Evolution of alternative transcriptional circuits with identical logic

Abstract

Evolution of gene regulation is an important contributor to the variety of life. Here, we analyse the evolution of a combinatorial transcriptional circuit composed of sequence-specific DNA-binding proteins that are conserved among all eukaryotes. This circuit regulates mating in the ascomycete yeast lineage. We first identify a group of mating genes that was transcriptionally regulated by an activator in a fungal ancestor, but is now transcriptionally regulated by a repressor in modern bakers' yeast. Despite this change in regulatory mechanism, the logical output of the overall circuit remains the same. By examining the regulation of mating in modern yeasts that are related to different extents, we deduce specific, sequential changes in both cis- and trans-regulatory elements that constitute the transition from positive to negative regulation. These changes indicate specific mechanisms by which fitness barriers were traversed during the transition.

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Figure 1: a-type mating is negatively regulated in modern S. cerevisiae , but was positively regulated in its ancestor.
Figure 2: Identification of a-specific genes in C. albicans.
Figure 3: Identification and validation of the C. albicans asg operator.
Figure 4: Analysis of cis - asg regulation across species.
Figure 5: Evolution of the α2–Mcm1 interaction.
Figure 6: Ordering the changes in cis - and trans -regulatory elements.

References

  1. 1

    Darwin, C. R. The Origin of Species (Gramercy, New York, 1859)

    Google Scholar 

  2. 2

    Carroll, S. B., Grenier, J. K. & Weatherbee, S. D. From DNA to Diversity (Blackwell Science, Malden, Massachusetts, 2001)

    Google Scholar 

  3. 3

    Davidson, E. H. Genomic Regulatory Systems (Academic, San Diego, California, 2001)

    Google Scholar 

  4. 4

    Gerhart, J. & Kirschner, M. Cells, Embryos, and Evolution (Blackwell Science, Malden, Massachusetts, 1997)

    Google Scholar 

  5. 5

    Levine, M. & Tjian, R. Transcription regulation and animal diversity. Nature 424, 147–151 (2003)

    ADS  CAS  Article  Google Scholar 

  6. 6

    Doebley, J. & Lukens, L. Transcriptional regulators and the evolution of plant form. Plant Cell 10, 1075–1082 (1998)

    CAS  Article  Google Scholar 

  7. 7

    Gompel, N., Prud'homme, B., Wittkopp, P. J., Kassner, V. A. & Carroll, S. B. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433, 481–487 (2005)

    ADS  CAS  Article  Google Scholar 

  8. 8

    Ihmels, J. et al. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309, 938–940 (2005)

    ADS  CAS  Article  Google Scholar 

  9. 9

    Ludwig, M. Z., Patel, N. H. & Kreitman, M. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 125, 949–958 (1998)

    CAS  PubMed  Google Scholar 

  10. 10

    Ronshaugen, M., McGinnis, N. & McGinnis, W. Hox protein mutation and macroevolution of the insect body plan. Nature 415, 914–917 (2002)

    ADS  Article  Google Scholar 

  11. 11

    Tanay, A., Regev, A. & Shamir, R. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc. Natl Acad. Sci. USA 102, 7203–7208 (2005)

    ADS  CAS  Article  Google Scholar 

  12. 12

    Wittkopp, P. J., Haerum, B. K. & Clark, A. G. Evolutionary changes in cis and trans gene regulation. Nature 430, 85–88 (2004)

    ADS  CAS  Article  Google Scholar 

  13. 13

    Galant, R. & Carroll, S. B. Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415, 910–913 (2002)

    ADS  CAS  Article  Google Scholar 

  14. 14

    Hull, C. M., Raisner, R. M. & Johnson, A. D. Evidence for mating of the “asexual” yeast Candida albicans in a mammalian host. Science 289, 307–310 (2000)

    ADS  CAS  Article  Google Scholar 

  15. 15

    Herskowitz, I., Rine, J. & Strathern, J. Mating-type determination and Mating-type interconversion in Saccharomyces cerevisiae (eds Jones, E. W., Pringle, J. R. & Broach, J. R.) 583–656 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1992)

