Several genes and promoters are commonly employed for genetic manipulations and studies with yeast. Some of these genes have special properties, whereas others were originally choosen arbitarily and are conveniently available in strains and plasmids. Several of the genes most commonly used for a variety of purposes are described below.

URA3 encodes orotidine-5’phosphate decarboxylase, an enzyme which is required for the biosynthesis of uracil. Ura3^- (or ura5^-) cells can be selected on media containing FOA. The URA3⁺ cells are killed because FOA appears to be converted to the toxic compound 5-fluorouracil by the action of decarboxylase, whereas ura3- cells are resistant. The negative selection on FOA media is highly discriminating, and usually less than 10^-2 FOA-resistant colonies are Ura⁺. The FOA selection procedure can be used to produce ura3 markers in haploid strains by mutation, and, more importantly, for expelling URA3-containing plasmids, including YCp and YEp replicating plasmids, and integated YIp plasmids, as discussed below for a number of genetic strategies (Section 11). Because of this negative selection and its small size, URA3 is the most widely used yeast marker in yeast vectors. The specfic allele, ura3-52, which is the most commonly used host marker, contains a Ty1 insertion, is not revertible, and does not allow integation of YIp-URA3 plasmids at the URA3 chromosomal locus in most, but not all strains.

The ADE1 and ADE2 yeast genes encode phosphoribosylamino-imidazole-succinocarbozamide synthetase and phosphoribosylamino-imidazole-carboxylase, respectively, two enzymes in the biosynthetic pathway of adenine. Ade1 and ade2 mutants, but no other ade^- mutants, produce a red pigment that is apparently derived from the polymerization of the intermediate phosphoribosylamino-imidazole (denoted AIR). Furthermore, the formation of AIR is prevented by blocks preceding the ADE1 and ADE2 steps. For example ade2 strains are red, whereas ade3 and the double mutant ade2 ade3 are both white, similar to the color of normal strains. Red colonies and red-white sectored colonies are easily detected by visual inspection.

The ade1 and ade2 red pigmentation, and the prevention of the coloration by ade3 or other ade^- mutation has been incorporated as a detection scheme in a number of diversed genetic screens. Also, the ade2-1 UAA mutation, and the suppression of formation of the red pigment by the SUP4-o suppressor has been used in a variety of genetic screens. Most of the screens are based on the preferential loss, or the required retention of a plasmid containing a component involved in the formation of the red pigment.

Examples of ade^- red genetic screens include the detection of conditional mutations (Section 11.5, Plasmid Shuffle), isolation of synthetic lethal mutations (Section 12.5, Synthetic Enhancement and Epistatic Relationships), detection of YAC transformants (Section 13.2, Yeast Artificial Chromosomes [YACs]), and the isolation of mutations that effect plasmid stability.

Cloned genes can be expressed with constitutive or regulatable promoters. The most commonly-used regulated promoter for yeast studies is P_GAL1.

There are two regulatory proteins, Gal4p and Gal80p, which effect the transcription of the following structural genes: GAL1, a kinase; GAL2, a permease; GAL7, a transferase; GAL10, an epimerase; and MEL1, a galactosidase. Gal3p appears to be required for the production of the intracellular inducer from galactose. In presence of the inducer, Gal4p binds to sites in the UAS (upstream activation sequence), and activates transcription. In the absence of the inducer, such as when cells are grown in media containing nonfermentable carbon sources, Gal80p binds to the carboxyl terminal region of Gal4p, masking the activation domain. Expression is repressed in cells exposed to glucose-containing media for several reasons in addition to the absence of the inducer, including the action of repressors at sites between the UAS and the TATA box and the inhibition of galactose uptake. Therefore, the addition of glucose to cells growing in galactose meduim causes an immediate repression of tramscription. The UAS of galactose structural genes contains one or more 17 base-pair palidromic sequences to which Gal4p binds, with the different levels of transcription determined by the number and combinations of the palidromes.

The UAS of the divergently transcribed GAL1 and GAL10 is contained within a 365-bp fragment, denoted P_GAL1, that is sufficient for maximal galactose induction and thorough glucose repression. P_GAL1 can rapidly induce the expression of downstream fused-genes over 1000-fold after the addition of galactose to cells growing in media with a nonfermentable carbon source. Furthermore, P_GAL1 can be turned off by the addition of glucose to the galactose containing medium.

P_GAL1 has been used in a wide range of studies with yeast, including the overproduction of yeast proteins as well as heterologous proteins (Section 13.3). Most importantly, the strong glucose repression of P_GAL1 has been used to investigate the terminal phenotype of essential genes, in much the same way that temperature shifts are used to control the activity of temperature-sensitive mutations (see Section 11.2). Also, the P_GAL1 system has been used to investigate suppression (Section 12.4) and growth inhibition by over expressed normal or mutant genes (dominant-negative mutations, Section 12.1). P_GAL1 is also an important component of one of the two-hybrid systems (Section 13.1).

Activities of promoters, and protein-protein and protein-DNA interactions involving promoter regions can be readily converted into selectable and quantifiable traits by fusing the promoter regions to reporter genes. Reporter genes can be used to determine the levels of transcription, or the levels of translation of the transcript, under various physiological conditions. The most common use of reporter genes has been to identify elements required for transcription by systematically examining series of mutations in promoter regions. Similarly, reporter genes have been used to identify trans acting factors that modulate expression by transcription or translation.

For positive selection, the reporter gene could include, for example, the translated region of the HIS3 gene, lacking a UAS (upstream-activating sequence). His⁺ colonies arise when active promoters are formed, such as in the cloning of heterologous components required for the activation of a defined DNA segment. Combining the HIS3 selection with a lacZ screen is a commomly used strategy; this approch of using two different reporters in parallel with the same promoter region is an efficient means for identifying trans-acting factors.