Part:BBa_J24813

URA3 Promoter from S. cerevisiae

This is the whole regulatory region from the URA3 gene coding for OMP decarboxylase, an essential protein in the uracil synthesis pathway in S. cerevisiae budding yeast.

Team Estonia_TUIT 2023 characterization of BBa_I766556 (pADH1)

The pURA3 promoter controls the URA3 gene. This gene is responsible for producing the enzyme orotidine 5-phosphate decarboxylase (ODCase), which is crucial for the synthesis of pyrimidine ribonucleotides (Umezu et al., 1971).

Plasmid formation

The promoters were PCR-amplified from the yeast genome using primers that contained SacI (forward primer) and BamHI (reverse primer) restriction sites in their 5’-overhangs. After PCR and restriction digestion, the DNA fragments containing the promoters were ligated into SacI/BamHI-restricted pRS304-based vector carrying EGFP coding sequence and tCYC1 terminator.

Promoter	Reporter	Assembly methods
pURA3	EGFP	Restriction-ligation

Yeast strain construction

Prior to yeast transformation, the integration plasmids were restricted with HindIII to linearise the plasmids for homologous recombination into the yeast genome TRP1 locus. The restricted plasmids were used to transform the S. cerevisiae DOM90 strain. Transformants were selected for Trp+ phenotype on tryptophan-dropout synthetic media (CSM-TRP) agar plates containing 2% glucose. All yeast strains generated and used for promoter characterization are listed in table:

Strain name	Genotype	Description
DOM90	MATa {leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15 bar1::hisG} [phi+]	Background strain used for transformation and as a negative control
I86	DOM90 trp1::pRS304-pURA3-sfGFP-tCYC1	Strain with sfGFP under pURA3 promoter, integrated into Trp1-1 locus

sfGFP fluorescence measurements Prior to fluorescence measurements, yeast cells were cultivated in complete synthetic media (CSM) with 2% glucose until the cultures reached an optical density (OD600) in the range of 0.6 to 1. Subsequently, 200 μl of the cell suspension was transferred into the designated wells on 96-well plates. To measure sfGFP fluorescence, a BioTek Synergy Mx Microplate Reader equipped with a 458 nm wavelength LED for GFP excitation was utilized. The emitted fluorescence was measured at a wavelength of 528 nm.

Results

In this study, we assessed the level of gene expression driven by the promoter pCYC1 by employing a fluorescent protein as a reporter. The promoter-containing constructs were integrated into the yeast genome, and the resulting reporter protein fluorescence was quantified in a 96-well plate. To establish a baseline of background fluorescence in the culture, we measured the fluorescence in a control strain, DOM90, which does not express any fluorescent proteins. Compared to the background fluorescence of DOM90, yeast strains with sfGFP under the control of pURA3 promoter displayed a 3.5-fold increase in sfGFP fluorescence intensity.

Bars indicate the mean fluorescence intensity (expressed in arbitrary units, AU) measured in pURA3-sfGFP strain or in DOM90 negative control strain. Error bars show standard deviation.

In our study, we examined three yeast promoters sourced from the iGEM part registry. We found that constitutive promoter pURA3 is suitable choice for achieving consistent moderate gene expression. Expanding the quantitative information on yeast promoter activities facilitates the engineering of fine-tuned synthetic biology applications.

References:

Umezu, K., Amaya, T., Yoshimoto, A., & Tomita, K. (1971). Purification and properties of orotidine-5’-phosphate pyrophosphorylase and orotidine-5’-phosphate decarboxylase from baker’s yeast. Journal of Biochemistry, 70(2), 249–262. https://doi.org/10.1093/oxfordjournals.jbchem.a129637

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]