    Google Scholar 

  16. 16

    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 

  17. 17

    Staben, C. & Yanofsky, C. Neurospora crassa a mating-type region. Proc. Natl Acad. Sci. USA 87, 4917–4921 (1990)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Kelly, M., Burke, J., Smith, M., Klar, A. & Beach, D. Four mating-type genes control sexual differentiation in the fission yeast. EMBO J. 7, 1537–1547 (1988)

    CAS  Article  Google Scholar 

  19. 19

    Kurischko, C., Schilhabel, M. B., Kunze, I. & Franzl, E. The MATA locus of the dimorphic yeast Yarrowia lipolytica consists of two divergently oriented genes. Mol. Gen. Genet. 262, 180–188 (1999)

    CAS  Article  Google Scholar 

  20. 20

    Philley, M. L. & Staben, C. Functional analyses of the Neurospora crassa MT a-1 mating type polypeptide. Genetics 137, 715–722 (1994)

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21

    Turgeon, B. G. et al. Cloning and analysis of the mating type genes from Cochliobolus heterostrophus. Mol. Gen. Genet. 238, 270–284 (1993)

    CAS  PubMed  Google Scholar 

  22. 22

    Butler, G. et al. Evolution of the MAT locus and its Ho endonuclease in yeast species. Proc. Natl Acad. Sci. USA 101, 1632–1637 (2004)

    ADS  CAS  Article  Google Scholar 

  23. 23

    Calderone, R. A. Candida and Candidiasis (ed. Calderone, R. A.) (ASM, Washington DC, 2002)

    Google Scholar 

  24. 24

    Hedges, S. B. The origin and evolution of model organisms. Nature Rev. Genet. 3, 838–849 (2002)

    CAS  Article  Google Scholar 

  25. 25

    Bender, A. & Sprague, G. F. Jr. Yeast peptide pheromones, a-factor and α-factor, activate a common response mechanism in their target cells. Cell 47, 929–937 (1986)

    CAS  Article  Google Scholar 

  26. 26

    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 

  27. 27

    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  Google Scholar 

  28. 28

    Acton, T. B., Mead, J., Steiner, A. M. & Vershon, A. K. Scanning mutagenesis of Mcm1: residues required for DNA binding, DNA bending, and transcriptional activation by a MADS-box protein. Mol. Cell. Biol. 20, 1–11 (2000)

    CAS  Article  Google Scholar 

  29. 29

    Tan, S. & Richmond, T. J. Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature 391, 660–666 (1998)

    ADS  CAS  Article  Google Scholar 

  30. 30

    Kjaerulff, S., Dooijes, D., Clevers, H. & Nielsen, O. Cell differentiation by interaction of two HMG-box proteins: Mat1-Mc activates M cell-specific genes in S. pombe by recruiting the ubiquitous transcription factor Ste11 to weak binding sites. EMBO J. 16, 4021–4033 (1997)

    CAS  Article  Google Scholar 

  31. 31

    Smith, D. L. & Johnson, A. D. A molecular mechanism for combinatorial control in yeast: MCM1 protein sets the spacing and orientation of the homeodomains of an α2 dimer. Cell 68, 133–142 (1992)

    CAS  Article  Google Scholar 

  32. 32

    van Beest, M. et al. Sequence-specific high mobility group box factors recognize 10–12-base pair minor groove motifs. J. Biol. Chem. 275, 27266–27273 (2000)

    CAS  PubMed  Google Scholar 

  33. 33

    Care, R. S., Trevethick, J., Binley, K. M. & Sudbery, P. E. The MET3 promoter: a new tool for Candida albicans molecular genetics. Mol. Microbiol. 34, 792–798 (1999)

    CAS  Article  Google Scholar 

  34. 34

    Rokas, A., Williams, B. L., King, N. & Carroll, S. B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798–804 (2003)

    ADS  CAS  Article  Google Scholar 

  35. 35

    Byrne, K. P. & Wolfe, K. H. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15, 1456–1461 (2005)

    CAS  Article  Google Scholar 

  36. 36

    Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71–76 (2003)

    ADS  CAS  Article  Google Scholar 

  37. 37

    Belloch, C., Querol, A., Garcia, M. D. & Barrio, E. Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene. Int. J. Syst. Evol. Microbiol. 50, 405–416 (2000)

