6.2: Genetic nomenclature
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When referring to genes and strains, it is important to use correct genetic nomenclature. Pay close attention to italics and capital letters as your prepare your reports.
Gene names are placed in italics, while proteins and phenotypes are referred to with normal font. Gene names that begin with capital letters refer to dominant alleles, while gene names beginning with lower case letters refer to recessive alleles. (One oddity about budding yeast: S. cerevisiaegene names are unique in that dominant alleles are described with three capital letters. In most other eukaryotic species, dominant alleles would be referred to as Met6 with only the first letter capitalized.) S. cerevisiae gene names consist of three letters, followed by a number. There
may be many different gene names that begin with the same three letters, e.g. there are over 20 different MET genes, but the number at the end of the gene name is specific for a particular gene. If some molecular detail is available for a particular mutant allele, the number may be followed by a hyphen and additional information about the allele.
As an example, let’s look at the nomenclature that would be used for the MET6 gene fromS. cerevisiae. The met prefix is used to describe loss-of-function alleles found in mutant strains, most of which were isolated in genetic screens based on their inability live in the absence of Met. The numbers associated with genes are usually arbitrary. The MET6 gene acquired its name before its gene product had been identified as homocysteine methyltransferase, the last step in methionine synthesis. The list below describes the naming conventions for genes, proteins, and strains related to S. cerevisiae MET6. These same rules apply for other genes in S. cerevisiae.
MET6 Dominant allele of the MET6 gene or the chromosomal locus
met6 Recessive allele of the MET6 gene (allele found in a met6 mutant)
met6-12 Recessive allele - number after the parentheses refers to specific mutation
met6-∆1 Recessive allele - met6 allele has a specific deletion (∆ indicates a deletion)
met6::LEU2 Recessive allele -insertion of a dominant LEU2 gene into the MET6 locus on the chromosome has inactivated the host MET6 gene
Met6p Protein encoded by the MET6 gene, i.e. homocysteine methyltransferase
We will be working with haploid strains of yeast in this course. To write the genotype of a particular strain, begin with the mating type and follow it with the mutant alleles in the strain. For example, we are using met strains constructed by inserting a bacterial kanamycin resistance (KANR) gene into yeast strain BY4742, which has the a mating type and carries mutations
in genes involved in the synthesis of histidine, leucine, lysine and uracil. BY4742 is derived from strain S288C, which was used for the genome project (Brachmann et al., 1998). Thus, the genotype of our met6 mutant would include the BY4742 mutations and be written:
MAT\(\alpha\) his3-∆1 leu2∆0 lys2∆0 ura3∆0 met6::KANR