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Systematic humanization of yeast genes reveals conserved functions and genetic modularity

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Science  22 May 2015:
Vol. 348, Issue 6237, pp. 921-925
DOI: 10.1126/science.aaa0769
  • Fig. 1 Systematic functional replacement of essential yeast genes by their human counterparts.

    (A) Of 547 human genes with 1:1 orthology to essential yeast genes, 469 human open reading frames (ORFs) were subcloned into single-copy yeast expression vectors under control of either the GAL or GPD promoters. Using three distinct assay classes (repressible yeast-gene promoter, temperature-sensitive yeast allele, and heterozygous diploid knockout strain), we obtained 126, 151, and 375 informative replaceability assays, respectively. (B) Representative examples of the three assay classes. (C) Combining assays and literature, 200 human genes could functionally replace their yeast orthologs and 224 genes could not. Some human genes were toxic using GAL induction but replaced their yeast orthologs upon reducing expression.

  • Fig. 2 Properties of gene modules can predict replaceability.

    (A) One hundred four quantitative features of proteins or ortholog pairs were evaluated for their ability to explain replaceability, assessing each feature’s predictive strength as the area under a ROC curve (AUC) and determining significance by shuffling replacement status 1000 times, measuring mean AUCs ± 1 SD (error bars). AUCs above 0.58 were generally individually significant with 95% confidence. Starred features were included in the integrated classifier (leftmost bar). (B) Distribution of amino acid identities among the tested ortholog pairs (left y axis) and fraction of replaceable genes in each sequence-identity bin (right y axis). (C) Relative proportion of replaceable and nonreplaceable genes among 12 broad KEGG (20) pathway classes.

  • Fig. 3 The modular nature of functional replacement.

    (A) None of the four tested human TRiC/CCT chaperonin genes replaced their yeast counterparts. (B) Similarly, no genes tested in the origin recognition complex (ORC) or the MCM complex were replaceable. (C) In contrast, 17 of 19 sterol biosynthesis genes were replaceable. In two cases, the yeast gene had two human orthologs but only one could complement. Human HMGCS1 (but not HMGCS2) replaced yeast ERG13; human IDI1 (but not IDI2) replaced yeast IDI1. Human PMVK, a nonhomologous protein that carries out the same reaction as yeast Erg8 (27), complemented temperature-sensitive allele erg8-1.

  • Fig. 4 Proteasome subunits are differentially replaceable.

    (A) Yeast 26S proteasome genes were generally replaceable, except for two interacting clusters, in the 19S regulatory “lid” particle and in the 20S core β-subunit ring. (B) The yeast α6-β6 subunit interface (top panel) sterically accommodates the human subunit (bottom panel, showing superposition of human α6 onto the yeast α6) despite 50% sequence identity at the interface. (C) Alpha subunits from diverse eukaryotes generally complemented the yeast mutant, but beta subunits did not (unlike plasmid-expressed S. cerevisiae genes, included as positive controls). ND, not determined. (D) In simulated evolution of interacting proteins Ubc9 and Smt3, if binding to the extant partner is not enforced (“Non-Bound”), a protein’s ability to bind its ancestral partner decays rapidly as sequences diverge. However, if extant binding is enforced (“Wild Type” and “Low Stability”), even highly diverged proteins often still bind to their ancestral partners. (Dots indicate right-censored data; see fig. S14.)

Supplementary Materials

  • Systematic humanization of yeast genes reveals conserved functions and genetic modularity

    Aashiq H. Kachroo, Jon M. Laurent, Christopher M. Yellman, Austin G. Meyer, Claus O. Wilke, Edward M. Marcotte

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S18
    • Tables S2, S4, and S6
    • Captions for Tables S1, S3, and S5
    • Captions for Data S1 to S3
    • Full Reference List
    Table S1
    Summary of complementation results.
    Table S3
    Summary of features and prediction performance.
    Table S5
    Oligonucleotide primers used in this study.

    Additional Data

    Data S1
    Weka machine learning feature file for the main gene set (.arff format).
    Data S2
    Weka machine learning feature file for the withheld literature test set (.arff format).
    Data S3
    BayesNet classifier (Weka .xml format).

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