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 › Blog › Cracking the Code: Evolutionary Changes in the Genetic Code of Yeasts

September 7, 2018

Cracking the Code: Evolutionary Changes in the Genetic Code of Yeasts

Yeasts are some of the most important microbes used in biotechnology. Saccharomyces cerevisiae, the type of yeast used for making bread and beer, is just one representative of more than 1,500 yeast species found around the world. Currently, only a fraction of these yeasts has been harnessed for biotechnological applications. However, researchers studying various “non-conventional” yeast species aim to capitalize on yeast physiology and genetic features to drive biotechnology. In the future, yeasts may play a large role in developing palm oil substitutes, ethanol products, and feedstocks, for example. As discussed below, yeasts are also unique in terms of their genetic code.

CUG is translated as Leu in the standard code, and as Ser or Ala in the modified codes. Codons are shown in uppercase. (From Krassowski et al. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun. doi: 10.1038/s41467-018-04374-7. CC BY 4.0)

In yeasts, the codon CUG can be reassigned to different amino acids. CUG is translated as Leu in the standard code, and as Ser or Ala in the modified codes. Codons are shown in uppercase. (From Krassowski et al. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun. doi: 10.1038/s41467-018-04374-7. CC BY 4.0)

We typically think of the universal genetic code as being stable, where mRNA is translated into protein as codons are assigned to either a stop codon or one of the 20 unquestioned amino acids. Occasionally, scientists see departures from this standard code in mitochondria which, because of their own ribosomes and tRNAs, are prone to genetic drift. In nuclear genomes, however, a genetic code change where the amino acid assignment of a sense codon is swapped for a different amino acid is very rare. Until 2016, the only such example in eukaryotes was the reassignment of CUG from leucine (its usual meaning) to serine in budding yeasts.

Robert Riley spoke at the 2016 DOE JGI Genomics of Enegry & Environment Meeting. Watch his talk at http://bit/ly/JGI2016Riley.

Click on the image above to watch Robert Riley on codon reassignments in yeasts at the 2016 JGI Genomics of Energy & Environment Meeting. Or go to http://bit/ly/JGI2016Riley.

Then in 2016, JGI researchers discovered a similar switch in Pachysolen tannophilus.  A close relative of the well-known yeast genus, Candida, P. tannophilus is a recently-sequenced yeast that can ferment the wood sugar, xylose. As reported in the Proceedings of the National Academy of Sciences, the team discovered another reassignment of the codon CUG. This time CUG was changed from serine to alanine in P. tannophilus. This change was only the second reported case of a non-stop codon reassignment. Scientists are not sure why or how the change came about, but knowing if yeasts’ genetic codes are the same is important for gene expression experiments. (Watch the paper’s first author Robert Riley discuss the CUG reassignment at the 2016 DOE JGI Genomics of Energy & Environment Meeting: http://bit.ly/JGI2016Riley.)

Building on this information, another group of scientists followed-up, investigating the phylogenetic relationships in yeasts with standard and non-standard genetic codes. Published earlier this year in Nature Communications, this study looked at the genomes of 52 yeast species, including seven newly sequenced, using whole-genome data and mass spectrometry to determine phylogeny and genetic codes, respectively. Within this data set, researchers observed all three CUG codon reassignments: CUG-Ser, CUG-Ala, and CUG-Leu.

Watch Tom Jeffries, president of Xylome and professor emeritus at the University of Wisconsin-Madison, on the importance of nonconventional yeasts for biotechnological applications at the 2018 JGI Genomics of Energy & Environment Meeting at http://bit.ly/JGI2018Jeffries.

Click on the image above to watch Tom Jeffries, president of Xylome and professor emeritus at the University of Wisconsin-Madison, on the importance of nonconventional yeasts for biotechnological applications at the 2018 JGI Genomics of Energy & Environment Meeting. Or go to http://bit.ly/JGI2018Jeffries.

So, why is the CUG codon unstable in yeasts? The study authors propose that natural selection caused by a toxin acted specifically against the ancestral tRNALeu(CAG). They hypothesize that this toxin may have come from a Virus-Like Element (VLE). VLEs, the so-called “killer plasmids” code for a toxin and antitoxin and are present in budding yeasts. The authors believe that a VLE with a tRNALeu(CAG)-specific toxin infected the common ancestor of five clades of yeasts. In response, yeast lineages either changed their genetic codes or altered the sets of tRNALeu genes they maintain. If this hypothesis is correct, these genetic code changes represent a profound defense mechanism.

Publications:

  • Krassowski T et al. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun. 2018 May 14;9(1):1887. doi: 10.1038/s41467-018-04374-7.
  • Riley R et al. Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113.

Related Links:

  • JGI 2016 News Release: “Expanding the Stable of Workhorse Yeasts”
  • Robert Riley at the 2016 Genomics of Energy & Environment Meeting: bit.ly/JGI2016Riley
  • Tom Jeffries at the 2018 Genomics of Energy & Environment Meeting: bit.ly/JGI2018Jeffries

 

Blog author: Cindi Hoover

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: Blog

More topics:

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

Related Content:

JGI at 25: Mapping Switchgrass Traits with Common Gardens

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

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

JGI at 25: Expanding Metagenomics to Capture Viral Diversity

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)

JGI at 25: Cow rumen and the early days of metagenomics

  • 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