Science Highlight

24-Mar-2020

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.

DOE/US Department of Energy

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 MAGIC approach synthesizes DNA sequences for CRISPR-based gene activation (in orange), silencing (in blue), and elimination (in pink), then uses those sequences on yeasts to identify the genes required in different growth conditions. Image courtesy of Nature Communications

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 "multi-functional genome-wide CRISPR." MAGIC can modify the expression of genes in yeast by combining CRISPR activation, interference, and deletion, and thereby allows 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.

Funding

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