    CAS  Article  Google Scholar 

  38. 38

    Wong, S., Butler, G. & Wolfe, K. H. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc. Natl Acad. Sci. USA 99, 9272–9277 (2002)

    ADS  CAS  Article  Google Scholar 

  39. 39

    Mead, J., Zhong, H., Acton, T. B. & Vershon, A. K. The yeast α2 and Mcm1 proteins interact through a region similar to a motif found in homeodomain proteins of higher eukaryotes. Mol. Cell. Biol. 16, 2135–2143 (1996)

    CAS  Article  Google Scholar 

  40. 40

    Jacobson, M. P. & Friesner, R. A. Protein local optimization program. http://francisco.compbio.ucsf.edu/~jacobson/plop_manual/plop_overview.htm (2006).

  41. 41

    Lengeler, K. B. et al. Signal transduction cascades regulating fungal development and virulence. Microbiol. Mol. Biol. Rev. 64, 746–785 (2000)

    CAS  Article  Google Scholar 

  42. 42

    Acton, T. B., Zhong, H. & Vershon, A. K. DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein. Mol. Cell. Biol. 17, 1881–1889 (1997)

    CAS  Article  Google Scholar 

  43. 43

    Kellis, M., Birren, B. W. & Lander, E. S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617–624 (2004)

    ADS  CAS  Article  Google Scholar 

  44. 44

    Wolfe, K. H. & Shields, D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708–713 (1997)

    ADS  CAS  Article  Google Scholar 

  45. 45

    Higgins, D. G. & Sharp, P. M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–244 (1988)

    CAS  Article  Google Scholar 

  46. 46

    Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502–504 (2002)

    CAS  Article  Google Scholar 

  47. 47

    Debuchy, R., Arnaise, S. & Lecellier, G. The mat- allele of Podospora anserina contains three regulatory genes required for the development of fertilized female organs. Mol. Gen. Genet. 241, 667–673 (1993)

    CAS  Article  Google Scholar 

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Acknowledgements

We are grateful to M. Jacobson for advice provided in modelling the K. lactis α2 and Mcm1 structures. We also thank S. Ästrøm for providing unpublished K. lactis strains and advice on their handling, P. Sudbury for providing the GFP reporter construct, M. Lorentz and G. Fink for the collaboration that produced the DNA microarrays used in this paper, and the Broad Institute (http://www.broad.mit.edu/annotation/fungi/fgi/), the Sanger Center (http://www.sanger.ac.uk/Projects/Fungi/), and the Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute (http://www.sanger.ac.uk/sequencing/Candida/dubliniensis/) for making sequence data available. M. Ptashne provided valuable comments on the manuscript. We thank B. Hromatka for overseeing microarray printing, and R. Bennett for microarray data and discussions. R. Zordan, A. Uhl, M. Lohse, M. Miller, R. Wu, C. Chaivorapol and other members of the Johnson and Li labs provided useful discussions. This work was supported by grants from the NIH to A.D.J. A.E.T was supported by a Howard Hughes Medical Institute Predoctoral Fellowship. B.B.T. is an NSF Predoctoral Fellow. B.B.T. and H.L. acknowledge partial support from a Packard Fellowship in Science and Engineering (to H.L.) and an NIH grant. Author Contributions A.E.T. determined the asgs of C. albicans, and validated the asg operator site. B.T. constructed the phylogenetic tree, analysed asg operators across multiple species, and modelled the K. lactis α2–Mcm1 interaction. H.L. and A.D.J. oversaw the work.

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Correspondence to Alexander D. Johnson.

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Microarray data are available in Supplementary Information and at http://genome.ucsf.edu/asg_evolution/. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file contains Supplementary Methods, Supplementary Figure Legends and Supplementary Tables (Position weight matrices for C. albicans and S. cerevisiae asg operators). (DOC 118 kb)

Supplementary Figure 1

Strategy used to identify asgs in C. albicans. (PDF 21 kb)

Supplementary Figure 2

Clustering analysis of putative asg operators (JPG 105 kb)

Supplementary Data

Microarray data used to identify the asgs in C. albicans (DOC 23 kb)

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Tsong, A., Tuch, B., Li, H. et al. Evolution of alternative transcriptional circuits with identical logic. Nature 443, 415–420 (2006). https://doi.org/10.1038/nature05099

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