Comprehensive genome-wide search enables discovery of multi-gene determinants of traits in yeast.
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.
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.
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.
BER Program Manager
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
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
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.
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].
University of Illinois: MAGIC system allows researchers to modulate activity of genes acting in concert
Contact: Pablo Rabinowicz, SC-23.2 (301) 903-0379
SC-33.2 Biological Systems Science Division, BER
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