PgmNr Y505: Deciphering common principles governing gene replaceability in yeast.

Authors:
Aashiq H. Kachroo ¹ ; Jon M. Laurent ¹ ; Azat Akhmetov ¹ ; Edward M. Marcotte ^1,2,3

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Institutes
1) Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; 2) Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX 78712, USA; 3) Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.

Keyword: Evolution/Comparative Genomics

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Abstract:

Owing to common ancestry, organisms share genes across vast evolutionary distances, with many eukaryotic genes shared among humans, yeast, plants, and even bacteria. “Swapping” such orthologous genes between species gives a simple, reasonably high-throughput, method for testing conserved functions and learning principles of replaceability. Recently, we showed that several hundred genes in yeast can be “humanized”, in the process learning some of the rules that govern functional replaceability. Notably, we found that replaceability is determined at the level of gene modules, such that genes in the same pathway or complex are often either largely replaceable or not (Kachroo et al. (2015) Science, 348:921-925).

            However, it is unknown if these trends are truly general in nature and apply equally well to other species. To learn general rules of replaceability, we have now replaced (one gene at a time) a large set of budding yeast (S. cerevisiae) genes with their orthologs from bacteria (E. coli), and to a lesser extent, from plants (A. thaliana). We find that a large proportion (roughly half) of the bacterial or plant genes tested can successfully replace their yeast orthologs and complement an otherwise lethal loss of an essential yeast gene. As with our systematic tests of yeast humanization, we observe genes in the same pathway and complex to be similarly replaceable or not. Strikingly, individual genes of the yeast heme biosynthesis pathway are almost entirely replaceable by their orthologs from E. coli, plants, or humans, indicating that this ancient pathway has remained functionally intact and largely unaltered—at least in terms of its critical, enzymatic functionality—since the divergence of the ancestors of modern eubacteria and eukaryotes. Finally, we’ll describe our extensions of this work, testing for the effects of mitochondrial localization, and using CRISPR-based integration of the donor genes directly into the yeast chromosomes, to more finely control the human/plant/bacterial-ized genes’ expression patterns.