Intercalation of a new tier of transcription regulation into an ancient circuit

Abstract

Changes in gene regulatory networks are a major source of evolutionary novelty1,2,3. Here we describe a specific type of network rewiring event, one that intercalates a new level of transcriptional control into an ancient circuit. We deduce that, over evolutionary time, the direct ancestral connections between a regulator and its target genes were broken and replaced by indirect connections, preserving the overall logic of the ancestral circuit but producing a new behaviour. The example was uncovered through a series of experiments in three ascomycete yeasts: the bakers’ yeast Saccharomyces cerevisiae, the dairy yeast Kluyveromyces lactis and the human pathogen Candida albicans. All three species have three cell types: two mating-competent cell forms (a and α) and the product of their mating (a/α), which is mating-incompetent. In the ancestral mating circuit, two homeodomain proteins, Mata1 and Matα2, form a heterodimer that directly represses four genes that are expressed only in a and α cells and are required for mating4,5,6. In a relatively recent ancestor of K. lactis, a reorganization occurred. The Mata1–Matα2 heterodimer represses the same four genes (known as the core haploid-specific genes) but now does so indirectly through an intermediate regulatory protein, Rme1. The overall logic of the ancestral circuit is preserved (haploid-specific genes ON in a and α cells and OFF in a/α cells), but a new phenotype was produced by the rewiring: unlike S. cerevisiae and C. albicans, K. lactis integrates nutritional signals, by means of Rme1, into the decision of whether or not to mate.

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Figure 1: The core hsgs are not directly regulated by a1–α2 in K. lactis.
Figure 2: RME1 is a direct activator of hsg expression and is required for K. lactis mating.
Figure 3: Overexpression of RME1 is sufficient for hsg expression in the absence of nutrient starvation.
Figure 4: A simplified model for the evolution of regulation of core hsgs in three yeasts.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

The gene expression array data have been deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE24874. For the ChIP-chip data the accession number is GSE25209.

References

  1. 1

    Carroll, S. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134, 25–36 (2008)

    CAS  Article  Google Scholar 

  2. 2

    Davidson, E. H. & Erwin, D. H. Gene regulatory networks and the evolution of animal body plans. Science 311, 796–800 (2006)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Wray, G. A. The evolutionary significance of cis-regulatory mutations. Nature Rev. Genet. 8, 206–216 (2007)

    CAS  Article  Google Scholar 

  4. 4

    Galgoczy, D. J. et al. Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae . Proc. Natl Acad. Sci. USA 101, 18069–18074 (2004)

    ADS  CAS  Article  Google Scholar 

  5. 5

    Tsong, A. E., Miller, M. G., Raisner, R. M. & Johnson, A. D. Evolution of a combinatorial transcriptional circuit: a case study in yeasts. Cell 115, 389–399 (2003)

    CAS  Article  Google Scholar 

  6. 6

    Srikantha, T. et al. TOS9 regulates white-opaque switching in Candida albicans . Eukaryot. Cell 5, 1674–1687 (2006)

    CAS  Article  Google Scholar 

  7. 7

    Herskowitz, I. A regulatory hierarchy for cell specialization in yeast. Nature 342, 749–757 (1989)

    ADS  CAS  Article  Google Scholar 

  8. 8

    Barsoum, E., Sjöstrand, J. O. O. & Aström, S. U. Ume6 is required for the MATa/MATα-cellular identity and transcriptional silencing in Kluyveromyces lactis . Genetics 184, 999–1011 (2010)

    CAS  Article  Google Scholar 

  9. 9

    Herskowitz, I. MAP kinase pathways in yeast: for mating and more. Cell 80, 187–197 (1995)

    CAS  Article  Google Scholar 

  10. 10

    Dignard, D., André, D. & Whiteway, M. Heterotrimeric G-protein subunit function in Candida albicans: both the α and β subunits of the pheromone response G protein are required for mating. Eukaryot. Cell 7, 1591–1599 (2008)

