DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    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

    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    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)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

News & Publications
Home › News Releases › Freedom and Flexibility: Thinking Outside the Cell for Functional Genomics

April 3, 2018

Freedom and Flexibility: Thinking Outside the Cell for Functional Genomics

Latest JGI-Funded Technology Development Proposal Focuses on Cell-Free Systems

Over the past two decades, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, has transitioned from a high-throughput genome sequencing center to a national user facility that provides researchers around the world with access to sequencing and computational analysis capabilities on projects relevant to the DOE missions of energy and environmental challenges. Along with advances in sequencing technologies and capacities, JGI has developed capabilities such as single-cell genomics, synthetic biology, and metabolomics to move beyond generating a DNA sequence to understanding gene functions for a myriad of applications.

The cell-free systems approach outlined in the proposal starts by lysing pre-optimized cells from selected strains, and then working with the lysates from these strains to express genes and pathways of interest in cell-free platforms (CFPS) which can be mixed in cocktails of varying ratios for easily and rapidly characterizing novel and improved pathways, speeding up the “build” and “test” portion of the design-build-test (DBT) cycle. (Diagram: Mike Jewett)

The cell-free systems approach outlined in the approved ETOP proposal starts by lysing pre-optimized cells from selected strains, and then working with the lysates from these strains to express genes and pathways of interest in cell-free platforms (CFPS) which can be mixed in cocktails of varying ratios for easily and rapidly characterizing novel and improved pathways, speeding up the “build” and “test” portion of the design-build-test (DBT) cycle. (Diagram: Ashty Stephen Karim)

“JGI’s strategic direction is to translate genomic information into functional understanding,” noted Director Nigel Mouncey. “Today, the scale and cost of DNA sequencing have afforded the generation of an unprecedented level of gene and genome information for which relatively little is known regarding function. Thus, there is a critical need to rapidly, and at scale, assign validated function of genes, pathways and genomes.”

Cell-based tests to determine metabolic function are challenging due to the need for cell growth, complex regulatory mechanisms, interference with or from other metabolic pathways and cellular processes. The latest proposal approved through the JGI’s Emerging Technologies Opportunity Program (ETOP) is led by Hal Alper of the University of Texas at Austin and Michael Jewett of Northwestern University. Aided by nearly $500,000 in funding over two years from the JGI, the project aims to develop an optimized cell-free platform that will enable researchers to speed up the “build” and “test” portion of the design-build-test-analyze cycle in synthetic biology. Cell-free systems have been used successfully for individual protein expression over decades, but more recent applications have focused on enzyme screening, metabolic pathway design and prototyping and immune system characterization.

Hal Alper, UT Austin

Hal Alper, UT Austin (courtesy photo)

“What we’re trying to develop is a generic platform that’s pathway-agnostic, a seamless pipeline from DNA design to prototype,” said Alper. “It’s a tool for both discovery and understanding, but always a way to speed up cell engineering.”

Launched in 2013, the ETOP aims to bring new technologies developed at other institutions into the JGI, making them available to its users for energy and environment applications and adding value to the high throughput sequencing and analysis currently being done for JGI users. (Click here for the list of previously approved proposals.)

The cell-free systems approach outlined in the proposal starts by lysing pre-optimized cells from selected strains, and then working with the lysates from these strains to express genes and pathways of interest which can be mixed in cocktails of varying ratios for easily and rapidly characterizing novel and improved pathways. Alper noted that this is a collaborative effort in which their labs will be handing off the technology development several times throughout the timeframe to enable progress.

“People have used cell-free frameworks to understand biochemistry for decades. What’s new is idea of treating a pathway as something that can be built from enzyme cocktails,” said Jewett. “In our design-build-test cycle, the unit isn’t a plasmid or a construct, but a lysate enriched with pathway enzymes. You have freedom and flexibility; direct access to reaction conditions because you don’t have cell walls, and it’s useful for non-model organisms. This can accelerate design loops and can lead to the question, rather than taking 10,000 shots on goal in a month, can we do it in a week?”

Mike Jewett, Northwestern University

Mike Jewett, Northwestern University (courtesy photo)

“This ETOP will develop novel and scaleable cell-free expression platforms that are optimized for particular key nodes of metabolism and will be demonstrated for a range of biosynthetic genes and pathways,” said Mouncey. “This technology is highly complementary to existing capabilities at JGI, and once in-house, will be combined in novel integrative workflows that allow for sophisticated genome mining to DNA synthesis to cell-free expression to high-throughput metabolomics to high-performance computing to characterize the function of 1000s of genes. Working with the leaders in this exciting field will lead to highly impactful and valuable technology for our Users.”

Jewett added that the cell-free systems framework wasn’t even possible two years ago. He cited the confluence of advances in DNA synthesis, improvements in cell-free biosynthesis capabilities, and genome engineering tools including novel strategies such as multiplexed CRISPR tools that have enabled this new platform.

“We hope to draw in researchers from the broader community that can leverage these new tools within the JGI,” he added.

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

More topics:

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

Related Content:

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"

JGI announces first round of 2023 New Investigator awardees

Digital ID card with 10 headshots reads: Congratulations to our 2023 New Investigator recipients!

JGI at 25: Following Fungi that Pry Apart Plant Polymers

A brown goat with white horns looks at green hay

Exploring Possibilities: 2022 JGI-UC Merced Interns

2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)

JGI at 25: Using team science to build communities around data

  • 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