Nature Amplified

The Engine
Dec 3, 2019 · 16 min read

The Synthetic Biology Revolution Is Here

By Deborah Halber for The Engine
Illustrations by
Andrés Rodríguez

Ajikumar Parayil reaches inside what looks like a black plastic wardrobe, tears a leaf from a bushy plant and sniffs it. A geranium, he guesses.

A chemical engineer and CEO, Parayil isn’t too concerned with exactly which species grow in a mini-hothouse in Manus Bio’s labs. His expertise lies in the molecular processes that let plants turn cheap, abundant resources into rare expensive chemicals such as essential oils.

Parayil’s MIT spin-off seeks to do what plants can’t — pump out large quantities of useful substances. By genetically programming fast-growing microbes to mimic the inner workings of plants, Manus Bio aims to mass-manufacture ingredients for new, cheaper, safer, more effective food and cosmetic ingredients, pharmaceuticals, and agricultural chemicals.

The global synthetic biology market is expected to surpass $55 billion by 2025. A dizzying array of potential applications stem from the notion that if nature can make a tiny amount of a pesticide or a healing agent, engineers can tweak nature to make a lot more. “Whatever you see biology in nature doing, we’d like to go in and harness that,” says MIT biological engineer Chris Voigt. “Cells are the ultimate engineering substrate. We view living cells as systems that can be reprogrammed to do things they don’t naturally do.”

Synthetic biology startups and research labs are working on biofuels, biodegradable plastics, microbes engineered to seek and destroy cells that cause disease, environmentally friendly industrial solvents, a better artificial sweetener, a new nontoxic pesticide, and other products.

Many synthetic versions of plant products are based on petrochemicals. By manipulating genes and organisms to produce naturally occurring substances like nootkatone in grapefruit oil, Parayil and others hope to transform traditional, fossil-fuel-intensive chemical manufacturing — one of the world’s worst polluters — into an environmentally friendly, sustainable industry.

Gee Whiz: Genetic Engineering

Synthetic biology sits at the juncture of biology and engineering. Its building blocks are genes, living cells — including human cells — and organisms such as yeast, fungi, and bacteria.

University of Texas researcher Randall Hughes believes that if the 20th century was the century of the atom, the 21st century will be dubbed the century of DNA or, in Voigt’s view, the century of genetic engineering.
Advances in sequencing and synthesizing DNA have led to “groundbreaking technologies for the design, assembly, and manipulation of DNA-encoded genes, materials, circuits, and metabolic pathways, which are allowing for an ever-greater manipulation of biological systems and even entire organisms,” Hughes wrote in a 2017 overview of synthetic biology.

In the early 2000s, members of the MIT Synthetic Biology Working Group — a pioneering consortium of researchers in and around Cambridge — wanted to provide an overview of their nascent field for a lay audience. They hired a cartoonist who had worked on a popular Spider-Man video game to produce a 12-page comic book called Adventures in Synthetic Biology. It was taken seriously enough to be published in the prestigious journal Nature in 2005.

In Adventures in Synthetic Biology, a kid reaching for a neon-green, googly eyed blob yells, “Check out that bacteria!” The boy is outfitted in goggles, cargo pants, a scuba shirt and boots suitable for walking on the moon — a mix of Back to the Future and Raiders of the Lost Ark. In a moment of gee-whiz science reminiscent of the 1950s, the boy exclaims, “Imagine what might become possible if they were working for us!”

Putting organisms to work isn’t new. For thousands of years, civilizations have used microorganisms to make alcoholic beverages, bread, and other products exploiting fermentation. It wasn’t until DNA’s structure was elucidated that biology proved open to manipulation at the genetic level.

In the early 1970s, scientists cut genes out of a frog’s DNA and inserted them into E. coli, a common gut bacterium. The microbe was able to translate the frog’s genetic information into proteins. And when the microbe divided, it made new copies of the frog genes along with its own. It was a Frankenstein creation, a bacteria-frog hybrid.

Altering the sequence of DNA’s four basic building blocks turned out to alter proteins, which altered an organism’s behavior. By adding the gene for a desired product or ramping up the expression of an existing gene, researchers found they could use living organisms such as yeast and bacteria as factories to churn out useful products.

