This web page was produced as an assignment for an undergraduate course at Davidson College.

My Favorite Yeast Genes

UBI4 and SET4

These genes can be found in brewer's yeast, Saccharomyces cerevisiae.  For more background information on S.cerevisiae visit the SGD "What are yeast?" page or the Wyeast Laboratory educational page.  For more information on the genetics of this yeast species visit the Saccharomyces Genome Database.

UBI4

UBI4 (ACC#: Z73144), also known as SCD2 or the polyubiquitin gene,  is found on chromosome 12 of S.cerevisiae.  The locus consists of 6209 base pairs (A: 1806, T: 2086, C: 1218,  G: 1099) which code for 1360 amino acids (ACC#: CAA97490.1). NCBI, 2001   Ozhaynak et al. reported that UBI4 "encodes a polyubiquitin precursor protein containing five ubiquitin repeats in a head-to-tail, spacerless arrangement." Ozkaynak, 1987; Finley, 1987  However, NCBI reports that the UBI4 encoded protein has no conserved domains. NCBI, 2001; <http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi>  UBI4 is related to UBI1, UBI2, and UBI3 which "encode hybrid proteins in which ubiquitin is fused to unrelated ('tail') amino acid sequences." Ozkaynak, 1987  UBI4 encodes for ubiquitin, a protein found in the cytoplasm of S.cerevisiae, similar to the proteins ubiquitin and polyubiquitin found in rats and humans. SGD, 2001;  <http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=YLL039c>, <http://genome-www.stanford.edu/cgi-bin/SGD/Sacch3D/getblast?name=UBI4&db=mammal>  UBI4's protein is involved in the processes of "deubiquitylation, monoubiquitylation, polyubiquitylation, sporulation (sensu Saccharomyces), and stress response."  Its biochemical activity is "protein degradation tagging" but the gene is only expressed under conditions of stress.  SGD, 2001; <http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=YLL039c>    Numerous studies link UBI4 expression to the S.cerevisiae stress response system which can be activated by heat shock elements (HSEs) and/or stress response elements (STREs).  Arnason, 1994; Barbet, 1996; Cheng, 1994; Finley, 1987; Fraser, 1991; Hazell, 1995; Lee, 1996; Ozkaynak, 1987; Simon, 1999; Tanaka, 1988; Timblin, 1997; Treger, 1988; Watt, 1997  According to Ozhaynak et al., "conjugation of ubiquitin to intracellular proteins mediate their selective degradation in vivo."  Ozkaynak, 1987  In December 1988, Tanaka et al. proposed "that the UBI4 gene is one of the genes which are part of the cAMP-effector pathway and required for G-0G-1 arrest in Saccharomyces cerevisiae." Tanaka, 1989

There is a mutant allele for UBI4, ubi4, caused by systematic deletion of the UBI4 gene. Winzeler, 1999  Finley et al. describe the mutant phenotypes: "ubi4 deletion mutants are viable as vegetative cells, grow at wild-type rates, and contain wild-type levels of free ubiquitin under exponential growth conditions.  However, although ubi4/UBI4 diploids can form four initially viable spores, the two ubi spores within the ascus lose viability extremely rapidly, apparently a novel phenotype in yeast.  Furthermore, ubi4/ubi4 diploids are sporulation-defective.  ubi4 mutants are also hypersensitive to high temperatures, starvation, and amino acid analogs.  These three conditions... are all known to induce stress proteins." Finley, 1987  SGD's description of ubi4 mutant phenotypes matches that published by Finley et al. SGD, 2001; <http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=YLL039c>

SET4

SET4 (ACC#: 249380.1) is found on chromosome 10 of S.cerevisiae.  The locus consists of 3999 base pairs (A: 1307, T: 1216, C: 735, G: 741) which code for 560 amino acids (ACC#: CAA89400). SGD, 2001; <http://genome-www2.stanford.edu/cgi-bin/SGD/getSeq?map=nmap&seq=YJL105W&flankl=0&flankr=0&rev=>, <http://genome-www2.stanford.edu/cgi-bin/SGD/getSeq?map=pmap&seq=YJL105W&flankl=0&flankr=0&rev=> GeneMark reports that SET4 has 1683 base pairs, with a CG value of 37.85%. GeneMark, 2001; <http://opal.biology.gatech.edu/GeneMark/>  SET4 shares conserved domains labeled "PHD" and "SET" with other genes; the e-values of these matches are low, 1e-6 and 4e-25 respectively, so these matches are probably not due to chance.  PHD tends to form zinc fingers.  NCBI describes SET domains: "SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction...  SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues." NCBI, 2001; <http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi>

The program, PREDATOR, can predict the secondary structure of a protein.  The figures below show the PREDATOR graphical output for SET4.



Figures 1A and 1B: X-axis refers to amino acid count.  Top figure shows secondary structure predicted states, where blue marks represent alpha helices, red marks represent extended strands and yellow marks represent random coil regions.  Bottom figure shows predicted reliability of state predictions.

