DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

News & Publications
Home › News Releases › Boosting Small Molecule Production in Super “Soup”

August 27, 2021

Boosting Small Molecule Production in Super “Soup”

Do metabolic pathways from engineered yeasts still work in cell-free environments? (Spoiler: Yes.)

Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)

Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)

Think of cells as tiny factories: within their walls they have both the machinery to make products such as proteins, and the mechanisms for maintenance to keep processes running smoothly.

As reported August 26, 2021, in Nature Communications, researchers led by Hal Alper at The University of Texas at Austin and Michael Jewett of Northwestern University describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system. The work complements efforts to further develop sustainable alternative approaches for manufacturing bioproducts and biofuels. This first report of their work, supported through the Emerging Technologies Opportunity Program at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory, indicates metabolic pathways could be more productive outside the cell environment, which would be transformative at industrial scales.

“Cell-free systems have been really powerful at finding ways to accelerate bio-design and identifying the best sets of enzymes that enable synthesis of sustainable chemical products,” said Jewett, one of the study’s senior authors. “But this has been done most commonly in bacterial-based systems, and so one of the things that I think is so special about this collaboration is that we’re doing work in yeast, a key platform organism that has been used historically for making sustainable products in industry.”

From Cell to “Soup”

The work started with yeast strains engineered by Alper’s team to convert the sugar glucose to the products including ethanol and 2,3-butanediol (BDO). To do so, the yeasts received fine-tuning of gene expression through genetic rewiring with CRISPR-Cas9 that enhanced their ability to redirect the carbon in the cells toward particular pathways. In this case, towards BDO and away from ethanol, an undesired product of the yeast’s native glucose metabolism

Alper’s graduate student Xiunan Yi visited the Jewett lab to provide a seamless transition between the in vivo (within the cell)and in vitro (outside the cell) efforts of this work when it started. Though such visits have been impossible for the past year and a half, “the logistics haven’t changed,” noted Northwestern graduate student Blake Rasor. He and Yi, one of the study co-authors, have maintained a regular shipment schedule, with plates arriving every couple of months.

The question for the researchers was, would the reactions in these engineered yeast strains continue to work in a cell-free system? At the Jewett lab, the engineered cells were lysed or burst, and the metabolic pathways were tested in the enhanced lysate “soup.” In this cell-free environment, reported Rasor, first author of the study, the lysate produced BDO at higher productivity rates than were noted inside the cell.

“One of the huge advantages of the cell-free system is that the cells are no longer growing,” Rasor said. “So they can push more of the carbon that we feed into a product molecule and so we’re able to make the same amount of a product in just eight hours that growing cells take three days to make, which is a really exciting jump in the rate of product formation.”

This was the first time CRISPR-Cas9 had been used to modify a cell’s genome in order to create lysates with altered metabolic performance, Alper noted. “This was really an unknown exercise,” he added. “It wasn’t a proven premise that if you rewire a cell in vivo that you’re going to get that same type of effect in vitro. This really demonstrates something that sounds feasible in retrospect – ‘Of course you can rewire one and get the other’ – but, that was not a known fact in the field whatsoever.”

Focusing on Carbon Flux and Future Directions

The team reported producing BDO at the rate of 0.9 grams per Liter-hour in a system optimized for developing small-scale prototypes. Additionally, the team also used a similar rewiring strategy to produce the small molecules glycerol and itaconic acid to see how the cell-free system allowed them to increase the productivity rates for pathways of varying complexity. Rasor cautioned that further optimization is needed to scale up for commercial viability.

“For context, commercially relevant biobased processes in cells often have synthesis rates on the order of one to five grams per Liter per hour,” Jewett said. “From the academic perspective we’re able to be in this range in the absence of cell walls. If we can continue to learn how to focus the carbon flux, we can avoid transport limitations to potentially reach even higher productivity and that’s one of these things that we’re really excited about in the future, to see if that’s possible.”

Alper and Jewett noted this paper is the first result of the collaboration with the JGI, where they are partnering with Yasuo Yoshikuni and Ian Blaby of the DNA Synthesis Science Program. “This collaboration brings tremendous strengths from each of the groups to allow us to do research that, frankly, neither one of us would have done alone,” Jewett said.

“To paraphrase a quote from an old movie, ‘This is the start of a beautiful collaboration,’” Alper said. “We’re exploring not just what can be enabled by this technology, but also what we can understand through this technology.”

“This is a fantastic example of rapid-prototyping systems for metabolic pathways that we plan to offer to users in the near term,” added JGI Director Nigel Mouncey.

Hal Alper will be speaking on “An Integrated Cell / Cell-free Metabolic Engineering Approach for Rapid Prototyping of Genes and Pathways” at the JGI Annual Genomics of Energy & Environment Meeting on September 1, 2021. Register here to hear him and others.

 

Publication: Rasor BJ et al. An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts. Nature Communications. 2021 Aug 26. doi: 10.1038/s41467-021-25233-y

 

Byline: Massie S. Ballon

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases Tagged With: 2022-progress-sci-highlight

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

You can move, but you can’t hide

Illustration of a magnifying glass identifying viruses and plasmids.

JGI announces second round of 2023 New Investigator awardees

From left to right: [above] Emma Bell, Mallory Choudoir, Sneha Couvillion, Tobin Hammer, Christina Hazard, Rachel Mackelprang, Brook Moyers, Mei, Ran,; [below] Benjamin Peterson, Dacheng Ren, Allison Rober, Neal Scott, Chikae Tatsumi, Vojtech Tlaskal, Fernando Torralbo, Luis Felipe Valdez-Nuñez

A Collaboration to Improve Plant Genome Annotations Across Species

A tiled collage of square photos of different plants - soybeans, and sorghum, for example.

From Berkeley to Binghamton: Tracking Strawberry Evolution

iPHoP: A Matchmaker for Phages and their Hosts

iPHoP image (Simon Roux)

Supercharging SIP in the Fungal Hyphosphere

Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California