Recoding Life

Amino acids are a fundamental building block of life. Crystalized amino acids beta-alanine and L-glutamine taurine captured via polarized light microscopy. Karl Gaff / Science Source

Scientists have created an organism that defies the rules of biology by using nonstandard amino acids. And you probably have some questions.

Dan Mandell, CEO of the biotech GRO Biosciences in Cambridge, Massachusetts, has a giant canvas poster in his office. It’s an artist’s rendition of Jeff Goldblum emerging from an egg with the famous Jurassic Park quote “Life finds a way” inscribed on it. The print is there, he says, “to remind us of what we are up against here.” 

Dan belongs to a relatively new breed of scientists who call themselves synthetic biologists. Just a couple of decades ago, the term was not yet a part of the professional nomenclature. They were just geneticists, molecular biologists, or chemical engineers working on the technologies to push the boundaries of science and help develop treatments for devastating diseases like cancer. Those scientists’ work, although bold, was limited by the fundamental rules of biology. You could take a gene from one organism, swap it into another, or make other modest tweaks to living systems. But you were still bound by the fundamental rules of biology like the universal DNA code and the limited set of twenty amino acid building blocks that every protein, enzyme, and living cell is made of. Those restrictions date back to the origins of life and have held for billions of years—until about a decade ago. 

In 2013, a paper came out in Science describing the first genomically recoded organism (GRO) that could use an expanded repertoire of building blocks, such as nonstandard amino acids which are not part of biology’s regular vocabulary. Although more than 500 possible amino acids exist in nature, only 20 of them make up proteins, and all of Earth’s mind-boggling biodiversity is made from those twenty canonical building blocks. Why would we need more than that? 

Dan Mandell of GRO Biosciences.

The pioneers of synthetic biology who came up with the first genomically recoded organisms would give a few reasons right off the bat. Unnatural amino acids could make genetically engineered organisms safer, for one. They could prevent the escape of modified organisms into the environment or make them resistant to viral infections. But perhaps the most compelling use case for recoded organisms is in therapeutics: If your enemy IS biology—as is the case with cancer, where your own body’s cells turn against you—you need to find ways to outsmart it. The expansion of the genetic code offered for the first time an opportunity to engineer biology to do things that nature has never done on its own.

“We started asking the question: What are some of the really difficult challenges facing patients that can’t be addressed using proteins comprised of the twenty natural amino acids? And that was really the genesis of GRO Biosciences,” says Mandell. 

Mandell, Chris Gregg, and Ben Stranges founded the company in 2017 after they met while working at Harvard Medical School in the laboratory of George Church, who is also a GRO Biosciences co-founder and chair of its scientific advisory board. Dan arrived in the lab as a postdoc with a background in computational protein design around the time of the first GRO paper publication, and he spotted the opportunity right away.

“GROs were the first forms of life that could allow us to expand the number of amino acids accessible to protein engineering,” he says. “With these new chemistries, we could make therapeutics that are safer and that could treat diseases that are, so far, impossible to cure.”

Not surprisingly, Dan was not the only one who thought about that. Another company that uses genomically recoded organisms is Pearl Bio, which is also based in Cambridge, Massachusetts. It was also co-founded by two former postdocs in Church’s lab, Michael Jewett and Farren Isaacs, who are now professors at Stanford and Yale. Similar to GRO Biosciences, Pearl Bio aims to produce molecules with new functions and make next-generation biomaterials to improve human health.

“We decided to build the seatbelt before the car.”

The molecules that can be made with the help of genomically recoded organisms combine the architectural precision of biology with the expanded functionality of the entire chemical repertoire to enable new treatments for cancers and metabolic and autoimmune diseases. One promising application of GRO-based therapeutics is to “trick” the immune system into not recognizing a foreign object by decorating it with custom sugar molecules like those covering the body’s own cells. These types of modifications can prolong the action of therapeutic enzymes and prevent the immune system’s reaction to and rejection of device implants or transplanted organs.