According to PREDATOR, SET4's 560 amino acids can be devided into nine regions of alpha helices (15%) and twenty regions of extended strand (16.07%) interspersed with regions of random coil (68.93%).  The reliability of these predictions ranges.  When the graph reaches or exceeds the value 0.8 on the Y-axis of the reliability graph the secondary structure state predictions in the upper graph are probable.  The reliability of the predicted secondary structure of SET4 is fairly high.  These results imply that SET4 may code for an integral membrane protein, like a G protein-coupled receptor, since it contains many regions of alpha helix.

 A hydropothy plot, also known as Kyte-Doolittle analysis, predicts whether or not a protein is an integral membrane protein.  If peaks occur at or above the value 2 on the graph then there is potential for a transmembrane domain.  The following figure is a hydropothy plot for SET4.


Figure 2: Courtesy of  J. Kyte and R. F. Doolittle (1982) J. Mol. Biol. 157:105-132.  X-axis refers to amino acid count.  Graph represents intermembrane domain potential.

According to the hydropothy plot, there is only one section of the protein encoded by SET4 which has high potential to be a transmembrane domain.  This domain occurs approximately at amino acid 100 of the sequence.  It should be noted that the PREDATOR secondary structure predictions show a region of alpha helix that between approximately amino acid 100 and amino acid 115 of the sequence.


Sources Consulted:
  1. Arnason, Terra and Michael J. Ellison.  (1994) "Stress resistance in Saccharomyces cerevisiae is strongly correlated with assembly of a novel type of multiubiquiton chain."  Molecular and Cellular Biology 14(12): 7876-7883.
  2. Barbet, Nik C., Ulrich Schneider, Stephen B. Helliwell, Ian Stansfield, Michael F. Tuite, and Michael N. Hall. (1996) "TOR controls translation initiation and early G1 progression in yeast."  Molecular Biology of the Cell 7(1): 25-42.
  3. Cheng, L. R.Watt, and P.W.Piper. (1994) "Polyubiquitin gene expression contributes to oxidative stress resistance in respiratory yeast." Molecular and General Genetics 243(3): 358-362.
  4. Finley, D., E.Ezkaynak, and A.Varshavsky.  (1987) "The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses."  Cell 48(6): 1035-1046.
  5. Fraser, J., H.A.Luu, J.Neculcea, D.Y.Thomas, and R.K.Storms. (1991) "Ubiquitin gene expression: Response to environmental changes."  Current Genetics 20(1-2): 17-24.
  6. "GeneMark." GeneMark, 2001. <http://opal.biology.gatech.edu/GeneMark/>
  7. "Genomic Sequence Total Analysis and Lookup Tool."  GESTALT, 2001. <http://sun01.systemsbiology.net/~gglusman/GESTALT/>
  8. Hazell, Brian W., Helena Nevalainen, and Paul V. Attfield. (1995) "Evidence that the Saccharomyces cerevisiae CIF1 (GGSI/TPSI) gene modulates heat shock response positively." FEBS Letters 377(3): 457-460.
  9. Kyte, J. and R.F.Doolittle (1982) J. Mol. Biol. 157:105-132.
  10. Lee, Jinhwa, Annette Romeo, and Daniel J. Kosman. (1996) "Transcriptional remodeling and G-1 arrest in dioxygen stress in Saccharomyces cerevisiae." Journal of Biological Chemistry 271(40): 24885-24893.
  11. "National Center for Biotechnology Information."  NCBI, 2001.  <http://www.ncbi.nlm.nih.gov/>
  12. Ozkaynak, E., D.Finley, M.J.Solomon and A.Varshavsky.  (1987) "The yeast ubiquitin genes: A family of natural gene fusions."  UMBO Journal 6(5):1429-1440.
  13. "Saccharomyces Genome Database."  SGD, 2001.  <http://genome-www.stanford.edu/Saccharomyces/>
  14. Simon, John R., Janet M. Treger, and Kevin McEntee.  (Feb. 1999) "Multiple independent regulatory pathways control UBI4 expression after heat shock in Sacharomyces cerevisiae."  Molecular Microbiology 31(3): 823-832.
  15. Takana, K., K.Matsumoto and E.A.Toh.  "Dual regulation of the expression of the polyubiquitin gene by cyclic AMP and heat shock in yeast." UMBO Journal 7(2):495-502, 1988.
  16. Timblin, Barbara K., and Lawrence W. Bergman.  (Dec.1997) "Elevated expression of stress response genes resulting from deletion of the PHO85 gene."  Microbiology 26(5): 981-990.
  17. Treger, J.M., K.A. Heichman, and K.McEntee. (1988) "Expression of the yeast UBI4 gene increases in response to DNA-damaging agents and in meiosis." Molecular and Cellular Biology 8(3): 1132-1136.
  18. Watt, R. and P.W.Piper.  (1997) "UBI4, the polyubiquitin gene of Saccharomyces cerevisiae, as a heat shock gene that is also subject to catabolite depression control."  Molecular and General Genetics 253(4): 439-447.
  19. Winzeler EA, et al. (1999) "Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis". Science 285(5429):901-906.

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updated 10/7/01