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Gene Review

URA3  -  orotidine-5'-phosphate decarboxylase

Saccharomyces cerevisiae S288c

Synonyms: OMP decarboxylase, OMPDCase, OMPdecase, Orotidine 5'-phosphate decarboxylase, UMP synthase, ...
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Disease relevance of URA3


High impact information on URA3

  • Our results contradict both models and show instead that transcriptional silencing at several URA3 transgenes, and at the naturally silenced endogenous HMRa and HMLalpha mating type genes, acts downstream of gene activator protein binding to strongly reduce the occupancy of TFIIB, RNA polymerase II, and TFIIE at the silenced promoters [5].
  • RNA3 derivatives carrying the yeast URA3 gene complemented ura3- yeast to prototrophy and were maintained as persistent RNA episomes [6].
  • Efficient repair also occurred in both strands of a disrupted TRP1 gene (ten PD sites), containing four unstable nucleosomes, and in a nucleosome gap at the 5' end of URA3 (two PD sites) [7].
  • The rate of excision repair of UV-induced pyrimidine dimers (PDs) was measured at specific sites in each strand of a yeast minichromosome containing an active gene (URA3), a replication origin (ARS1), and positioned nucleosomes [7].
  • Repression was due to proximity to the telomere itself since an 81 bp tract of (TG1-3)n positioned downstream of URA3 when URA3 was approximately 20 kb from the end of chromosome VII did not alter expression of the gene [8].

Chemical compound and disease context of URA3


Biological context of URA3

  • The proportions of 5-FOA-resistant cells in cultures from isogenic RAD+ and rad7-delta strains containing a telomeric URA3 gene were similar, suggesting that the RAD7 gene is not involved in the production or structure of transcriptionally silent chromatin at the telomeres [14].
  • RAD7-dependent DNA repair of transcriptionally silent chromatin was shown not to induce expression of a telomeric copy of the URA3 gene, suggesting that repair of transcriptionally silent chromatin differs from transcriptionally active chromatin [14].
  • The repression of URA3 inserted in different subtelomeric positions at several chromosome ends was investigated [15].
  • A pol3-01/pol3-01 pms1/pms1 diploid was viable and displayed an estimated URA3 relative mutation rate of 2 x 10(4), which we calculate to be catastrophically high in a haploid [16].
  • Using high-resolution repair analysis, we determined the in vivo repair kinetics of cyclobutane pyrimidine dimers positioned around the transcription initiation site of RNAPII-transcribed genes RPB2 and URA3 [17].

Anatomical context of URA3


Associations of URA3 with chemical compounds


Physical interactions of URA3

  • The interaction is biologically significant, since the deletion of the TUP1 gene as well as the removal of the Tup1p-binding domain from Ppr1p results in an increased expression of the URA3 gene [24].

Enzymatic interactions of URA3

  • We constructed strains containing two ura3 segments on one side of the HO cut site and one ura3 region on the other side to characterize how flanking repeats find each other [25].
  • Southern blot analysis of DNA extracted from a nam7 :: URA3 deleted strain revealed the presence of a second gene whose sequence is related to that of the NAM7 gene and which could participate in the same process [26].

Regulatory relationships of URA3

  • On the other hand, both GAL1 and URA3 transcripts expressed from the SSA4 promoter accumulated in nuclei following heat shock [27].
  • In comparison, a nontelomeric URA3 could be activated by PPR1 at all times [28].
  • Having proposed that regulation of 3' end formation dictates the amount of each CBP1 transcript, we now show that a 146-bp fragment from the middle of CBP1 is sufficient to direct carbon source-regulated production of two transcripts when inserted into the yeast URA3 gene [29].
  • Spontaneous and double-strand break (DSB)-induced allelic recombination in yeast was investigated in crosses between ura3 heteroalleles inactivated by an HO site and a +1 frameshift mutation, with flanking markers defining a 3.4-kbp interval [30].

Other interactions of URA3

  • In active genes (URA3, HIS3), photolyase repairs the non-transcribed strand faster than the transcribed strand and can match fast removal of lesions from the transcribed strand by NER (transcription-coupled repair) [31].
  • In contrast to NER, photolyase rapidly repairs CPDs in non-nucleosomal regions, including promoters of active genes (URA3, HIS3, DED1) and in linker DNA between nucleosomes [31].
  • The cloned C. albicans URA3 gene was disrupted with the C. albicans ADE2 gene, and the linearized DNA was used for transformation of two ade2 mutants, SGY-129 and A81-Pu [32].
  • Likewise, rad6-delta reduces silencing of the telomere-located RNAP II-transcribed genes URA3 and ADE2 [33].
  • In contrast, transcription of the MET3-URA3 fusion did not alter the Ty1 target-site distribution in wild-type or other mutant strains [34].

