BER Research Highlights

Search Date: July 11, 2020

17 Records match the search term(s):


December 19, 2019

A MAGIC Approach to Understanding the Genetic Basis of Complex Biological Functions

Comprehensive genome-wide search enables discovery of multi-gene determinants of traits in yeast.

The Science
Researchers use a strategy called metabolic engineering to improve how microbes produce bioproducts such as biofuel. Typically, scientists modify one or a few genes to understand how those genes affect bioproduct production. However, some traits are controlled by many genes. Identifying all the genes involved in complex traits is difficult and time consuming. Now, researchers have developed a new system for altering the expression of each gene in the yeast genome to identify multiple genes that control complex traits.  

The Impact
Researchers know the sequence of nearly all genes in organisms ranging from bacteria to humans. However, they do not understand the functions of most of those genes. If researchers can determine what genes do, they can engineer organisms for biotechnological applications such as biofuel production. That task is hardest for traits that arise from the interaction of many genes. Researchers have developed a method called MAGIC to activate, silence, or eliminate the expression of each gene in the yeast genome. This method allows them to identify the genes responsible for different traits, regardless of how many genes are involved.

Summary
Researchers use CRISPR, for “Clustered Regularly Interspaced Short Palindromic Repeats,” to edit the genomes of living things by activating, silencing, or deleting the activity of specific genes. However, previous methods could not easily combine these editing tools. Researchers have addressed that limitation with a new system called MAGIC, for “multifunctional genome-wide CRISPR.” MAGIC can modify the expression of genes in yeast by combining CRISPR activation, interference, and deletion, thereby allowing researchers to understand how genes work in concert, not just on their own, to produce specific traits.

The researchers first created a comprehensive mutant library of the approximately 6,000 genes in the yeast genome. Once the researchers used MAGIC to identify genes of interest, they could permanently modify those genes in a new strain of yeast. The team identified three genetic modifications that confer tolerance to furfural, a growth inhibitor that can limit the ability of yeast to produce biofuels. The modified strain grows and ferments ethanol much more effectively than unmodified yeast. Additional rounds of screening identified more genes for furfural tolerance. These additional genetic modifications required the presence of the modifications found in the first round of screening. This demonstrates the importance of MAGIC and its ability to piece together complex synergistic interactions of genes.

Contacts
BER Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Principal Investigator
Huimin Zhao
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

Funding
This work was supported by Biosystems Design research within the Genomic Science program of the U.S. Department of Energy’s Office of Biological and Environmental Research.

Publication
Lian, J., C. Schultz, M. Cao, M. HamediRad, and H. Zhao.“Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping.” Nature Communications 10(1)5794 (2019). [DOI:10.1038/s41467-019-13621-4].

Related Links
University of Illinois: MAGIC system allows researchers to modulate activity of genes acting in concert

Contact: Pablo Rabinowicz, SC-23.2 (301) 903-0379

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 18, 2019

How Many Copies Does It Take to Change a Trait?

The number of copies of genes a poplar tree has influences its traits.

The Science
New research shows that the number of copies of genes in a poplar tree affects its traits. Scientists developed a group of poplar trees in which different plants have DNA segments that are repeated or deleted. They found that the number of copies of certain regions of the genome influences traits important to agriculture, the bioenergy industry, and the tree’s ecological role. Because poplars and other plants commonly show variation in copy number, these results highlight an important source of genetic variation.

The Impact
Sequencing plant genomes (an organism’s set of genes) has revealed many new features. A significant fraction of plant genes have either fewer or extra copies compared to others. However, the impact of these differences on wood yield and other important traits has been hard to measure. This study demonstrates a practical method to identify regions of the genome whose copy number is important for these traits. These findings help researchers understand how genomes balance their many components. It should also improve predictions of which forest trees will be most useful for bioenergy.

Summary
Scientists have developed a large collection of poplar trees carrying genomic insertions and deletions. Each tree was sequenced to determine the exact location of their genomic change, then measured for numerous phenology and biomass production traits relevant to bioenergy production. These results show that a large proportion of the genome is represented by regions that are sensitive to changes in gene dosage and that these regions are correlated with phenology and biomass traits important for bioenergy applications. These results thus indicate that copy number variation and gene dosage are fundamental to explaining quantitative trait variation in poplar trees. In a broader sense, because copy number variation has been recently identified as common in numerous plant species, these results indicate that copy number variation and gene dosage should be considered when trying to predict phenotypic performance based on genotypic information.

Contacts
(BER Program Manager)
Cathy Ronning
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Environmental Genomics
catherine.ronning@science.doe.gov

(Principal Investigator)
Luca Comai
University of California Davis, Genome Center and Plant Biology
lcomai@ucdavis.edu

Funding
Office of Biological and Environmental Research (award number DE-SC0007183), within the U.S. Department of Energy Office of Science.

Publications
Bastiaanse, H., M. Zinkgraf, C. Canning, H. Tsai, M. Lieberman, L. Comai, I. Henry, and A. Groover. “A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees.” Proceedings of the National Academy of Sciences USA 116(27), 13690-13699 (2019). [DOI:10.1073/pnas.1903229116].

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 17, 2019

Microbial Evolution: Nature Leads, Nurture Supports

(Microbial Evolution: Nature Leads, Nurture Supports

Across ecosystems, microbial traits are preserved along lineages, much like in multicellular organisms, and can improve the development of soil models.

The Science
To better predict how microbes influence how much carbon moves through the water, air, and land, scientists want to compare the influence of evolution (“nature”) and the surrounding climate (“nurture”). Based on an extensive study across environments, from mixed conifer forest to high-desert grassland, the team suggests that microbes are not so different from larger, more complex forms of life. That is, in determining species traits, nature takes the lead, while nurture plays a supporting role.

The Impact
With microbial species, less is known about the relative role of nature versus nurture than desired. Why? Microbes’ small size and great diversity make measuring their traits in nature challenging. This study offers an improved understanding of microbial trait distribution, which influences nutrient cycling, such as growth rate and carbon usage. How bacterial species influence soil carbon cycling may help enhance models to reduce uncertainty when forecasting soil carbon feedbacks to global change.

