About
We are a systems genetics and synthetic biology group interested in repurposing model organisms by replacing human genes in yeast and other simplified cells. Our laboratory engineers human biological processes in simplified cells to study disease and evolution.
News
Recent News
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Decoding human genetic variation_a short perspective on a research article
Decoding human genetic variation using a synthetic paradigm).
This short journal club article by Aashiq Kachroo in Nature Reviews Genetics highlights a recent paper by van Loggerengerg et al that demonstrates the experimental power of “humanized yeast” to gain insight into the genetic variations underlying disease.
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Canada Research Chair Award
Dr. Aashiq Kachroo successfully renewed the Canada Research Chair Award (2023-2028).
We thank Tri-agency Institutional Programs Secretariat and the reviewers for positive criticism, tremendous enthusiasm and endorsement of our research program.
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Humanization of the yeast Proteasome
We published two articles focusing on the replaceability of yeast proteasome genes with their human equivalents. 1.Rapid, scalable, combinatorial genome engineering by marker-less enrichment and recombination of genetically engineered loci in yeast.
Highlights:
• Cas9-induced gene drive efficiently converts heterozygous to homozygous yeast locus
• Yeast mating and Cas9 selection combines two or more separate edits into a single strain
• The method enables marker-less enrichment, recombination of genetically engineered loci
• MERGE reveals a fitness-driven path to humanize α-proteasome core subunits in yeast
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2.Species-specific protein–protein interactions govern the humanization of the 20S proteasome in yeast.
Highlights: We identified multiple replacement-competent variants of human β2c (PSMB7) in yeast. Structural modeling of the human mutants indicated at least 2 modes of suppression:
• Mutations close to the interacting surfaces of neighboring proteins in the complex suggested multiple Protein-Protein Interactions critical to β-core assembly. Specifically, the mutations in the C-terminal tail extension of human β2c suggested the importance of PPIs with the β3 subunit for optimal assembly.
• Mutations that affected the catalytic activity of the human β2c also enabled its assembly into the yeast proteasome core, presumably through retention of the entire or partially trimmed 43-residue propeptide.
Cover art made for the Genetics journal (Not selected). The cover art features the crystal structure of the yeast 20S proteasome core particle (1ryp.pdb) with human PSMB7 (Hsβ2) in a translucent surface and cartoon view, rendered using ChimeraX. While Hsβ2 cannot functionally replace the yeast PUP1 (Scβ2), mutations in Hsβ2, such as the active site mutant (T44A, represented by the red sphere), or the tail swap variant (with the yeast PUP1 tail in cyan transplanted into Hsβ2), enable functional rescue of the loss of the yeast gene. Additionally, by restoring human-like local protein-protein interactions (achieved by providing the neighboring Hsβ3, depicted as a adjascent yellow surface rendering), the wild type Hsβ2 can also function in yeast.
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Humanization of yeast genes with multiple human orthologs
We published two articles focusing on the replaceability of yeast genes with their human equivalents, particularly the duplicated human genes.
- Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. This completes most of the testable essential gene humanizations in yeast. This work demonstrated that the duplicated human genes still retained functional similarity; however, differentially. The systematic assays allowed us to identify the features explaining the divergence between human paralogs.
- Systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human Genes. In this work, we focused on Eukaryotic cytoskeletal families (conserved back to Opisthokonts). These genes are particularly interesting because of having undergone extensive duplications across broad eukaryotic clades. After ~1 billion years of divergence between humans and yeast, we wondered, to what extent were core elements of the yeast cytoskeleton humanizable. We found several cystoskeletal elements in yeast replaceable by their human counterparts (Actins, Myosins, Tubulins and Septins), albeit only a subset from an orthogroup. The study appears on the Cover of the Genetics journal.
Summary of the Cover “Cytoskeleton genes are responsible for forming the structural (architectural) components of cells and have expanded into multigene families in humans relative to earlier ancestors. In this issue, Garge and colleagues studied the evolutionary divergence of such duplicated genes by “humanizing” yeast, replacing yeast cytoskeletal genes with different versions of the corresponding human genes. This is symbolized in the image by human workers constructing yeast from the inside out, as inspired by Fernand Léger’s “The Builders” and illustrated by Ella Marushchenko.