[L-R] Ajikumar Parayil, Founder & CEO, Manus Bio, Chris Voigt, Professor of Advanced Biotechnology, MIT, Pamela Silver, Professor of Biochemistry and Systems Biology, Harvard Medical School

With its relatively straightforward 4,000 genes, E. coli became the organism of choice to manipulate. “Bacteria really are the powerhouses of molecular biology research, because their genes are much easier to modify in the lab and they can grow and evolve much more quickly than other organisms,” says Pamela Silver, the Elliot T. and Onie H. Adams Professor of Biochemistry and Systems Biology at Harvard Medical School, whose lab works on reprogramming bacteria and other cells to perform a variety of new functions.

Within a decade of the landmark gene-splicing experiment, insulin and human growth hormone were being generated by genetically modified bacteria. One of the first biotechnology companies in 1971 promised that by 2000, virtually all diseases would be cured with proteins made through genetic engineering.

Fast forward to the early 2000s. Companies synthesized long fragments of DNA at a reasonable price, but researchers struggled to systematically engineer large-scale genetic systems. Even relatively simple organisms were too complex to predictably alter. The process was painstaking and labor-intensive, and largely hit-or-miss.

In the 18th century in New Haven, Conn., inventor Eli Whitney figured out how to mass-produce muskets — previously assembled painstakingly by hand — by using interchangeable parts. Early stages of synthetic biology at MIT revolved around a Registry of Standard Biological Parts: a library of well-characterized parts and modules that could be assembled in cells in different combinations, resulting in predictable outcomes.

With BioBricks created and submitted to the registry through an MIT-initiated global competition, student teams developed a bioengineering device that “prints” genetic circuits a water purification system, and a way to save the honeybees. In time, hyper-precise genome engineering tools such as CRISPR further expanded the scope of what’s possible to coax cells to do for our own purposes.

In Adventures in Synthetic Biology, the kid thinks it would be fun to change the genome of the green blob so it blows up like a balloon. “First you need to assemble the DNA parts that encode your program,” says a young woman in a white lab coat and oversized glasses, her hair pulled back in a messy bun. She hands him a thick blue book. “Get them from the catalog.”

E.coli

Foundries for Cells

In Ginkgo Bioworks’ Bioworks3 foundry, a robotic arm systematically dips a thin black probe into tiny wells on a grid-patterned tray. It’s doing what bench scientists do — inserting custom-designed DNA into cells — but it does it 24/7 at a higher level of output than humans could manage.

Ginkgo Bioworks designs genetic codes to build custom microorganisms. It was co-founded in 2008 by CEO Jason Kelly and three other former MIT biological engineering grad students, along with former MIT research scientist Tom Knight — at 68, considered the godfather of synthetic biology.

Knight, an electrical engineer and computer scientist who made the leap to biology in the 1990s, wanted biology to be more like engineering, where you could grab chips and other components off the bench, put them together, and have them work as expected. In a nod to semiconductor fabrication, Ginkgo calls its labs “foundries.”

[L-R] Barry Canton, Co-Founder and CTO, Ginkgo Bioworks, Kristala Prather, Professor of Chemical Engineering, MIT & Co-founder, Kalion

Working with partner companies, accelerators Y Combinator and Petri, and independent researchers, Ginkgo has reprogrammed cells to produce yeast that generates the fragrance of extinct flowers, bacteria that can decrease farmers’ reliance on chemical fertilizers, and through its partnership with Cambridge, Mass., biotech firm Synlogic, so-called “living medicine.” Synlogic and Ginkgo are developing a therapeutic that will break down toxic levels of the amino acid phenylalanine in the gut of patients with the metabolic disease phenylketonuria (PKU).

Yet Ginkgo is “application agnostic,” says CTO Barry Canton. Its business model is to make synthetic biology itself cost-effective and accessible to any industry — especially ones that never imagined they could employ yeast, bacteria, or Chinese hamster ovary cells (used commercially to produce therapeutic proteins) to make products.