Summary
How much of a microbe’s makeup and destiny is determined by where it finds itself in the world, and how much is explained by its evolutionary past? While evolutionarily encoded traits (nature) have been more predictive in plants and animals than environmental variation (nurture), the small size and great diversity of microbial species have made it challenging to answer this question in life’s microscopic realm. Now, a team of researchers at West Virginia University, Northern Arizona University, University of Massachusetts Amherst, Lawrence Livermore National Laboratory, and Pacific Northwest National Laboratory used a new approach to determine the traits of microbial species by tracking isotopes into their DNA, indicating rates of carbon assimilation and growth. The team measured these traits in four ecosystems along a gradient in elevation, temperature, and moisture.

They found that, as with plant and animal species, the evolutionary history of soil bacteria (that is, nature) explained more variation in the measured traits than did their local environment (that is, nurture). Evolutionary history explained up to 65 percent of the variation in trait values, while the variation explained by the ecosystem never exceeded 20 percent. Even across vast changes in temperature and precipitation, the traits of microbial species remained relatively consistent. For example, microbial species and families that rapidly used carbon in soil from warm desert grassland showed very similar activity rates when assessed in soil from a comparatively cool and wet forest.

Determining whether nature or nurture has more influence has practical value: if traits are hard-wired by evolution, they are consistent and can be used to make predictions about the natural world.

(Contacts)
BER Program Manager
Dawn Adin
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research
dawn.adin@science.doe.gov

(Principal Investigator)
Bruce Hungate
Northern Arizona University
Bruce.Hungate@nau.edu

Funding
This work was supported by the Biological Systems Science Division’s Genomic Science program (No. DE-SC0016207) of the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy (DOE) Office of Science. It also was supported by the National Science Foundation’s Dimensions of Biodiversity (Nos. DEB-1645596 and DEB-1241094).

Publications
Morrissey, E. M., R. L. Mau, M. Hayer, et al., “Evolutionary history constrains microbial traits across environmental variation.Nature Ecology and Evolution 3, 1064–1069 (2019). [DOI:10.1038/s41559-019-0918-y].

Related Links
Northern Arizona University: Center for Ecosystem Science and Society

Contact: Cathy Ronning, SC-23.2, (301) 903-9549

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 11, 2019

Droughts Spell Changes for Soil Microbes

Researchers found that soil drying altered metabolic pathways within soil microbial communities.

The Science
Scientists predict a warming Earth will cause more droughts that are more severe in the grasslands of the central United States. Soils in these fertile, productive grasslands store large reserves of carbon. Previously, scientists did not know how the decrease in soil moisture due to drought would affect carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. This research found that soil drying affects the microbial community in several ways. First, it affects which microbes are there. In addition, it influences the relationship between those microbes and the organisms that produce compounds that help microbial species survive during a drought.

The Impact
Researchers used multiple methods to study the community of microbes, including analyzing its rRNA, how it expresses its genes, and the molecules cellular processes produce. They showed that despite the soil habitat’s complexity, it is possible to better understand the effect of environmental change on the community of microbes (microbiome) in the soil. They also gained insight into how that microbiome functions. This large-scale approach lays the groundwork for future, targeted studies. Other scientists could also use this approach to study other complex microbial systems.

Summary
Warming temperatures are causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community (i.e., the metaphenome). In this study, researchers used an untargeted omics approach to determine the soil microbial community’s metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, they aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies.

The research team collected soil from three locations at a field station in Kansas, incubated the samples for 15 days under dry or wet conditions, and compared them to field-moist controls. The team determined the microbiome response to wetting or drying through 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics. Researchers then assessed the resulting shifts in taxa, gene expression, and metabolites. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome, such as changes in metabolic pathways that lead toward the production of sugars and other osmoprotectant compounds. By contrast, few changes occurred after wetting. The team used the combined metabolic and metatranscriptomic data to generate metabolite-reaction networks to determine the metaphenomic response to soil moisture transitions, such as generation of trehalose under dry conditions.

(Contacts)
BER Program Manager
Dawn Adin
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research
dawn.adin@science.doe.gov

(Principal Investigator)
Janet Jansson
Pacific Northwest National Laboratory
janet.jansson@pnnl.gov

Funding
This research was supported by the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy (DOE) Office of Science, and is a contribution of the Scientific Focus Area Phenotypic Response of the Soil Microbiome to Environmental Perturbations. This research was also supported by the Environmental Molecular Sciences Laboratory (EMSL). EMSL is a DOE Office of Science user facility sponsored by DOE BER and located at Pacific Northwest National Laboratory (PNNL). A portion of the research was conducted using PNNL Institutional Computing (PIC) resources and partially supported by the Microbiomes in Transition Initiative under the Laboratory Directed Research and Development Program at PNNL.

Publications
Chowdhury, T. R., J.- Y. Lee, E. M. Bottos, C. J. Brislawn, R. A. White III, L. M. Bramer, J. Brown, J. D. Zucker, Y.-M. Kim, A. Jumpponen, C. W. Rice, S. J. Fansler, T. O. Metz, L. A. McCue, S. J. Callister, H.-S. Song, and J. K. Jansson, “Metaphenomic responses of a native prairie soil microbiome to moisture perturbations.” mSystems 4(4), e00061-19 (2019). [DOI:10.1128/mSystems.00061-19].

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 11, 2019

Predicting How Microbial Neighbors Influence Each Other

A new computational method reliably predicts interactions that depend on neighboring organisms in an environment.

The Science
Microbes in the soil form networks, which in turn make up larger communities. As the environment changes, so do the microbes and their relationships. For scientists to design or control these microbes, they must first understand their communities in nature (microbiomes). Soil ecologists know well that neighboring species influence some microbial interactions.  Researchers developed a new theoretical framework called minimal interspecies interaction adjustment (MIIA). It predicts how surrounding organisms and other factors drive changes in interactions in microbial communities.

The Impact
This new computational method improves the understanding of how microbes organize themselves into communities. It describes in detail how neighboring species affect interactions between microbes. This method also predicts major shifts in microbes’ influence on carbon and nitrogen cycles. This information could enable scientists to design and engineer groups and communities of microbes in the future.

Summary
Microbial community dynamics in soil and other habitats involve nonlinear interspecies interactions, so these dynamics are notoriously difficult to predict. Yet understanding how such microbiomes are organized in nature is necessary for designing them (such as for biofuel production) and for controlling them—for example, as a way to ensure that soils do not emit too much carbon into the Earth’s atmosphere. Meanwhile, ecologists know that interactions in microbial communities are influenced by neighboring species, or which organisms are around them. Until now, however, there has been no theoretical framework that can predict such context-dependent microbial interactions.

