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

Our Science
Home › Science Highlights › Mining Metagenomes for Cas Proteins

October 19, 2018

Mining Metagenomes for Cas Proteins

Cas14 proteins discovered from JGI’s IMG/M database and biochemically characterized at UC Berkeley and the Innovative Genomics Institute. 

The Science

Click on the image above or click here (https://youtu.be/iSEEw4Vs_B4) to watch a CRISPR Whiteboard Lesson from the Innovative Genomics Institute, this one focuses on the PAM sequence.

Click on the image above or click here to watch a CRISPR Whiteboard Lesson from the Innovative Genomics Institute, this one focuses on the PAM sequence.

Researchers report the discovery of miniature Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated proteins that can target single-stranded DNA (ssDNA). The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at the University of California (UC), Berkeley, which is also affiliated with the Innovative Genomics Institute.

The Impact

The ability to accurately edit genomes (that is, repair gene mutations, and either delete or add genes in a precise fashion) has applications across many areas. In particular, gene editing is being used to develop drought, flooding, pest-resistant, and better-yielding crops. On the clinical side, gene editing is being advanced as a potential therapy for both genetic and complex disease. Finally, gene editing is being used to understand how a person’s genetic makeup predisposes them to, or protects them from, disease. Much of the work on genome editing has focused on the seminal CRISPR-Cas9 system, which targets double-stranded DNA. The discovery of Cas proteins that can target single-stranded DNA molecules broadens the range of applications for CRISPR-Cas systems. It also underscores the untapped potential waiting to be unearthed in sequencing and analyzing uncultivated microbes.

Summary

The CRISPR-Cas system is an immune mechanism in bacteria that confers resistance to foreign genetic elements by incorporating short sequences from infecting viruses and phages. In the event of a new infection, the microbes use the genetic information encoded in CRISPR sequences to target the virus and release attack enzymes in the form of Cas enzymes to cut the DNA and disable the virus. In Science, a team led by researchers from the University of California, Berkeley, report the identification of active Cas enzymes – dubbed Cas14 – that target ssDNA. In contrast, the seminal Cas9 proteins cleave double-stranded DNA.

Co-first author Lucas Harrington was a graduate student from study senior author Jennifer Doudna’s lab, and he worked with co-first author David Burstein, then a postdoctoral fellow with Doudna and longtime JGI collaborator Jill Banfield, also at UC Berkeley. Harrington is now at Mammoth Biosciences while Burstein is now at Tel Aviv University.

The Cas14 proteins are ~400–700 amino acids (aa) in size, half that of previously known class 2 CRISPR enzymes that are typically 950—1400 aa. They were initially identified by searching for Cas12d homologs across IMG/M’s assembled metagenomic data. It turned out that some of these were shorter than the typical Cas12d proteins and were also found next to cas1 genes. Further analysis led to the identification of a new family of Cas proteins, named Cas14. Using these sequences as a starting point, JGI data scientist David Paez-Espino in Nikos Kyrpides’ Microbiome Data Science group mined the IMG/M system with its large collection of publicly accessible metagenomic datasets from a wide variety of ecosystems around the world, conducting iterative searches using statistical analyses to continuously refine and improve the process.

The results yielded several CRISPR-Cas systems, and based on several experiments conducted by Doudna’s lab at UC Berkeley, close to 40 CRISPR-Cas14 systems belonging to eight subtypes were identified. Additionally, using Cas14a, the team was able to develop a Cas14-DETECTR that allows for CRISPR-based detection of ssDNA pathogens.

With few exceptions, the Cas14 proteins identified were found within the archaeal superphylum DPANN, named by a JGI-led team for the first five groups discovered: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaea. This work represents an excellent showcase of the unique capabilities provided from the IMG/M database in enabling new discoveries and is a continuation of previous collaboration of the JGI with the Doudna lab on the discovery of thermostable Cas9 genes.

The work also used resources at the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory.

Contacts:

BER Contact
Ramana Madupu, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Ramana.Madupu@science.doe.gov

PI Contact
Jennifer Doudna
University of California, Berkeley
doudna@berkeley.edu

Funding:

The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The work was supported in part by grants from the Paul Allen Frontiers Group, the National Science Foundation Graduate Research Fellowships and the Howard Hughes Medical Institute. Support was also provided by the National Science Foundation, and the the Lawrence Berkeley National Laboratory’s Sustainable Systems Scientific Focus Area is funded by the U.S. Department of Energy.

Publication:

  • Harrington LB et al. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science. 2018 October 18. doi: 10.1126/science.aav4294.

Related Links:

  • UC Berkeley News Release: “Smallest life forms have smallest working CRISPR system”
  • Jennifer Doudna’s Lab at UC Berkeley: http://doudnalab.org/
  • Jill Banfield’s Lab at UC Berkeley: http://geomicrobiology.berkeley.edu/
  • Innovative Genomics Institute: https://innovativegenomics.org/
  • IGI video: “CRISPR-Based Diagnostic Tools – A CRISPR Whiteboard Lesson”
  • Integrated Microbial Genomes and Microbiomes (IMG/M): https://img.jgi.doe.gov/
  • JGI News Release: “Tracking Microbial Diversity Through the Terrestrial Subsurface”
  • JGI News Release: “Unveiled: Earth’s Viral Diversity”
  • JGI News Release: “Boldly Illuminating Biology’s “Dark Matter”
  • Supercomputing 17 (SC17) video: “#HPCConnects – CRISPR“

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)

Filed Under: Science Highlights

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.

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.

New Research Sheds Light on Diversity in the Deep Sea

A photo taken in the deep sea. Black clouds billow out of hydrothermal vents.

Sequencing Sphagnum Leads to Discovery of Sex Chromosomes

A photo of two sphagnum species: S. divinum (red) and S. angustifolium (green)]

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.
  • 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