“There are a lot of heads of R&D at big companies who are trying to figure out how to make their development dollars go further and who understand — or are beginning to understand — the potential of synthetic biology,” Canton says. “They’re looking for cheaper ways to make existing products or how biology can make products that they can’t make or buy via chemistry. And then they come and talk to us.”

A Game of Whack a Mole

“There it is — the genome,” Ms. Scientist tells the boy in the goggles as they soar past, a la The Magic School Bus, oversized corkscrews of blue and violet DNA. “The master program that’s running the cell.”

“So this is what we change to reprogram this critter?” the boy says. “Looks easy!”

At MIT, Kristala Prather designs new ways to engineer bacteria to synthesize drugs and biofuels. Prather, the Arthur D. Little Professor of Chemical Engineering, is co-founder of Kalion, a company commercializing the first microbial fermentation process to produce glucaric acid, a powerful biodegradable and non-toxic corrosion inhibitor.

Prather and her team were among the first to control how cells make chemicals relative to how they do their primary jobs: growing and reproducing. Prather’s lab devised an internal switch that compels the cell to stop using all its ingested food for its own purposes and use it to make the product the researchers want it to make.

Prather says advances in computation, molecular and cell biology, data science, and machine learning have been game-changing for synthetic biology. And then there are the time-saving robotic lab workers, and software that models and simulates the function of new genetic circuits before they go near a petri dish.

But living cells are incredibly complex, dynamic systems. “As soon as you start adding a bunch of stuff, it changes how the rest of the system behaves in ways that can be very unpredictable,” Prather says. It’s like whack-a-mole: You push down on one part and another one pops up.

Inside Ginkgo Bioworks

At Ginkgo, Canton says that to get a cell to produce a specific substance or act in a desired way, “We have to come up with, let’s say 10,000 different designs (of assembled strains of DNA). We need to manufacture all of those, test all of them.

“We have to come up with a new set of designs informed by that first round and go through that process again,” he says. “And we need to do that multiple times for every project.” Canton compares the resulting knowledge to Google’s proprietary software. “Ginkgo accumulates codebase in the form of enzymes, genes, entire strains that we’ve developed that we’ve shown to be productive,” he says. The hope is that researchers will use that knowledge to piece together products to benefit people and rescue the planet, which is drowning in waste and struggling with an industrial base built around fossil fuels.

Better Bioplastics

A few years ago, bioplastics made from fermented corn seemed like great alternatives to petroleum-based plastics.

Shannon Nangle and Marika Ziesack aren’t so sure. To break down commonly used bioplastics called polylactic acid, or PLA, you have to run an industrial composter containing a specific set of microbes at specific temperatures and durations. “Most composters don’t even do that,” Nangle says. “Few composters fully degrade PLA, so the PLA remnants end up in landfills and, like petrochemical plastics, they will not degrade. PLAs that find their way into the environment also will not degrade readily.”

Public awareness of the millions of tons of plastic waste polluting the oceans is spurring governments to impose bans on single-use plastics. Consumer product companies are looking for alternatives. Nangle and Ziesack think they have a better one than PLA.

Nangle shows a visitor around the Harvard Medical School lab where she and Ziesack work as postdocs. A machine jiggles glass jars of bacteria growing in mixtures of gases. Ziesack, Nangle, and Pam Silver have engineered bacteria to produce a variety of compounds called polyhydroxyalkanoates (PHAs), a class of biodegradable, bio-based polymers. PHAs are promising, but have found limited applications in niche markets because of their high production costs.

Unlike PLA, PHAs will degrade in the ocean and land, where they are a food source for local microbes. By diversifying and enhancing the existing range of PHAs, Nangle hopes to tailor PHAs to have similar properties to many types of petrochemical plastics.

Nangle and Ziesack have produced new varieties of PHAs directly from carbon dioxide and hydrogen by engineering the metabolic pathways of hydrogen-oxidizing bacteria called Knallgas bacteria — an accomplishment that could change the long-term sustainability of bioplastics.

“By using carbon dioxide waste streams instead of corn as input for our fermentation, we hope to scale up bioplastics production without competing for cropland,” Ziesack says. The team is working to fine-tune these new bioplastics at a reasonable manufacturing cost.