Analytical, diagnostic and therapeutic context of URA3


  1. A Tn3 derivative that can be used to make short in-frame insertions within genes. Hoekstra, M.F., Burbee, D., Singer, J., Mull, E., Chiao, E., Heffron, F. Proc. Natl. Acad. Sci. U.S.A. (1991) [Pubmed]
  2. Yeast shuttle and integrative vectors with multiple cloning sites suitable for construction of lacZ fusions. Myers, A.M., Tzagoloff, A., Kinney, D.M., Lusty, C.J. Gene (1986) [Pubmed]
  3. A new method for the isolation of recombinant baculovirus. Patel, G., Nasmyth, K., Jones, N. Nucleic Acids Res. (1992) [Pubmed]
  4. Adaptation of the yeast URA3 selection system to gram-negative bacteria and generation of a {delta}betCDE Pseudomonas putida strain. Galvão, T.C., de Lorenzo, V. Appl. Environ. Microbiol. (2005) [Pubmed]
  5. Mechanism of transcriptional silencing in yeast. Chen, L., Widom, J. Cell (2005) [Pubmed]
  6. RNA-dependent replication, transcription, and persistence of brome mosaic virus RNA replicons in S. cerevisiae. Janda, M., Ahlquist, P. Cell (1993) [Pubmed]
  7. Site-specific DNA repair at the nucleosome level in a yeast minichromosome. Smerdon, M.J., Thoma, F. Cell (1990) [Pubmed]
  8. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Gottschling, D.E., Aparicio, O.M., Billington, B.L., Zakian, V.A. Cell (1990) [Pubmed]
  9. A series of yeast/Escherichia coli lambda expression vectors designed for directional cloning of cDNAs and cre/lox-mediated plasmid excision. Brunelli, J.P., Pall, M.L. Yeast (1993) [Pubmed]
  10. Protection against chloroethylnitrosourea cytotoxicity by eukaryotic 3-methyladenine DNA glycosylase. Matijasevic, Z., Boosalis, M., Mackay, W., Samson, L., Ludlum, D.B. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  11. The use of proline as a nitrogen source causes hypersensitivity to, and allows more economical use of 5FOA in Saccharomyces cerevisiae. McCusker, J.H., Davis, R.W. Yeast (1991) [Pubmed]
  12. Evidence for transcriptional regulation of orotidine-5'-phosphate decarboxylase in yeast by hybridization of mRNA to the yeast structural gene cloned in Escherichia coli. Bach, M.L., Lacroute, F., Botstein, D. Proc. Natl. Acad. Sci. U.S.A. (1979) [Pubmed]
  13. Isolation and characterization of the orotidine 5'-monophosphate decarboxylase domain of the multifunctional protein uridine 5'-monophosphate synthase. Floyd, E.E., Jones, M.E. J. Biol. Chem. (1985) [Pubmed]
  14. Interaction of the yeast RAD7 and SIR3 proteins: implications for DNA repair and chromatin structure. Paetkau, D.W., Riese, J.A., MacMorran, W.S., Woods, R.A., Gietz, R.D. Genes Dev. (1994) [Pubmed]
  15. Limitations of silencing at native yeast telomeres. Pryde, F.E., Louis, E.J. EMBO J. (1999) [Pubmed]
  16. Pathway correcting DNA replication errors in Saccharomyces cerevisiae. Morrison, A., Johnson, A.L., Johnston, L.H., Sugino, A. EMBO J. (1993) [Pubmed]
  17. Transitions in the coupling of transcription and nucleotide excision repair within RNA polymerase II-transcribed genes of Saccharomyces cerevisiae. Tijsterman, M., Verhage, R.A., van de Putte, P., Tasseron-de Jong, J.G., Brouwer, J. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  18. Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae. Thorsness, P.E., Fox, T.D. Nature (1990) [Pubmed]
  19. Yeast artificial chromosome fragmentation vectors that utilize URA3 selection. Cook, J.R., Emanuel, S.L., Pestka, S. Genet. Anal. Tech. Appl. (1993) [Pubmed]
  20. cis- and trans-acting regulatory elements of the yeast URA3 promoter. Roy, A., Exinger, F., Losson, R. Mol. Cell. Biol. (1990) [Pubmed]
