target of making a synthetic genome in a month using some of the techniques we’ve learned,” he reveals.

Why E. coli?

Those familiar with E. coli –which has a public reputation lying somewhere between Clostridium difficile and salmonella – may wonder at its selection.

But in addition to the strain that leads to a hideous bout of diarrhoea and vomiting, E. coli is very useful as a biological model. Experiments on hardy, non-pathogenic strains have helped us advance our understanding of biology, and it is used in therapeutics, including to create insulin to treat diabetes, and to treat haemophilia, gout, cancer and other diseases.

E. coli is a real workhouse in biology,” says Dr Chin. “So this is a practical choice both for studying basic biology and for biotechnology.”

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