The research was motivated by the following fundamental ecological questions: How are interspecies interactions modulated by shifts in community composition and species populations? To what extent can interspecies relationships observed in simple cultures be translated into complex communities?

The researchers addressed these questions by demonstrating that the theoretical framework enables microbial interactions in binary, or one-to-one, cultures to be translatable into complex communities. The researchers also demonstrated the utility of this method in designing and engineering microbial consortia. In this regard, they found that microbial interactions can be significantly modulated when perturbed by a small number of neighboring species—but that the level of modulation diminishes as the number of new neighboring species increases.

This work, the authors say, can also be applied to questions of community ecology beyond microbes. It may provide a theoretical platform for better understanding all biological interaction systems.

(Contacts)
BER Program Manager
Dawn Adin
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research
dawn.adin@science.doe.gov

(Principal Investigators)
Hyun-Seob Song
Pacific Northwest National Laboratory
HyunSeob.Song@pnnl.gov

Janet Jansson
Pacific Northwest National Laboratory
janet.jansson@pnnl.gov

Funding
This research was supported by the Office of Biological and Environmental Research within the U.S. Department of Energy Office of Science, as part of the Foundational Scientific Focus Area (SFA), Soil Microbiome and the Subsurface Biogeochemistry Research (SBR) SFA at Pacific Northwest National Laboratory.    

Publications
Song, H-S., J-Y. Lee, S. Haruta, W. C. Nelson, D-Y. Lee, S. R. Lindemann, J. K. Fredrickson, and H. C. Bernstein, “Minimal interspecies interaction adjustment (MIIA): Inference of neighbor-dependent interactions in microbial communities,” Frontiers in Microbiology 10, 1264 (2019). [DOI:10.3389/fmicb.2019.01264].

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 10, 2019

Fungus Fuels Tree Growth

The Science
The fungus Mortierella elongata enjoys a dual lifestyle. It can thrive in the soil as a saprophyte, an organism that lives off decaying organic matter. It can also live as an endophyte, an organism that lives inside a plant between root cells. The fungus is almost always found among and within poplar trees. In an effort to understand the fungus’s influence on the plant, a team of scientists studied what happens to the tree’s physical traits and gene expression when the fungus is present.

The Impact
Black cottonwood, or poplar (Populus trichocarpa), is the fastest growing hardwood tree in the western United States. This characteristic makes it a promising feedstock for bioenergy. By better understanding how poplar responds to endophytes, scientists can improve their work on both plant and root microbiomes to grow energy crops more efficiently.

Summary
To interrogate the close partnership of endophyte M. elongata and poplar, a team collected forest samples of poplar and soil from Washington and Oregon. The cuttings included genotypes from the U.S. Department of Energy’s (DOE) BioEnergy Science Center (BESC), predecessor of DOE’s Center for Bioenergy Innovation (CBI) at Oak Ridge National Laboratory. To see how the fungus affected poplar growth, the team compared poplar cuttings grown with and without an inoculation of the M. elongata strain PM193 that was added to a diluted soil mixture. The results were striking. Adding PM193 caused poplar cuttings to grow about 30 percent larger by dry weight than without PM193. By contrast, a different endophytic fungus, Ilyonectria europaea, had no effect on growth. The team partnered with the DOE Joint Genome Institute (JGI), a DOE Office of Science user facility, through its Community Science Program to sequence and annotate the M. elongata and I. europaea genomes for this study. The team found that, unlike pathogenic or mycorrhizal fungi (mutualist symbionts that induce structural changes in plant roots), M. elongata does not have as many gene products that directly influence plant phenotype, such as secreted proteins. However, M. elongata seems to encourage the plant to have leakier cell walls and weaker defenses in general; the fungus decreased the expression of poplar genes associated with plant defense (e.g., jasmonic acid and salicylic acid). The team also observed that the plants instead put more energy into growth, noting an increased expression of genes involved in signaling of gibberellin, one of the best-known plant growth hormones. One other tidbit that caught the researchers’ attention is that the poplar cuttings had increased expression of lipid signaling genes when they were inoculated with M. elongata. Poplar might be detecting lipids from M. elongata; the fungus produces them so prolifically it oozes. The team hypothesizes that lipids could act as a bridge of interkingdom communication between the plant and fungus. Discovering how microbes can influence plant physiology helps scientists better understand how to optimize characteristics like growth rate. Harnessing that power could help usher widespread use of biofuel as a replacement to fossil fuel.

(Contacts)
BER Program Managers
Cathy Ronning
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Environmental Genomics
catherine.ronning@science.doe.gov

Ramana Madupu
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research, Computational Biosciences, and DOE Joint Genome Institute
ramana.madupu@science.doe.gov

(Contact)
Hui-Ling Liao, Ph.D.
University of Florida
sunny.liao@ufl.edu

 

 

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 15, 2019

Trees Consider the Climate When Choosing Their Partners

Forest trees establish symbiotic relationships with microbes depending on how the climate determines the rate of soil organic matter decomposition.

The Science
Bacteria and fungi living inside plant roots help plants capture mineral nutrients from the soil while benefiting from the food that the plant produces using energy from the sun. Trees can establish several types of symbiotic relationships with fungi and bacteria. Researchers constructed a global map of the types of tree symbioses across the world. With the map, they determined that the type of fungal symbiosis found in trees depends on how quickly the organic matter in the soil decomposes. The team also found that bacteria that convert nitrogen gas from the atmosphere into plant-usable products form tree symbioses in arid environments.

The Impact
The health of the world’s forest is of critical importance for the well-being of the planet. Symbiotic microbes that associate with trees affect their capacity to acquire essential nutrients from the soil and air around them. Our knowledge of the effects of geographic and climatic factors on these symbioses has so far come from analyses of a limited number of environments. The study provides a global map of tree symbioses across large numbers of species and ecosystems. This comprehensive analysis not only sheds light on the important role of microbes in shaping the landscape of the world’s forests, but it will also help improve global biogeochemical models.

Summary
To understand how tree-microbial symbioses affect the state of forests at the global scale, an international consortium of researchers surveyed tree-microorganism symbioses in 1.1 million locations around the world. These ecosystems included over 28,000 tree species and a vast climatic and geographic diversity. This comprehensive study demonstrated that the majority of tree symbioses are ectomycorrhizal, although they represent a small percentage of all tree species. This type of tree symbiosis is predominant in seasonally cold and dry climates as well as at high latitude and elevation. In these conditions, decomposition of soil organic matter is slow. In warm tropical forests, where decomposition is faster, trees prefer to establish arbuscular mycorrhizal associations, and the researchers observed a fairly sudden geographical transition between the two types of symbioses. On the other hand, the research showed that symbioses with nitrogen-fixing rhizobia and actinobacteria occur in arid and hot ecosystems. The global microbial biogeographical map of forest symbioses constructed in this study shows that forests transition from low-latitude arbuscular mycorrhizal through nitrogen-fixer to high-latitude ectomycorrhizal ecosystems, confirming predicted rules of mycorrhizal distribution.