Another example is creating next-generation antibody-drug conjugates, which are potent cancer treatments that target and kill tumor cells while sparing healthy cells. Antibody-drug conjugates combine two essential elements: the antibody that binds specifically to cancer cells and a cytotoxic (cell-killing) drug attached to it via a chemical linker. The antibodies will seek out cancer in the body and carry their payload to it. The challenge in creating these therapies is that there are many attachment points on the antibody that the drug can be linked to. As a result, it is hard to dial in how many drug molecules each antibody carries and how quickly those drug molecules get released. 

Using genomically recoded organisms to produce these treatments allows the scientists to incorporate the precise number of non-natural amino acids into the antibodies, which serve as exclusive attachment points for the drug. This could solve many of the current problems with antibody-drug conjugates by improving their stability, narrowing down the drug-to-antibody ratio to reduce side effects, and fine-tuning the therapeutic window to make sure that the treatment can get to the tumor before the drug is released. 

Building the seatbelt before the car

While protein-based therapeutics are so far the most promising application for genomically recoded organisms, there are potentially many others. These semi-synthetic organisms are much more than just factories for biological drugs. 

“In a certain sense, it’s in a whole new kingdom of life,” says George Church, the famed Harvard professor whose lab could be considered the birthplace of GROs. 

“The genetic code has been shared by all life for three and a half billion years, and [these are] really the first kind of organisms that depart from that fundamental principle,” says Mandell. 

All that makes this a pivotal moment in synthetic biology: The creation of organisms that run on different operating systems than every other life form on Earth is quite a feat. But, as Jeff Goldblum’s character in Jurassic Park said, “The fact that you can doesn’t mean you should.”

“One of the aspects of recoded organisms, which is an emergent property, is that as you deviate further and further from the standard genetic code, these organisms become more and more resistant to viruses and phages,” explains Mandell. While this property is useful for developing virus-resistant microbes for bioindustrial applications, there is also a potential risk of creating virus-resistant superbugs that could proliferate uncontrollably in the environment. 

“We took this very seriously from the beginning,” says Church. “Before we came up with an organism that was resistant to viruses, we had to make sure it was bio-contained.”

Mandell was the lead on the biocontainment project, and he assures me that “there isn’t a great risk of them running amok in the wild.” First of all, engineered organisms such as these are actually pretty weak relative to their wild-type counterparts. And secondly, his team has developed a mechanism to ensure that they cannot survive and replicate in the wild.  

“We have made an organism that is resistant to—as far as we know—all viruses.”

“We decided to build the seatbelt before the car,” he says. The biocontainment strategy relies on a property called “synthetic auxotrophy.” Auxotrophy means the organism cannot itself make the compounds essential for its growth, which must be supplied externally. Synthetic auxotrophy means that this essential component—such as a synthetic amino acid—does not exist in nature. 

“If you withdraw that amino acid from the food source, or if the organism were to escape the laboratory, it can’t scavenge this synthetic amino acid from nature,” explains Mandell. 

This is a far better approach than the one used in Jurassic Park. Having a bulletproof biocontainment mechanism in place provided the insurance to keep pushing the research forward: “Initially, we made an organism that was resistant to just a few viruses. Then, as soon as possible, we started working on the biocontainment project, just in case we got to the next step,” says Church. “We have now gotten to that step: We have made an organism that is resistant to—as far as we know—all viruses.”

More than meets the eye

Although the idea of creating synthetic life has been around for a long time, it was intractable until just a couple of decades ago. Why? The reasons are technical.

The ability to introduce non-natural amino acids into proteins required recoding the entire genome of the cell to free up one of the three-letter DNA codons for alternative use. In a way, the first genomically recoded organism back in 2013 was the easiest to make. The team had to replace only 321 codons—the rarest of the three-letter combinations called the “amber” stop codon, which provides a signal for the ribosome to stop translating the protein. (The ribosome is the molecular machine that reads DNA genes and translates them into proteins.) But in the early 2000s, before CRISPR genome editing and high-fidelity DNA synthesis became available, that painstaking process took almost ten years. 