From Cancer to Chemicals

In 2016, Gaurab Chakrabarti was in medical school, studying the role of chemicals in cancer progression.

Years earlier, a friend of Chakrabarti’s from medical school had introduced him to Sean Hunt, who was pursuing a PhD at MIT in chemical engineering. “Sean would come down to Dallas,” Chakrabarti recalled. “One night, we were playing poker and somehow we started talking about our research.” That conversation would propel Hunt and Chakrabarti to Forbes’ 2017 list of “30 Under 30” in manufacturing and industry.

Chakrabarti was looking at a protein that helps cells detoxify in the presence of quinones — toxic free radical byproducts of cell metabolism. In pancreatic cancer cells, clearing up quinones produces high levels of hydrogen peroxide, which cancer cells have evolved to withstand.

Chakrabarti told Hunt he had stumbled on a kind of super enzyme that efficiently turned sugar into hydrogen peroxide.

At MIT, Hunt was exploring ways to use nanoparticles to improve traditional methods of manufacturing hydrogen peroxide, an all-natural germicidal agent. The global market for hydrogen peroxide — used in electronics fabrication, water purification, agriculture, textile and paper pulp bleaching, plastics production, and rocket propulsion — is projected to reach $6.3 billion by 2026. Right now, it’s expensive and environmentally unfriendly to produce.

At the time, Hunt was all about traditional chemical manufacturing. He considered enzymes — chemical reaction catalysts within a cell — too expensive and not very stable. “No, man,” Chakrabarti told him. “Things have changed.”

Capable of generating high concentrations of peroxide without losing effectiveness, the cancer cell enzyme worked far better than metal catalysts, which tended to degrade the peroxide at high concentrations. Now, Houston-based Solugen’s bio-inspired reactions use enzymes derived from microorganisms that break down biodegradable, cheap plant material and turn them into hydrogen peroxide. Their process is cheaper and produces no harmful byproducts.

“We do water treatment, which is industry-agnostic. So we can be in up-stream oil and gas-produced water, we can be in mining, agriculture, soil remediation,” Hunt says. “The problems we’re solving are all slightly different. But fundamentally, it’s the same core chemical solutions.”

In 2010, MIT chemical engineer Gregory Stephanopoulos and Parayil — a postdoc at the time — were hoping to find a way to induce bacteria to yield an intriguing substance called taxadiene isolated from the bark of the Pacific yew tree. A precursor of the potent anticancer drug Taxol, taxadiene was tricky to generate in quantity. Stephanopoulos and Parayil rejiggered E.coli to churn out one gram per liter — 15,000 times more than previously possible.

[L-R] Marika Ziesack, Postdoctoral Researcher, Harvard University, Gaurab Chakrabarti, Co-Founder & CEO, Solugen

The researchers were investigating plant pathways that generated isoprenoids, an ancient and diverse set of metabolites that help plants do everything from make chlorophyll to germinate seeds. Industrial companies immediately saw the potential of this pathway “to alleviate a lot of their sourcing needs, particularly for natural ingredients,” says Manus CTO Christine Santos, a graduate student in the lab who completed her PhD in 2010.

Manus’ fermentation technology replicates how plants manufacture natural chemical compounds. “What we’re doing is taking biosynthetic pathways that typically exist in plants and translating them into a microbial system,” Santos says. “There’s quite a bit of work that we do to optimize the performance of those enzymes, which have evolved in a very different cellular context.”

Lately, the food industry has been abuzz about a substance found in the leaves of the stevia plant. Rebaudioside M or Reb M is sweeter than Reb A used in Truvia and other products. But it’s trickier to extract.

Manus has engineered bacteria that mimic Reb M’s metabolic pathway, and Manus’ manufacturing facility in Augusta, Ga., is ramping up production of a zero-calorie sweetener based on Reb M. Among Manus’ other products in various stages of development is a component of grapefruit oil that repels and kills mosquitoes, ticks, head lice, and bedbugs. Unlike DEET, nootkatone is nontoxic. It’s FDA-approved for citrus-flavored soft drinks and perfumes; the EPA may soon green-light it as a pesticide and insect repellent that could protect against Lyme disease, malaria, Zika, and more.