Contact
Kabir Gabriel Peay
Stanford University
kpeay@stanford.edu  

Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Funding
This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Early Career Research Program. The authors also acknowledge support from other sources listed in https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-019-1128-0/MediaObjects/41586_2019_1128_MOESM3_ESM.pdf.

Publication
Steidinger, B. S., T. W. Crowther, J. Liang, et al. “Climatic controls of decomposition drive the global biogeography of forest-tree symbioses.” Nature 569, 404 (2019). [DOI:10.1038/s41586-019-1128-0]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 14, 2019

Simplifying Microbial Consortia Opens a Path to Understanding Soil Community Ecology

Representative communities of reduced complexity provide new experimental context for investigating how soil microbial communities function.

The Science
Soil microbiomes are among the most diverse communities of microbes on Earth. They play a huge role in cycling soil carbon, nitrogen, and other nutrients. These cycles underpin land-based food webs. Soil microbes also regulate many of the planet’s other biogeochemical cycles. It is notoriously difficult to study how these natural microbial communities interact, function, and respond to changing environments. New research demonstrates that microbial communities that are simplified but still representative may offer a way to explore more complex ones. In particular, they can help scientists uncover the mechanisms that drive the ecology of groups of soil microbes.

The Impact
Soil microbial communities that are simpler than real ones but still represent their basic functions can be useful tools for scientists. They can offer insights into how the microbes in these communities remain stable or change over time. They provide scientists with new contexts to understand how environments shape soil microbiomes. These communities can also reveal how the different types of microbes and their environment can influence the community’s stability. By observing these simplified communities, scientists can learn more about how to potentially control similar ones in complex native soils.

Summary
Scientists need a deeper understanding of the ecological properties that control the structure and function of soil microbiomes. These communities are globally consequential and are now undergoing little-known pressures in a changing world environment. Understanding them is difficult because of the sheer number of species present. In addition, scientists have cultivated and thoroughly studied very few soil microbes in laboratory conditions. Now a team of researchers report on representative, reduced-complexity microbial communities that can serve as tools for better understanding soil microbiology. To cultivate their simplified soil microbiomes, the researchers looked at both bacteria and fungi. Many other studies use only liquid and focus only on bacteria, making it impossible to simulate a full view of the soil microbiome in its native environment.

They found that an environment of soil, rather than liquid, leads to a community of microbes that is representative of native soil sites. The researchers used a dilution procedure to obtain simplified, naturally adapted cohorts to serve as an experimental resource that recapitulates at least some soil microbiome behaviors. Finally, they showed that such reduced-complexity communities are reproducible and that the communities are stable across time.

Contacts
BER Program Manager
Dawn Adin
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research
dawn.adin@science.doe.gov

Principal Investigators
Elias Zegeye
Pacific Northwest National Laboratory
elias.zegeye@pnnl.gov

Janet Jansson
Pacific Northwest National Laboratory
janet.jansson@pnnl.gov 

Funding
This work was supported by the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy (DOE) Office of Science, and is a contribution of the Scientific Focus Area Phenotypic Response of the Soil Microbiome to Environmental Perturbations (70880). The Pacific Northwest National Laboratory (PNNL) is operated for DOE by Battelle Memorial Institute.

Publication
Zegeye, E. K., C. J. Brislawn, Y. Ferris, S. J. Fansler, K. S. Hofmockel, J. K. Jansson, A. T. Wright, E. B. Graham, D. Naylor, R. S. McClure, and H. C. Bernstein, “Selection, succession, and stabilization of soil microbial consortia.” mSystems 4, e00055-19 (2019). [DOI:10.1128/mSystems.00055-19].

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 01, 2019

A Viral Gold Rush

Scientists develop a new tool to find viruses in complex genomic datasets.

The Science
Researchers developed open-source software that can classify viruses in ways that previous tools could not. Scientists have limited data on viruses that they cannot grow in laboratories. That lack of information makes the viruses especially hard to classify. This new system uses viral genes to separate out viruses that are difficult to distinguish from each other into distinct groups. This separation is a key step in organizing and isolating viruses that are particularly interesting to scientists. Tests using information from known viruses have shown the new software to be very accurate.

The Impact
Research on viruses is an important frontier in environmental science. In fact, viruses that invade bacteria and archaea are most likely critical to all ecosystems. Every environment contains myriad viruses that scientists cannot grow in the laboratory. However, the lack of a framework that can classify large numbers of viruses and includes viruses’ relationship with their hosts holds back progress in this area. This software tool provides a new standard for classifying viruses that scientists have detected in DNA from field and other environmental samples.

Summary
Classification of environmental viruses, specifically uncultivated viral genomes (called UVIGS) is a key step to organizing the virosphere and isolating viral groups of potential interest. Single-gene or full-genome phylogenies are commonly used to classify viruses within a known framework of virus classification. However, a high rate of gene exchange in and between bacterial viruses (i.e., phages) makes it difficult to classify highly divergent phages with the limited data available. A team of researchers developed vConTACT 2.0, an open-source, community-available, network-based software application to establish prokaryotic virus taxonomy that scales to thousands of uncultivated virus genomes or fragments, while integrating multiple confidence scores for all taxonomic predictions. Performance tests show the predictions of the new software with currently classified viruses to be very accurate (International Committee on Taxonomy of Viruses: >91% genus-level assignments at 97% accuracy). This approach can also resolve highly recombinogenic taxa through an integrated distance-based hierarchical approach, and remaining discrepancies likely will require changes to current viral taxonomy guides. vConTACT 2.0 also automatically classified 1,364 previously unclassified reference viruses. The software application can be scaled to modern metagenomic datasets with a robust reference network and could potentially uncover thousands more viral sequences. Together, these efforts provide a systematic reference network and a robust, scalable taxonomic analysis tool that is critically needed by the research community.