    CAS  Article  Google Scholar 

  11. 11

    Coria, R. et al. The pheromone response pathway of Kluyveromyces lactis . FEMS Yeast Res. 6, 336–344 (2006)

    CAS  Article  Google Scholar 

  12. 12

    Chang, F. & Herskowitz, I. Identification of a gene necessary for cell cycle arrest by a negative growth factor of yeast: FAR1 is an inhibitor of a G1 cyclin, CLN2. Cell 63, 999–1011 (1990)

    CAS  Article  Google Scholar 

  13. 13

    Butty, A. C., Pryciak, P. M., Huang, L. S., Herskowitz, I. & Peter, M. The role of Far1p in linking the heterotrimeric G protein to polarity establishment proteins during yeast mating. Science 282, 1511–1516 (1998)

    CAS  Article  Google Scholar 

  14. 14

    Côte, P. & Whiteway, M. The role of Candida albicans FAR1 in regulation of pheromone-mediated mating, gene expression and cell cycle arrest. Mol. Microbiol. 68, 392–404 (2008)

    Article  Google Scholar 

  15. 15

    Bailey, T. L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994)

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    Goutte, C. & Johnson, A. D. Recognition of a DNA operator by a dimer composed of two different homeodomain proteins. EMBO J. 13, 1434–1442 (1994)

    CAS  Article  Google Scholar 

  17. 17

    Hull, C. M. & Johnson, A. D. Identification of a mating type-like locus in the asexual pathogenic yeast Candida albicans . Science 285, 1271–1275 (1999)

    CAS  Article  Google Scholar 

  18. 18

    Covitz, P. A. & Mitchell, A. P. Repression by the yeast meiotic inhibitor RME1. Genes Dev. 7, 1598–1608 (1993)

    CAS  Article  Google Scholar 

  19. 19

    Toone, W. M. et al. Rme1, a negative regulator of meiosis, is also a positive activator of G1 cyclin gene expression. EMBO J. 14, 5824–5832 (1995)

    CAS  Article  Google Scholar 

  20. 20

    Barsoum, E., Martinez, P. & Astrom, S. U. α3, a transposable element that promotes host sexual reproduction. Genes Dev. 24, 33–44 (2010)

    CAS  Article  Google Scholar 

  21. 21

    Kassir, Y. & Simchen, G. Regulation of mating and meiosis in yeast by the mating-type region. Genetics 82, 187–206 (1976)

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Mitchell, A. P. & Herskowitz, I. Activation of meiosis and sporulation by repression of the RME1 product in yeast. Nature 319, 738–742 (1986)

    ADS  CAS  Article  Google Scholar 

  23. 23

    Hickman, M. A. & Rusche, L. N. The Sir2-Sum1 complex represses transcription using both promoter-specific and long-range mechanisms to regulate cell identity and sexual cycle in the yeast Kluyveromyces lactis . PLoS Genet. 5, e1000710 (2009)

    Article  Google Scholar 

  24. 24

    Herman, A. Interspecies sex-specific growth responses in Kluyveromyces . Antonie van Leeuwenhoek 36, 421–425 (1970)

    CAS  Article  Google Scholar 

  25. 25

    Tuch, B. B., Galgoczy, D. J., Hernday, A. D., Li, H. & Johnson, A. D. The evolution of combinatorial gene regulation in fungi. PLoS Biol. 6, e38 (2008)

    Article  Google Scholar 

  26. 26

    Kurtzman, C. P. & Fell, J. W. The Yeasts: A Taxonomic Study 4th edn (Elsevier, 2000)

    Google Scholar 

  27. 27

    Ezov, T. K. et al. Molecular-genetic biodiversity in a natural population of the yeast Saccharomyces cerevisiae from ‘Evolution Canyon’: microsatellite polymorphism, ploidy and controversial sexual status. Genetics 174, 1455–1468 (2006)

    CAS  Article  Google Scholar 

  28. 28

    Gehring, W. J. & Ikeo, K. Pax 6: mastering eye morphogenesis and eye evolution Trends Genet . 15, 371–377 (1999)