[L-R] Christine Santos, CTO, Manus Bio, Alexander Titus, Head of Biotechnology, United States Department of Defense

Safety on the Road Ahead

In Adventures in Synthetic Biology, the little dude sets to work making the googly eyed green blob generate and trap hydrogen gas so it inflates like a party balloon.

To his delight, the blob starts to fill with hydrogen. Then it keeps going. It expands until it takes over the entire lab, pops and splats, flinging sickly green splotches everywhere.

“Hmm,” muses the scientist. “Are you sure you understand enough about what you want to do? You don’t want to make things worse.”

As synthesis technology becomes cheaper and more widely available
(“You can start a biotech company out of your dorm,” Solugen’s Hunt says) questions become increasingly worrisome: Who owns rewired organisms? What happens if they escape — or are inserted — into the wild? Could freely available DNA sequences of viruses or the genes encoding lethal substances such as anthrax become a threat to public safety?

Alexander Titus is Assistant Director for Biotechnology in the Office of the Under Secretary of Defense for Research & Engineering. He’s responsible for developing and overseeing the U.S. Department of Defense’s biotechnology roadmap.

The U.S. bio-economy — economic activities based on renewable biological resources — emerged in the early 2000s, and its economic promise has ratcheted steadily upward. “In the future, we see biotechnology impacting nearly every aspect of business or technology,” Titus says. The U.S. is already a world leader in the field, with 300-plus companies founded in 2017 alone.

“It will be a challenge to scale up critical biomanufacturing processes to realize the new class of manufacturing technologies,” Titus says. “There are technical hurdles that need to be overcome to quickly and cost-effectively produce and isolate robust quantities of bio-based materials, molecules, and other products, as well as platforms that will need to be created in order to test and evaluate said products.” Titus believes partnerships among industry, academia, and government will be key to leveraging existing resources.

Plus, he says, the DOD wants the U.S. to be a global biotech leader “so that we can help to ensure that biotechnology is used responsibly,” he says.

Biosecurity and biosafety issues could hinder industry growth, Silver says. If technology relies on releasing organisms into the environment — such as through soil-dwelling microbes that boost crop yields — how do you ensure that doesn’t get out of hand?

In the not-too-distant future, synthetic biology may go beyond pairing an enzyme from a human cell with a structural protein from a yeast cell to create living systems unlike any existing organisms. In April 2019, the Swiss Federal Institute of Technology announced that researchers there had created the world’s first fully computer-generated genome of a living organism. While the organism itself does not yet exist, it’s only a matter of time.

Harvard geneticist George Church and an international team of scientists have been working on “yeast 2.0,” known as the synthetic yeast project — synthesizing a form of S. cerevisiae in which engineered chromosomes within a mostly intact original genome steer the organism to evolve along a desired path.

Silver, Church, and others founded a company called 64-x (64 minus x), which engineers organisms with entirely new genetic codes to function in otherwise inaccessible environments. These new life forms are immune — the company says — to “every virus on Earth.” “Why we like them: These geniuses invented a new life form,” wrote TechCrunch in August 2018.

Take the “living medicine” in development at Ginkgo Bioworks. CTO Barry Canton says the current goal is to engineer bacteria that help degrade harmful amino acids for those suffering from metabolic disorders. One day, the target product might be a much more extensively engineered cell that can sense — and respond to — changing disease conditions inside the body.

“We’ll probably go through an evolution where you’ll go from putting a handful of genes into a cell to totally redesigning almost every aspect of what the cell does,” Canton says. “It will increasingly look like a specialized cell for making product X or treating disease Y. Today’s relatively modest reprogramming of cells that exist in nature will, over time, create cells that are more pared-down, more and more focused on the objective at hand.” Such a cell, presumably, would no longer be a yeast cell or a bacterium, but something altogether different.

At the end of Adventures in Synthetic Biology, the scientist and the boy gaze, wide-eyed, as a perfect, smiley bacteria balloon floats gently off into the cosmos. “Look at us,” the kid exclaims. “We’re building stuff!” +

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