Today, a recoded genome can be assembled from long stretches of synthetic DNA in about two years. In theory, it should now be much easier to create new types of GROs with an expanded range of functions. But while the process got easier, the goal got harder. If you want to introduce not one, but two or more distinct non-standard amino acids into a synthetic protein, you need to free up additional codons—the ones that code for natural amino acids, such as arginine, lysine, or serine. Since those are a lot more common than the stop codon, creating new GROs now requires making close to 20,000 genomic modifications.

This is tricky because changing so much of the organism’s DNA can affect its viability. “One of the hardest challenges is actually keeping the organisms alive,” says Jewett, the Stanford professor who co-founded Pearl Bio after working for Church as a postdoc. There are many hidden signals in the sequence of the genome, such as essential mRNA structures, cryptic promoters, overlapping genes, and a gazillion other known and unknown nuances that, if messed with, could have a deleterious or even lethal effect on the organism. 

As scientists keep tweaking these synthetic organisms, is it possible that they will accidentally create one that we cannot control?

“If you just make a synthetic copy of the genome, it’s probably going to work,” says Church. His lab has been building a GRO with seven reassigned codons, the most ambitious genome recoding project yet. “But if you are trying to change seven codons, there’s just a bunch of things that can go wrong.” 

On top of that, recoding the genome is only part of the challenge. The other part is engineering cellular machinery to introduce unfamiliar building blocks into the proteins. This machinery consists of many parts: there is the ribosome, the protein-making machine, the transfer RNA (tRNA), a molecule that pairs with the mRNA’s triplet codons, and the aminoacyl-tRNA synthase which loads the tRNA with the cargo to add to the growing protein chain. And if you want to introduce a new building block, you need to re-engineer each of those parts.

“How do you get a system which has perfected itself to make proteins from standard amino acids to do something different?” asks Jewett, who is working on engineering alternative translation machinery systems for GROs. “It requires understanding evolutionary biology, protein and RNA design, and using AI to guide evolution.”

“It’s the ultimate synthetic biology problem,” he says.

Moving the goalposts

But so far, technical challenges have not stopped scientists from pushing biology more and more into synthetic territory. Even though the first GRO was born in an academic lab, the technology is maturing in the industry. As the Church Lab prepares to publish the latest GRO version with seven reassigned codons, Pearl Bio and GRO Biosciences have already shown that they can expand the range of functions and develop real-life use cases for GRO technology.  

“We’re actually now finishing a new organism that will explicitly allow the incorporation of multiple non-standard amino acids using different codons in the same protein,” says Mandell. That means they will be able to encode more novel functions into these synthetic proteins, which can ultimately lead to creating better medicines. 

“We’ve also dramatically expanded the non-standard amino acid chemistries available to our platform and we now have positive animal data for two distinct disease indications.” GRO Biosciences plans to declare its first candidates for development in the clinic in 2024. With backing from Leaps by Bayer that co-led their series A financing, GRO Biosciences is going after autoimmune and metabolic diseases like multiple sclerosis and diabetes. 

Pearl Bio is thinking even more broadly as they envision new applications of protein-based materials endowed with unique properties, from smart therapeutics to wearable electronics or next-generation Kevlar. But to get to that point, there is more work to be done.

“If we develop better strategies to engineer ribosomes to work with novel monomers, I see a significant opportunity to provide a path to polymers with previously unimaginable structures and functions,” says Jewett. “It could lead to new classes of peptidomimetic [protein-like] drugs to address the rising antibiotic resistance or new kinds of functional materials.”

The question remains: As scientists keep tweaking these synthetic organisms, is it possible that they will accidentally create one that we cannot control? Or could an organism evolve to escape on its own?

“You can never drive the risk to zero. But I think it’s fair to say that the value that we can realize from these organisms far outweighs the risks, provided we continue to develop and use them responsibly,” says Mandell. 

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