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 › Fungal Enzymes Team Up to More Efficiently Break Down Cellulose

May 26, 2017

Fungal Enzymes Team Up to More Efficiently Break Down Cellulose

Collaborative science initiative enables resolution of fungal protein complexes.

Scanning electron micrograph (SEM) of Neocallimastix californiae, a representative of the Neocallimastigomycetes, a clade of the early-diverging fungal lineages that are not well-studied. It's one of three Neocallimastigomycetes sequenced and annotated by the DOE JGI for this study. (Chuck Smallwood, PNNL)

Scanning electron micrograph (SEM) of Neocallimastix californiae, a representative of the Neocallimastigomycetes, a clade of the early-diverging fungal lineages that are not well-studied. It’s one of three Neocallimastigomycetes sequenced and annotated by the DOE JGI for this study. (Chuck Smallwood, PNNL)

One of the biggest barriers in the commercial production of sustainable biofuels is to cost-effectively break down the bioenergy crops into sugars that can then be converted into fuel. To reduce this barrier, bioenergy researchers are looking to nature and the estimated 1.5 million species of fungi that, collectively, can break down almost any substance on earth, including plant biomass.

As reported May 26, 2017 in Nature Microbiology, a team led by researchers at the University of California (UC), Santa Barbara has found for the first time that early lineages of fungi can form complexes of enzymes capable of degrading plant biomass. By consolidating these enzymes, in effect into protein assembly lines, they can team up to work more efficiently than they would as individuals. The work was enabled by harnessing the capabilities of two U.S. Department of Energy (DOE) Office of Science User Facilities: the DOE Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (Berkeley Lab); and, the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL).

“There are protein complexes in bacteria called cellulosomes that pack together the enzymes to break down plant biomass,” said study senior author Michelle O’Malley of UC Santa Barbara. “The idea is that these clusters are better at attacking biomass because they are keeping the different enzymes in place with plugs called dockerins so they work more efficiently. This has been detailed in bacteria for more than 20 years, but now seen for the first time in fungi.”

Omics Lend Insights to Fungal Enzyme Complexes

With help from both the DOE JGI and EMSL, the team has now found protein complexes in anaerobic gut fungi that O’Malley said in principle do the same thing—attack plant biomass as a cluster of enzymes. While they found that many of enzymes in these complexes resulted from horizontal gene transfers with gut bacteria, they also noted differences in the composition compared to the bacterial cellulosomes. For one thing, both dockerins and scaffoldin are not similar between fungi and bacteria. Also, the bacterial cellulosomes are species-specific. Think of them as the high school clique that does everything together. In contrast, the fungal structures that appear analogous to the bacterial cellulosomes are like the high school kids who could easily move among various social groups and are comprised of clusters of enzymes that can “dock” and work in other fungi.

The study involved a comparative genomics analyses of five fungi that belong to the Neocallimastigomycetes, a clade of the early-diverging lineages that are not well-studied. Three of the fungi were isolated from animal gut samples collected by the UC Santa Barbara team and sequenced and annotated by the DOE JGI. “Proteomics data and genomics data enabled us to figure out what these complexes are and go hunting for them in other genomes,” O’Malley said. “The three genomes are really well resolved to the point where you can start looking at what’s there, what’s regulating enzyme production, and how enzymes have evolved.”

Study co-senior author and DOE JGI Fungal Genomics Program head Igor Grigoriev noted that a multi-omics approach that harnessed the genomics and molecular characterization capabilities through a collaborative science initiative allowing researchers to access multiple user facilities in one proposed project known as Facilities Integrating Collaborations for User Science (FICUS), was critical for the research.

“It’s the first time we’ve seen parts of the fungal cellulosome,” Grigoriev said. “Through the JGI-EMSL FICUS initiative, proteomics allowed us to find the first of these really large ~700 kiloDaltons (kDa) fungal proteins that hold all enzymes together (compared to the molecular weight of 34 kDa of an average protein). Then the high quality of genome assemblies enabled identification of multiple copies of this protein in each of the gut fungi genomes. Just having proteomics or sequencing tools isn’t enough since these proteins are not similar to anything else outside of Neocallimastigomycetes. Though the fungal cellulosome was discovered through proteomics, we needed genomics and transcriptomics to decode all its parts.”

Digging Deeper with High-Resolution Genomes

The O'Malley Lab at UC Santa Barbara with principal investigator Michelle O'Malley in the center. (Courtesy of Michelle O'Malley)

UC Santa Barbara researcher Michelle O’Malley and her lab led the work published in Nature Microbiology. (Courtesy of Michelle O’Malley)

The work is an extension of O’Malley’s studies of anaerobic gut fungi, which appeared in Science last year (watch her talk from the 2016 DOE JGI Genomics of Energy & Environment Meeting at bit.ly/JGI2016OMalley). It’s a lot of the same players, but we’re digging deeper now because we have high-resolution genomes, and we didn’t have them then,” she said. “We’re able to conduct more comparative genetics and now we’re trying to figure out the ecological roles in their microbiome.”

Understanding in greater detail the protein mechanisms of biomass degradation is crucial to advancing DOE’s agenda to develop sustainable biofuels from plant feedstocks. High throughput sequencing, combined with sophisticated proteomics, illuminates not just the diversity and complexity of fungal biomass degradation capacities but also furnishes a knowledge basis for exploitation of these abilities with synthetic biology and metabolic engineering approaches.

Support for this work was provided by the DOE Office of Science, including an Early Career Research Program award, as well as the National Science Foundation, the U.S. Department of Agriculture, the U.S. Army Research Office, and the University of California.

***

EMSL, the Environmental Molecular Sciences Laboratory, is a DOE Office of Science User Facility. Located at Pacific Northwest National Laboratory in Richland, Wash., EMSL offers an open, collaborative environment for scientific discovery to researchers around the world. Its integrated computational and experimental resources enable researchers to realize important scientific insights and create new technologies. Follow EMSL on Facebook, LinkedIn and Twitter.

Interdisciplinary teams at Pacific Northwest National Laboratory address many of America’s most pressing issues in energy, the environment and national security through advances in basic and applied science. Founded in 1965, PNNL employs 4,400 staff and has an annual budget of nearly $1 billion. It is managed by Battelle for the U.S. Department of Energy’s Office of Science. As the single largest supporter of basic research in the physical sciences in the United States, the Office of Science is working to address some of the most pressing challenges of our time. For more information on PNNL, visit the PNNL News Center, or follow PNNL on Facebook, Google+, LinkedIn and Twitter.

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:

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