UK scientists have created an artificial version of the stomach bug E. coli that is based on an entirely synthetic form of DNA.
At the same time, Syn61 as they are calling it, has had its genetic code significantly redesigned.
It’s been done in a manner that will pave the way for designer bacteria that could manufacture new catalysts, drugs, proteins and materials.
Other scientists working in synthetic biology have hailed the development.
Genetic engineer Prof George Church, from Harvard University, US, has hailed the work as “a major breakthough”.
Dr Tom Ellis, a reader in synthetic biology at Imperial College London called it super-impressive.
Syn61’s 4 million genetic letters make this the largest entire genome to be synthesised from scratch.
They were ordered in short segments from a laboratory supplies company, before being assembled into half-million-letter lengths in yeast cells by natural cellular machinery.
At this point, the genome engineers’ job became a bit like a railway engineer’s maintenance programme – replacing the E. coli genome piecewise – section by section – rather than all at once.
“The bacterial chromosome is so big,” team leader Jason Chin told the BBC, “we needed an approach that would let us see what had gone wrong if there had been any mistakes along the way.”
So it was only after each half-million-letter segment had been tested in partially synthetic bacteria that the eight segments were brought together in Syn61.
The approach is more cautious than that used by bio-entrepreneur, Craig Venter, whose microbial replicant based on the tiny organism Mycoplasma genitaliumwas presented to the world in 2010.
That was a milestone, Tom Ellis recalls, but consumed the efforts over many years of an entire institute, set up, run and named by Venter.
The new work was conducted by a small team at Cambridge’s world-famous Laboratory for Molecular Biology, and could readily be scaled up to bigger genomes in any well equipped lab, according to Dr Chin.
In the event, the team found only four mistakes out of the entire four million synthesised genetic letters, and they were easily corrected.
But Dr Chin’s ambitions go well beyond record-breaking chromosomes.
The new genome has also been recoded, as a first step allowing the synthetic biologists to incorporate components into biomolecules that do not exist in nature.
The code on DNA carries instructions for the cell for how to assemble proteins, the primary biomolecules of a body.
Just as DNA is composed of strings of single nucleic acid elements, so proteins are made of strings of simple amino acids.
Nature has a palette of 20, with names like serine, leucine and alanine. Their chemistry dictates the properties of the protein they make – from hair to muscle proteins, to stomach enzymes.
But although nature relies on only 20, the DNA code could accommodate up to 64. DNA biologist Francis Crick, who worked at the LMB in its early days, called this a frozen accident.
As a result, many of the DNA “words” or codons, lead to the same amino acid. There are six ways, for example, of writing the instructions for serine – which Chin sees as wasteful.
“We have stripped out some of the duplications in the natural code to make it more efficient,” says his colleague Julius Fredens, who oversaw much of the detailed lab work.
They set out to find all instances of two variants of the serine instruction, and synthetically replace them with two of the other synonyms – a task similar in scale to finding all the “C’s and Q’s” in the bible and replacing them with “K’s”, so that “quick” becomes “kwikk”.
The team also reduced the number of codons (like full stops) marking the ends of genes from three to two. There were over 18,000 replacements in all.
“This was a really radical transformation,” Chin argues.
There were further edits to remove the cellular machinery that reads the lost codons – it was no longer needed.
Syn61 turns out not to be quite so vigorous as its natural E. coli cousin – it grows about 60% slower. Although that could suggest there may be something fundamentally important about the alternative spellings in the genetic code, Julius Fredens believes they have identified smaller issues in Syn61, which should be readily corrected to fully restore the organism’s health.
Tom Ellis is impressed the bacterium works at all, saying: “These 18,000 changes mean that every gene on the chromosome will have been altered – and yet it’s still alive!”
One effect of the recode is that it separates Syn61 from all other life. Until now, organisms have been able to swap genes, often via viruses, because they all share the same basic language. Now, a virus trying to infect Syn61 will find the host cell lacks the tools to translate the viral DNA; the attempt would fail.
George Church calls this the “cliffhanger”. In an earlier attempt in his lab, with a more limited set of edits, one in five viruses still managed to replicate.
“Chin’s success will embolden the rest of us working to make many organisms (industrial microbes, plants, animals, and human cells) resistant to all viruses by this recoding approach,” Church wrote in an email.
Chin says that test has not been tried yet with Syn61, but it is high on their to-do list.
But Chin’s grand plan is to make biochemistry more diverse.
With only 61 of Syn61’s 64 possible codons taken up as instructions for natural amino acids (hence the name), that leaves three that can now be reassigned to unnatural ones that could introduce entirely new chemistry into the cell.
Chin has pioneered this kind of synthetic biology introducing elements that make proteins glow, or respond to light by becoming active, or turned off.
Fredens reckons there may already be 200 unnatural building blocks that could be brought into protein chemistry this way, and that these would work with the techniques already developed at LMB and elsewhere.
“It’s pretty mind blowing that you can expand the genetic alphabet this way,” Fredens admits. “I think we’re pretty far from realising how much we can do with it, producing things we have never seen before.”
Chin’s focus is very much on what the opportunities will do for science, talking of alternative proteins that will spy on the inner workings of cells, or help pharmaceuticals companies build better drugs. But the possibilities are endless. Tom Ellis speculates on the idea of connecting molecular hooks onto proteins that would allow them to click together to make vast molecular networks in smart materials.
It may sound like a brave new molecular world, but Chin says it should not be scary.
“People have legitimate concerns,” he accepts. “There is a dual use to anything we invent. But what’s important is that we have a debate about what we should and shouldn’t do. And that these experiments are done in a well controlled way.”