Contacts
BER Program Manager

Dawn Adin
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research
dawn.adin@science.doe.gov

Ramana Madupu
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research, Computational Biosciences, and DOE Joint Genome Institute
ramana.madupu@science.doe.gov

Principal Investigators
Matthew Sullivan
Ohio State University
sullivan.948@osu.edu

Jennifer Pett-Ridge
Lawrence Livermore National Laboratory
pettridge2@llnl.gov

Funding
Funding was provided in part by the Office of Biological and Environmental Research Genomic Sciences program’s Soil Microbiome Scientific Focus Area, within the U.S. Department of Energy (DOE) Office of Science, award to Lawrence Livermore National Laboratory; National Science Foundation Biological Oceanography awards; and a Gordon and Betty Moore Foundation Investigator Award to M. B. Sullivan. Funding was provided to J. R. Brister by the Intramural Research Program of the U.S. National Institutes of Health (NIH) National Library of Medicine. The work conducted by the DOE Joint Genome Institute is supported by the DOE Office of Science. This work was also funded in part through Battelle Memorial Institute’s prime contract with the NIH National Institute of Allergy and Infectious Diseases.

Publication
Jang, H. B., B. Bolduc, O. Zablocki, J. H. Kuhn, S. Roux, E. M. Adriaenssens, J. R. Brister, A. M. Kropinski, M. Krupovic, R. Lavigne, D. Turner, and M. Sullivan. “Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.” Nature Biotechnology 37, 632–39 (2019). [DOI:10.1038/s41587-019-0100-8].

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 16, 2019

Feeding Sugars to Algae Makes Them Fat

Adding glucose to a green microalga culture induces accumulation of fatty acids and other valuable bioproducts.

The Science
Algae can make dramatic shifts in their metabolism in response to changes in their environment. Some microscopic green algae stop photosynthesizing and start accumulating fats and other valuable molecules when certain changes happen. However, scientists don’t know the details of those swift metabolic changes. A team examined a green microalga to better understand this process. After a few days of feeding this microbe sugar, it completely dismantled its photosynthetic apparatus while accumulating fat. In contrast, after the team stopped feeding it sugar, the microbe returned to its normal metabolism.

The Impact
Algae could be a sustainable source of biofuels and other valuable chemicals. As they trap carbon dioxide from the air by photosynthesis, they convert greenhouse gases into oils and other useful industrial products. Scientists need to know how algae control their metabolism to engineer strains that can make desirable products. This study showed that feeding glucose (sugar) to this alga affects one-third of its genes. This extensive catalog of affected genes opens the door to identify and manipulate critical genes that will dramatically increase oil production along with other tailored bioproducts.

Summary
Microalgae can produce large quantities of valuable oils and other chemicals, but their tight metabolic regulation poses a challenge for engineering these organisms for industrial-level production of biofuels and bioproducts. Using a variety of imaging and genomics technologies, a team from the University of California and national laboratories determined that only a few days after adding glucose to a culture of the green alga Chromochloris zofingiensis growing in the light, algal cells accumulate large amounts of the biofuel precursors triacylglycerols, as well as economically important products such as carotenoids. Further, they observed that photosynthesis shut off and the photosynthetic apparatus disappeared, while the overall culture biomass increased. At the same time, nearly one-third of the genes in the genome changed their expression during these growth and metabolic alterations. The researchers also discovered that these changes were readily reversed when they removed the glucose from the culture. Elucidation of the pathways that lead to high accumulation of those biofuels and bioproducts will allow scientists to engineer algae as sustainable biofactories.

Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Principal Investigators
Melissa Roth
University of California, Berkeley
melissa.s.roth@gmail.com

Krishna K. Niyogi
University of California, Berkeley
niyogi@berkeley.edu

Funding
This research was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research. The authors acknowledge work performed by the DOE Joint Genome Institute (a DOE Office of Science user facility), the DOE Joint BioEnergy Institute, and the National Center for X-ray Tomography. The cryo-soft X-ray tomography was supported by the Photosynthetic Systems program in the DOE, Office of Science, Office of Basic Energy Sciences. The authors also acknowledge funding and support from the U.S. Department of Agriculture National Institute of Food and Agriculture, the National Institutes of Health, the National Science Foundation, and the Howard Hughes Medical Institute. 

Publications
Roth, M. S., S. D. Gallaher, D. J. Westcott, et al. “Regulation of oxygenic photosynthesis during trophic transitions in the green alga Chromochloris zofingiensis.” The Plant Cell 31, 579–601 (2019). [DOI:10.1105/tpc.18.00742]

Related Links
University of California, Los Angeles news release: Discovery of an alga’s ‘dictionary of genes’ could lead to advances in biofuels, medicine

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 04, 2019

Testing the Toughness of Microbial Cell Walls

Some cells stand firm against techniques to extract the biological material inside, while others dot not stand a chance.

The Science
Microbial cells contain biological material that can be important for research or industrial use, such as DNA or proteins. Yet, reaching this cellular material can be a challenge. Different methods to disrupt cells have a wide range of effects on microbial communities and their environments. Researchers compared different cell disruption techniques. They found that fungal and gram-positive bacteria cells (which have a thicker cell wall and do not have an outer membrane) resisted common cell disruption techniques. In contrast, the same techniques destroyed gram-negative bacterial cells (which have a thin cell wall and an outer membrane).

The Impact
This work measured differences between microbial populations’ resistance to cell disruption. In particular, it increases what is known about how long microbial cells persist in the soil. Microbial residues-what is left of microbes when they die-create soil organic matter. They are believed to persist in soil for decades. The susceptibility of microbes’ cell walls to breaking down as a result of natural cycles (i.e., freeze-thaw and wet-dry cycles) influences how much residues build up. How soil microbial populations differ in their resistance to cell disruption could affect long-term soil carbon storage. Differences in soil carbon storage may influence soil structure, fertility, and water-holding capacity. These differences could also influence which microbes that research and development efforts detect.

Summary
Previous research showed some bacterial and fungal resistance to cell disruption, but it did not quantify differences in the efficiencies and yields of cell disruption techniques. This led to uncertainty in the potential magnitude of differences in cell disruption among soil microbial communities. Scientists compared how different types of microbes responded to common cell disruption methods. Researchers studied the effects of bead-beating (shaking the sample in a combined solution with glass beads) and ultrasonication (applying high-frequency sound energy to the sample) to demonstrate differential resistance of cell disruption. Fungal and gram-positive bacterial cells remained almost intact after ultrasonication, indicating a strong resistance to some forms of cell disruption. After bead-beating and ultrasonication, fungi produced lower DNA yields than expected, supporting the idea of fungal resistance to cell disruption. The team did not find any intact cells in the gram-negative bacterial enrichment culture. Implications of these findings could include increased extraction of biomolecules from microbes with less rigid cell walls and underrepresentation of resistant microbes—particularly fungi—in ecological studies. Next, researchers aim to understand how differences in resistance to cell disruption may influence the turnover of microbial populations in soil and their contribution to the generation and persistence of soil organic matter.

