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Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways

A special issue of Synthetic Biology celebrates research enabled by the JGI DNA Synthesis Science Program.

Fashioning DNA outside a cell is key to interrogating what genes do, how they work, and applying them to environmental and energy challenges. But not all scientists have the expertise and resources to do DNA design and synthesis work. This is where the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), comes in. The JGI is uniquely positioned to enable this kind of science; through its DNA Synthesis Science Program, the JGI enables large-scale synthesis support, sequencing, integrative -omics, and data mining, empowering research collaborators to take on ambitious synthetic biology experiments.

A recent special issue of the journal Synthetic Biology puts the spotlight on JGI’s DNA design and synthesis superpower. Through a series of case studies, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program, which started in 2012, and what they’ve discovered through their collaborations.

One review article in the collection, Genomics-enabled analysis of specialized metabolism in bioenergy crops: current progress and challenges, details how an interdisciplinary collaboration between three different principal investigators (PIs) harnessed JGI’s DNA synthesis capability to better understand a special class of compounds, or secondary metabolites, called terpenes. Terpenes are made via a tangled network of enzymes in plants. To better pinpoint the biosynthetic routes that produce terpenes, the JGI synthesized several of the underlying genes. These genes then provided a foundation that allowed the scientists to interrogate the roles that terpenes play in nature. The research collaboration has been incredibly productive; more than 10 papers, including two Nature Plants publications, in five years, have come out of the JGI-supported project.

“The JGI DNA Synthesis Science Program has been instrumental in establishing larger-scale research projects in our group. It’s enabled us to accelerate gene, enzymes, and pathway discovery approaches and provided the resources needed to foster interdisciplinary collaborations,” says Philipp Zerbe, the lead PI on this project. “I view the program as an excellent platform to build collaborative research initiatives.”

Yasuo Yoshikuni, who heads the JGI DNA Synthesis Science Program and was the guest editor of the issue, points to the terpene project as a demonstration of how JGI’s capabilities — and their applications — are evolving. “JGI is famous for its work sequencing human and environmental genomes. But we now have these DNA synthesis capabilities that push the frontier in areas like plant secondary metabolites, as well.” 

Another paper in the Synthetic Biology special issue, Modular cell-free expression plasmids to accelerate biological design in cells,  recounts how the JGI has enabled Michael Jewett, a synthetic biologist at Northwestern University, and researchers at the biotech company LanzaTech to develop a “cell-free” gene expression system. Developed through the JGI DNA synthesis Community Science Program (CSP) Functional Genomics, the system allows scientists to test enzymatic pathways, which make valuable products, more quickly. In the cell-free approach, cells are grown and then basically exploded, so that the molecules and enzymes that were once trapped inside are now, still functional, in a kind of biomolecular soup. The soup permits researchers to quickly test different ways of controlling the pathway enzymes, and thus evaluate changes to the pathway more quickly. 

Zhiying Jean Zhao at work in the JGI DNA Synthesis Science Program. (Marilyn Sargent)

Zhiying Jean Zhao at work in the JGI DNA Synthesis Science Program. (Marilyn Sargent)

The JGI has also helped LanzaTech researchers tame gene expression in the organism Clostridium autoethanogenum. The microbe can utilize carbon oxides, including the greenhouse gas carbon dioxide, to make valuable chemicals, such as ethanol and acetone. To help reduce production of byproducts, the JGI DNA Synthesis Science program developed thousands of DNA constructs encoding a molecular tool to repress targeted genes in the organism. The team demonstrated that this tool, called CRISPR inhibition or CRISPRi, works (see the article Transcriptional control of Clostridium autoethanogenum using CRISPRi). Now, they’ll be able to further explore how best to use it in order to optimize C. autoethanogenum as a biochemical factory. 

“These large-scale research efforts are accelerating the transition into real-world applications,” says Michael Köpke, the vice president of synthetic biology at LanzaTech. “JGI has always been a leader in DNA sequencing technologies. The DNA synthesis program combines these capabilities with state-of-the-art DNA design and construction, providing a unique resource for the international community and fostering academia-industry collaborations.”

A third story from the issue — Machine learning-based prediction of activity and substrate specificity for OleA enzymes in the thiolase superfamily — featured a team working on thiolases, a superfamily of enzymes found only in microbes, which make carbon-carbon bonds. This ability is attractive as an alternative to fossil fuels to make hydrocarbon products, ranging from gasoline to furniture polish and even cosmetics. Helped by the JGI, who built the enzyme-encoding constructs, the team studied more than 70 enzymes and how they grab hold of different substrates. By analyzing these relationships with machine learning, they predicted key features of the enzymes, including particular amino acid residues that influence their activity on different substrates.

“Working with amazing colleagues at the JGI, we were able to design large-scale functional screens for characterization of new enzymes and use the data we generated to train machine learning models now publicly available for the research community,” says lead author Serina Robinson, a postdoctoral fellow at the ETH Zürich, who will be starting an independent group at the Swiss Federal Institute of Aquatic Science and Technology in September 2021.

Robinson stressed that the DNA Synthesis Science team’s expert advice was critical to both the project’s success and her own as an early career researcher. “We were able to study hydrocarbon biosynthesis at a scale that would absolutely not have been possible without JGI’s support,” she says.

Scientists can  harness the expertise and capabilities of the DNA Synthesis Science Program by applying to the year-round Community Science Program Functional Genomics call for proposals.

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By Alison F. Takemura