  21. GAL11 protein, an auxiliary transcription activator for genes encoding galactose-metabolizing enzymes in Saccharomyces cerevisiae. Suzuki, Y., Nogi, Y., Abe, A., Fukasawa, T. Mol. Cell. Biol. (1988) [Pubmed]
  22. Identification and isolation of the gene encoding the small subunit of ribonucleotide reductase from Saccharomyces cerevisiae: DNA damage-inducible gene required for mitotic viability. Elledge, S.J., Davis, R.W. Mol. Cell. Biol. (1987) [Pubmed]
  23. Molecular genetic properties of the yeast Torulaspora pretoriensis: characterization of chromosomal DNA and genetic transformation by Saccharomyces cerevisiae-based plasmids. Oda, Y., Tonomura, K. Curr. Genet. (1995) [Pubmed]
  24. Why Ppr1p is a weak activator of transcription. Pätzold, A.J., Lehming, N. FEBS Lett. (2001) [Pubmed]
  25. Characterization of double-strand break-induced recombination: homology requirements and single-stranded DNA formation. Sugawara, N., Haber, J.E. Mol. Cell. Biol. (1992) [Pubmed]
  26. NAM7 nuclear gene encodes a novel member of a family of helicases with a Zn-ligand motif and is involved in mitochondrial functions in Saccharomyces cerevisiae. Altamura, N., Groudinsky, O., Dujardin, G., Slonimski, P.P. J. Mol. Biol. (1992) [Pubmed]
  27. Regulation of mRNA export in response to stress in Saccharomyces cerevisiae. Saavedra, C., Tung, K.S., Amberg, D.C., Hopper, A.K., Cole, C.N. Genes Dev. (1996) [Pubmed]
  28. Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Aparicio, O.M., Gottschling, D.E. Genes Dev. (1994) [Pubmed]
  29. Yeast CBP1 mRNA 3' end formation is regulated during the induction of mitochondrial function. Mayer, S.A., Dieckmann, C.L. Mol. Cell. Biol. (1991) [Pubmed]
  30. Multiple heterologies increase mitotic double-strand break-induced allelic gene conversion tract lengths in yeast. Nickoloff, J.A., Sweetser, D.B., Clikeman, J.A., Khalsa, G.J., Wheeler, S.L. Genetics (1999) [Pubmed]
  31. Chromatin structure modulates DNA repair by photolyase in vivo. Suter, B., Livingstone-Zatchej, M., Thoma, F. EMBO J. (1997) [Pubmed]
  32. Directed mutagenesis in Candida albicans: one-step gene disruption to isolate ura3 mutants. Kelly, R., Miller, S.M., Kurtz, M.B., Kirsch, D.R. Mol. Cell. Biol. (1987) [Pubmed]
  33. The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae. Huang, H., Kahana, A., Gottschling, D.E., Prakash, L., Liebman, S.W. Mol. Cell. Biol. (1997) [Pubmed]
  34. Host genes that affect the target-site distribution of the yeast retrotransposon Ty1. Huang, H., Hong, J.Y., Burck, C.L., Liebman, S.W. Genetics (1999) [Pubmed]
  35. Development of an integrative transformation system for the opportunistic pathogenic yeast Candida lusitaniae using URA3 as a selection marker. François, F., Chapeland-Leclerc, F., Villard, J., Noël, T. Yeast (2004) [Pubmed]
  36. Sequence analysis of the DdPYR5-6 gene coding for UMP synthase in Dictyostelium discoideum and comparison with orotate phosphoribosyl transferases and OMP decarboxylases. Jacquet, M., Guilbaud, R., Garreau, H. Mol. Gen. Genet. (1988) [Pubmed]
  37. Use of polymerase chain reaction epitope tagging for protein tagging in Saccharomyces cerevisiae. Schneider, B.L., Seufert, W., Steiner, B., Yang, Q.H., Futcher, A.B. Yeast (1995) [Pubmed]
  38. The use of a double-marker shuttle vector to study DNA double-strand break repair in wild-type and radiation-sensitive mutants of the yeast Saccharomyces cerevisiae. Jha, B., Ahne, F., Eckardt-Schupp, F. Curr. Genet. (1993) [Pubmed]
  39. A new type of fusion analysis applicable to many organisms: protein fusions to the URA3 gene of yeast. Alani, E., Kleckner, N. Genetics (1987) [Pubmed]
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