Contacts
BER Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

PrincipaI Investigator
Kirsten Hofmockel
Environmental Molecular Sciences Laboratory/Iowa State University
kirsten.hofmockel@pnnl.gov

Funding
The research was supported by the Early Career Research program (award number FWP 68292) of the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy (DOE) Office of Science. The research was performed using the Environmental Molecular Sciences Laboratory (EMSL; grid.436923.9), a DOE BER Office of Science user facility.

Publications
Starke, R., N. Jehmlich, T. Alfaro, A. Dohnalkova, P. Capek, S. L. Bell, and K. S. Hofmockel, “Incomplete cell disruption of resistant microbes.” Scientific Reports 9, 5618 (2019). [DOI:10.1038/s41598-019-42188-9].

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


February 26, 2019

Microbes Retain Toxicity Tolerance After They Escape Toxic Elements

Groundwater microbes living outside a contaminated area contain mobile genetic elements that give them resistance to heavy metals.

The Science
Bacteria and other microbes contain mobile genetic elements called plasmids that are circular DNA molecules. Plasmids often encode traits that confer some advantage to the harboring microbe such as antibiotic resistance. A team of researchers has developed a method to purify and study plasmids from groundwater microbial communities. Using this method, they discovered several hundred different plasmids in samples from a U.S. Department of Energy site in Tennessee. The most common trait encoded in those plasmids was resistance to toxic metals such as mercury. The team also found that the plasmids were diverse but not as much as the microbial community from which they came.

The Impact
Studying plasmids from microbial communities that live in groundwater is difficult because of the low concentration of cells in those habitats. Researchers knew that heavy metal resistance genes were present in groundwater microbes, but their new method allowed them to prove that these mobile elements harbor metal resistance genes. The method will also facilitate the discovery of new plasmids in other water environments.

Summary
Plasmids are mobile genetic elements that often contain genes that confer important functions to the microbial host. They are composed of circular DNA molecules and are easy to purify. However, plasmid purification methods do not work well if the concentration of cells is low, as is the case in samples of microbial communities from groundwater environments. To solve this problem, a team of researchers developed a method to purify and analyze plasmids from such environments. With this method, the team uncovered over 600 different plasmids that showed an enrichment in metal tolerance genes in addition to antibiotic- and virus-resistance genes. Given that the team did not detect heavy metals in the microbial habitat, they hypothesize that plasmids may represent a mechanism to maintain latent resistance within a microbial community. The discovery of new plasmid genes allowed by this research will provide new possibilities for engineering novel and useful microbial strains.

Contact
Aindrila Mukhopadhyay
Lawrence Berkeley National Laboratory
amukhopadhyay@lbl.gov  

Program Managers
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Todd Anderson
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
todd.anderson@science.doe.gov

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research.

Publications
Kothari, A., Y. W. Wu, J. M. Chandonia, M. Charrier, L. Rajeev, A. M. Rocha, D. C. Joyner, T. C. Hazen, S. W. Singer, and A. Mukhopadhyay. “Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multimetal resistance genes.” mBio 10, e02899-18 (2019). [DOI:10.1128/mBio.02899-18]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


February 20, 2019

Discovering an Internal Metabolic Switch in Algae

Discovering hexokinase as an algal regulator of lipids and high-value antioxidants will enable sustainable sources of biofuels and bioproducts.

The Science
Algae can accumulate lipids such as oils and waxes, as well as other useful chemicals. Scientists do not completely understand the genetic mechanisms that regulate how algae build up these chemicals. By analyzing algae’s genes, researchers discovered that an enzyme called hexokinase plays a key role in how algae accumulate lipids. It also plays an important role in how green algae build up large amounts of the antioxidant astaxanthin. This enzyme is also responsible for shutting off photosynthesis when sugars are present.

The Impact
Studying microalgae helps scientists better understand biological pathways that are also in many other species. It is then easier for scientists to manipulate these systems. This research expands what is known about how algae and plants regulate photosynthesis. It also reveals different ways species use energy under different metabolic conditions. This discovery could enable increased production of biofuels and bioproducts.

Summary
Photosynthesis and metabolism in plants and algae drive global carbon fixation. Algae also have the potential to contribute to a sustainable bioeconomy by delivering valuable chemicals with reduced environmental impacts. Unlocking the biology behind relevant phenotypes can reveal new opportunities for bioengineering and creating commercially viable sources of biofuels and bioproducts in a sustainable fashion.

The unicellular green alga Chromochloris zofingiensis accumulates high amounts of lipids in the form of triacylglycerols (TAGs), which are biodiesel precursors, and the high-value antioxidant astaxanthin. This study used forward genetics to reveal that the widely conserved glycolytic enzyme hexokinase (HXK1) is necessary for a photosynthetic and metabolic switch. Glucose represses photosynthesis both in plants and algae, but in C. zofingiensis, it also causes rapid accumulation of TAG and astaxanthin. Algae with mutations in HXK1 showed that this enzyme is necessary for shutting off photosynthesis and amassing bioproducts. C. zofingiensis is a promising candidate for bioproduction, and insights into its regulation of photosynthesis and metabolism will enable engineering of this organism to improve its commercial prospects. Nutrients such as glucose play essential regulatory roles in gene expression, metabolism, growth and aging in plants, animals, yeast, and bacteria. This study introduces C. zofingiensis as a simpler system to investigate HXK function, shedding light onto fundamental and evolutionarily conserved mechanisms of glucose signaling and regulation of photosynthesis at the base of the plant evolutionary tree.

Contacts
BER Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Principal Investigator
Melissa Roth
University of California, Berkeley
MRoth@berkeley.edu

Funding
This work was supported by the Office of Biological and Environmental Research within the U.S. Department of Energy Office of Science; U.S. Department of Agriculture National Institute of Food and Agriculture, and the National Science Foundation.

Publications
Roth, M. S., D. J. Westcott, M. Iwai, and, K. K. Niyogi, “Hexokinase is necessary for glucose-mediated photosynthesis repression and lipid accumulation in a green alga.” Communications Biology 2, 347 (2019). [DOI:10.1038/s42003-019-0577-1].