  29. 29

    Nobile, C. J. et al. Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol. 7, e1000133 (2009)

    Article  Google Scholar 

  30. 30

    Homann, O. R. & Johnson, A. D. MochiView: versatile software for genome browsing and DNA motif analysis. BMC Biol. 8, 49 (2010)

    Article  Google Scholar 

  31. 31

    Sherman, F. Getting started with yeast. Methods Enzymol. 350, 3–41 (2002)

    CAS  Article  Google Scholar 

  32. 32

    Wach, A. PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae . Yeast 12, 259–265 (1996)

    CAS  Article  Google Scholar 

  33. 33

    Longtine, M. S. et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae . Yeast 14, 953–961 (1998)

    CAS  Article  Google Scholar 

  34. 34

    Janke, C. et al. A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21, 947–962 (2004)

    CAS  Article  Google Scholar 

  35. 35

    Wolf, K., Breunig, K. & Barth, G. Non-Conventional Yeasts in Genetics, Biochemistry and Biotechnology (Springer, 2003)

    Google Scholar 

  36. 36

    Gojkovic, Z., Jahnke, K., Schnackerz, K. D. & Piskur, J. PYD2 encodes 5,6-dihydropyrimidine amidohydrolase, which participates in a novel fungal catabolic pathway. J. Mol. Biol. 295, 1073–1087 (2000)

    CAS  Article  Google Scholar 

  37. 37

    Janbon, G., Sherman, F. & Rustchenko, E. Monosomy of a specific chromosome determines L-sorbose utilization: a novel regulatory mechanism in Candida albicans . Proc. Natl Acad. Sci. USA 95, 5150–5155 (1998)

    ADS  CAS  Article  Google Scholar 

  38. 38

    Mitrovich, Q. M., Tuch, B. B., Guthrie, C. & Johnson, A. D. Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans . Genome Res. 17, 492–502 (2007)

    CAS  Article  Google Scholar 

  39. 39

    Rouillard, J.-M., Zuker, M. & Gulari, E. OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 31, 3057–3062 (2003)

    CAS  Article  Google Scholar 

  40. 40

    Lemoine, S., Combes, F., Servant, N. & Le Crom, S. Goulphar: rapid access and expertise for standard two-color microarray normalization methods. BMC Bioinformatics 7, 467 (2006)

    Article  Google Scholar 

  41. 41

    de Hoon, M. J., Imoto, S., Nolan, J. & Miyano, S. Open source clustering software. Bioinformatics 20, 1453–1454 (2004)

    CAS  Article  Google Scholar 

  42. 42

    Saldanha, A. J. Java Treeview—extensible visualization of microarray data. Bioinformatics 20, 3246–3248 (2004)

    CAS  Article  Google Scholar 

  43. 43

    Bennett, R. J., Uhl, M. A., Miller, M. G. & Johnson, A. D. Identification and characterization of a Candida albicans mating pheromone. Mol. Cell. Biol. 23, 8189–8201 (2003)

    CAS  Article  Google Scholar 

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Acknowledgements

We thank Q. Mitrovich, O. Homann, A. Hernday, M. Miller, C. Cain, T. Sorrells and H. Madhani for helpful discussions and technical contributions; and S. Åström for generously providing the K. lactis strains used in this study. The S. cerevisiae strains were a gift from the H. Madhani and J. Li laboratories. The work was funded by grant RO1 GM037049 from the National Institutes of Health. L.N.B. is a National Science Foundation Graduate Research Fellow.

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L.N.B. performed all experiments. L.N.B. and B.B.T. analysed data. L.N.B., B.B.T. and A.D.J. designed the study and wrote the paper.

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Correspondence to Alexander D. Johnson.

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Booth, L., Tuch, B. & Johnson, A. Intercalation of a new tier of transcription regulation into an ancient circuit. Nature 468, 959–963 (2010). https://doi.org/10.1038/nature09560

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