Roth, M. S., S. D. Gallaher, D. J. Westcott, M. Iwai, K. B. Louie, M. Mueller, A. Walter, F. Foflonker;, B. P. Bowen, N. N. Ataii , J. Song, J.-H Chen, C. Blaby-Haas, C. Larabell, M. Auer, T. Northen, S. S. Merchant and, K. K. Niyogi. “Regulation of oxygenic photosynthesis during trophic transitions in the green alga Chromochloris zofingiensis.” The Plant Cell 31, 579-601 (2019). (DOI:10.1105/tpc.18.00742).

Related Links

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 29, 2019

Cultivating an Understanding of Microbial Diversity

Plant diversity, soil structure, and seasonality all influence microbial diversity in soil.

The Science
Biodiversity protects ecosystems from stressors, increases ecosystem services, and promotes sustainability by enhancing resilience. Researchers studied how plant growth, agricultural management, and season influence the diversity of microbial communities. Within soil clumps called aggregates, scientists saw that smaller soil aggregates had more bacterial and fungal diversity than larger ones. They also found that microbial diversity increases with plant diversity and changes seasonally. Larger soil aggregates were less diverse. But they had communities of microbes, known as microbiomes, that are more sensitive to environmental changes over the course of seasons.

The Impact
Understanding what controls the diversity and function of soil microbes can help researchers better predict how productive and healthy soil will be. This information can also help scientists predict how climate and environmental changes will influence the soil. Land-management services might use this knowledge to enhance biodiversity and the benefits soil provides to society.

Summary
Within soil systems, microbes maintain nutrient cycling, influence plant productivity, enhance drought tolerance, and impact soil health and fertility. However, the ecological rules that reinforce soil biodiversity and microbial activities are not clearly defined at a microbial scale. This study helps close an important knowledge gap by investigating how the spatial structure of soil is vital to understanding the impact of microbiomes on ecosystem and biogeochemical services. Historically, researchers have examined microbial diversity in soils at ecosystem or landscape scales. In this study, researchers chose different size soil aggregates as a way to represent microbially relevant scales. Over years and seasons, soil aggregate turnover is dynamic and thereby structures soil microbial habitats. Temporal data from different size soil aggregates and three different bioenergy management systems revealed discrete microbial communities. This research is pertinent to evaluating how different management practices impact spatially discrete microbial communities in the soil. Management practices that increase plant diversity across growing seasons, the authors demonstrate, influence soil aggregate habitats and therefore increase microbial diversity. The study underscores the importance of including both spatial and temporal dynamics in investigations in order to fully understand microbial community assembly and persistence in soil.

Contacts
BER Program Manager
Dawn Adin
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research
dawn.adin@science.doe.gov

PrincipaI Investigator
Kirsten Hofmockel
Pacific Northwest National Laboratory
Kirsten.Hofmockel@pnnl.gov

Funding
This research was supported by the Office of Biological and Environmental Research, within the U.S. Department of Energy Office of Science, under award DE-SC0010775.

Publications
Upton, R. N., E. M. Bach, and K. S. Hofmockel. “Spatio-temporal microbial community dynamics within soil aggregates.” Soil Biology and Biochemistry 132, 58-68 (2019). [DOI:10.1016/j.soilbio.2019.01.016].

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 11, 2019

New Method Knocks Out Yeast Genes with Single-Point Precision

Researchers can precisely study how different genes affect key properties in a yeast used industrially to produce fuel and chemicals.

The Science
How do you make yeast work harder? Not to make bread, but in processes that yield chemicals and pharmaceuticals. Industries currently use a yeast called Saccharomyces cerevisiae. They’d like it to work better. The answer is in manipulating the yeast’s genetic code. To get at that code, researchers developed a method that turns off targeted genes in the yeast, introducing mutations. The team’s approach deletes specific points in the DNA sequence. They study how each deletion affects the yeast. Does a deletion cause the yeast to stop working in certain chemicals? Does a deletion make the yeast grow more slowly? The team’s approach lets them study each gene, as well as in combination with other genes. With this approach, scientists can construct libraries of mutants for use in discovering how each gene works.

The Impact
Libraries of genetic mutations have so far only been achieved in simpler organisms, specifically prokaryotes. Now, scientists can build such libraries for more complex organisms. The new technique lets scientists rapidly engineer tens of thousands of genes. They can target the genes with 98 percent efficiency. The results ease identifying and isolating mutant strains that show desired traits, such as tolerance to toxic compounds necessary to produce industrial products.

Summary
Researchers developed a method called CRISPRCas9- and homology-directed-repair-assisted genome-scale engineering (CHAnGE) using libraries of synthetic oligonucleotides (cassettes) containing a CRISPR guide sequence, gene-specific sequences to target homologous recombination to those selected genes, and unique barcodes to track each mutant strain. The oligonucleotide library was cloned into a plasmid and introduced into Saccharomyces cerevisiae. Nearly 25,000 sequences representing almost every one of the 6,500 yeast open reading frames were synthesized. More than 98 percent of the CHAnGE cassettes resulted in mutations in the target genes at least 82 percent of the time, demonstrating a high editing efficiency. The technology proved to be effective for the introduction of both small deletions and single-base mutations, as well as for saturation mutagenesis of a single gene or domain. CHAnGE was successfully applied to engineer yeast strains that are tolerant to furfural, indicating that it could be used to engineer industrially relevant eukaryotes to advance toward renewable production of biofuels and valuable chemicals.

Contact
Program Manager
Pablo Rabinowicz
Department of Energy, Office of Science, Biological and Environmental Research
pablo.rabinowicz@science.doe.gov

Principal Investigator
Huimin Zhao
University of Illinois at Urbana-Champaign 
zhao5@illinois.edu  

Funding
This work was supported by the Office of Biological and Environmental Research within the Department of Energy’s Office of Science and the Carl R. Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign.

Publications
Z. Bao, M. HamediRad, P. Xue, H. Xiao, I. Tasan, R. Chao, J. Liang, and H. Zhao, “Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision.” Nature Biotechnology 36, 505 (2018). [DOI: 10.1038/nbt.4132]

Related Links
University of Illinois press release: New CRISPR technology ‘knocks out’ yeast genes with single-point precision

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 09, 2019

How Plants Regulate Sugar Deposition in Cell Walls

Identified genes involved in plant cell wall polysaccharide production and restructuring could aid in engineering bioenergy crops.

The Science
Ultimately, researchers want to engineer bioenergy crops to accumulate large amounts of easy-to-use sugars. Researchers from the Great Lakes Bioenergy Research Center identified a major part of the sugar production process in a model leafy grass. They discovered a transcription factor, which turns a gene on and off. The gene triggers the synthesis of a sugar, called mixed-linkage glucan (MLG). Characterizing downstream genes regulated by this transcription factor provides insight into how plants make MLG. This information is vital to overcoming growth defects associated with engineering plants to produce large quantities of MLG.

The Impact
To make fuels from grasses or other plants, scientists often focus on certain sugars, such as mixed-linkage glucan. Understanding the genes that produce and restructure such sugars should lead to a better understanding of how the bioenergy grass sorghum stores sugar in cell walls. With such information, Great Lakes Bioenergy Research Center researchers aim to engineer bioenergy crops like sorghum to accumulate large amounts of the sugar in the stem. They aim to do it without disrupting plant growth.

Summary
Mixed-linkage glucan (MLG) is an energy-rich polysaccharide found at high levels in some grass endosperm cell walls and at lower amounts in other tissues. Cellulose synthase-like F and cellulose synthase-like H genes synthesize MLG, but it is unknown if other genes participate in the production and restructuring of MLG. Working with the model grass Brachypodium distachyon, GLBRC researchers identified a trihelix family transcription factor (BdTHX1) that is highly co-expressed with the BdCSLF6 gene and which appears to help regulate MLG biosynthesis. They showed that BdTHX1 protein can bind with high affinity to BdCSLF6 as well as BdXTH8, which encodes a grass-specific endotransglucosylase, an enzyme involved in cell wall structuring. The team found that BdXTH8 preferentially interacts with MLG and xyloglucans, suggesting it may mediate their binding in plant tissues. In addition, B. distachyon shoots grown from cells overexpressing BdTHX1 showed abnormal growth and early death. These results indicate that the transcription factor BdTHX1 likely plays an important role in MLG biosynthesis and restructuring by regulating the expression of BdCSLF6 and BdXTH8. This knowledge will be instrumental for engineering the bioenergy grass sorghum to accumulate large amounts of MLG in its stem tissue.

Contact
Program Manager
N. Kent Peters
Department of Energy, Office of Science, Office of Biological and Environmental Research
kent.peters@science.doe.gov; (301) 903-5549

Principal Investigator
Curtis Gene Wilkerson
Michigan State University 
wilker13@msu.edu

Funding
This work was supported by the Department of Energy Great Lakes Bioenergy Research Center and the United Kingdom Biotechnology and Biological Sciences Research Council.

Publications
M. Fan, K. Herburger, J.K. Jensen, S. Zemelis-Durfee, F. Brandizzi, S.C. Fry, and C.G. Wilkerson, “A trihelix family transcription factor is associated with key genes in mixed-linkage glucan accumulation.” Plant Physiology 178, 1207 (2018). [DOI: 10.1104/pp.18.00978]

Related Links
Plant Physiology article: A Trihelix Family Transcription Factor Is Associated with Key Genes in Mixed-Linkage Glucan Accumulation

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 09, 2019

Scientists Identify Gene Cluster in Budding Yeasts with Major Implications for Renewable Energy

How yeast partition carbon into a metabolite may offer insights into boosting production for biofuels.

The Science
Yeasts are complex organisms that may become the workhorses of biofuel production. To move yeasts into this larger role, scientists need to understand the genetic machinery that leads to the production of complex molecules like the iron-binding molecule pulcherrimin in budding yeasts. Scientists revealed a four-gene cluster associated with pulcherrimin production. Further tests revealed likely functions for each of the genes: two biosynthetic enzymes, a transporter, and a transcription factor involved in both biosynthesis and transport.

The Impact
Yeasts use the same pathway to make pulcherrimin and an alcohol, isobutanol, of interest for biofuels. Some yeast strains direct a significant amount of carbon into pulcherrimin. Since both pulcherrimin and isobutanol are made from a common pathway, this suggests that the metabolic control of high pulcherrimin producers may be harnessed for increased isobutanol production in yeast. This could help engineer yeast to make larger quantities of isobutanol.

Summary
Despite the discovery of an iron-binding pigment known as pulcherrimin 65 years ago, the genes responsible for its biosynthesis remained uncharacterized. Using a comparative genomics approach among 90 genomes from the budding yeast subphylum Saccharomycotina, researchers from the Great Lakes Bioenergy Research Center identified the first yeast secondary metabolite gene cluster and showed that it’s responsible for pulcherrimin biosynthesis. Targeted gene disruptions in Kluyveromyces lactis identified putative functions for each of the four genes: two pulcherriminic acid biosynthesis enzymes, a pulcherrimin transporter, and a transcription factor involved in both biosynthesis and transport. The requirement of a functional putative transporter to utilize extracellular pulcherrimin-complexed iron demonstrates that pulcherriminic acid is a siderophore, an iron-chelating compound secreted by microorganisms. This research also characterized and named two genes that previously lacked assigned functions in the fuel-producing model yeast Saccharomyces cerevisiae. The evolution of this gene cluster in budding yeast suggests an ecological role for pulcherrimin akin to other microbial public goods systems. Because some yeasts species are particularly adept at funneling carbon into pulcherrimin, studying how high-level pulcherrimin producing strains are altered in their metabolic control may inform strategies for increased biofuel production in model organisms.

Contact
Program Manager
N. Kent Peters
Department of Energy, Office of Science, Office of Biological and Environmental Research
kent.peters@science.doe.gov; (301) 903-5549

Principal Investigator
Chris Todd Hittinger
University of Wisconsin-Madison
cthittinger@wisc.edu

Funding
This material is based upon work supported by the Department of Energy, Office of Science, Office of Biological and Environmental Research, as well as the National Science Foundation. Additional funding was provided by the Pew Charitable Trusts and the Vilas Trust Estate.

Publications
D.J. Krause, J Kominek, D.A. Opulente, X. Shen, X. Zhou, Q.K. Langdon, J. DeVirgilio, A.B. Hulfachor, C.P. Kurtzman, A. Rokas and C.T. Hittinger, “Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts.” Proceedings of the National Academy of Sciences USA 115(43), 11030 (2018). [DOI: 10.1073/pnas.1806268115]

Related Links
Great Lakes Bioenergy Research Center news release: Red-hued yeasts hold clues to producing better biofuels

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER