Baker’s yeast Saccharomyces cerevisiae is both an important model organism for eukaryotic biology and a very important industrial microorganism. The genome sequence was one of the first ever completed (even before E. coli) and is still regarded as the one of the highest quality.

Saccharomyces Genome Database (SGD), as the name implies, is a database for baker's yeast only. Here we can find the sequence for all yeast genes and a lot of additional information about almost every gene in the organism.

Saccharomyces cerevisiae has 12 linear chromosomes and about 12 Mbp. This is very compact for a eukaryote as this is only about three times the size of the E. coli genome.

Find SGD by googling “sgd” in your web browser.

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You should be able to view a page similar to the one in Fig 1. You can use the search box at the top right corner to search for information.

Genes in S. cerevisiae have a systematic name with seven letters following the syntax below:

Y(A-P)(R or L)(NNN)(w/c)

Y is short for Yeast. A-P is the chromosome number where the gene is located. There are 16 chromosomes designated with the first 16 letters of the alphabet. R or L is the right or left side of the centromere of the chromosome. NNN is a three digit number, counting the genes between this gene and the centromere. w or c Watson or Crick, whether the gene is transcribed from the upper or lower strand of the DNA.

For example YAR002c is the name of a gene on the first chromosome (A) on the right arm (R) of the chromosome two genes away from the centromere (002) on the crick strand.

Question 1:

What is the location of the gene with the systematic name YGR194c? Fill in the table below. Use the same reasoning as for YAR002 above.

Gene	YGR194c
chromosome	?
number of genes from centromere	?
direction --> or <--	?

Many yeast genes have a standard name in addition to the systematic name. The standard name is often an acronym that may say something about the function of a gene. The gene URA3 is a good example of this. Search for URA3 in the search box on the top left corner. You will then see the summary page for this gene (below).

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Question 2:

What is the systematic name for URA3?

For S. cerevisiae there is a convention to write active genes in upper case like “URA3” and use lower case “ura3” for a gene that is inactive.

See lines two and three in the table below (Table 2 from "Getting started with yeast").

Gene symbol	Definition
ARG+	All wild-type alleles controlling arginine requirement
ARG2	Locus or dominant allele
arg2	Locus or recessive allele conferring an arginine requirement
arg2-	Any arg2 allele conferring an arginine requirement
ARG2+	Wild-type allele
arg2-9	Specific allele or mutation
Arg+	Strain not requiring arginine
Arg-	Strain requiring arginine
Arg2p	Protein encoded by ARG2
Arg2 protein	Protein encoded by ARG2
ARG2 mRNA	mRNA transcribed from ARG2
arg2-∆1	Specific complete or partial deletion of ARG2
ARG2::LEU2	Insertion of the functional LEU2 gene at the ARG2 locus; ARG2 remains functional and dominant
arg2::LEU2	Insertion of the functional LEU2 gene at the ARG2 locus; arg2 is or became nonfunctional
arg2::KanMX4	Insertion of the functional KanMX4 gene at the ARG2 locus; arg2 is or became nonfunctional
arg2-10::LEU2	Insertion of the functional LEU2 gene at the ARG2 locus, and the specified arg2-10 allele which is nonfunctional
cyc1-arg2	Fusion between the CYC1 and ARG2 genes, where both are nonfunctional
PCYC1-ARG2	Fusion between the CYC1 promoter and ARG2, where the ARG2 gene is functional

There is a link on the left side of the page called “phenotype” (Fig 4). This link will take us to a short text describing the observable consequences of deleting the gene.

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Question 3:

The phenotype of a deletion of the URA3 gene includes auxotrophy for a certain compound. Which one? Read the text at the top of the page after clicking on the “phenotype” link as described above.

Question 4:

What is the standard name for gene YCL018W? The deletion of the gene produces auxotrophy for a certain compound, which one?

In the laboratory, mutant strains are most often used. A popular strain is a strain called “CEN.PK2-1C”. It has the genotype described by this string:

MATa; his3D1; leu2-3_112; ura3-52; trp1-289; MAL2-8c; SUC2

The MATa refers to the mating type, which is this case is a. There are also strains of the α mating type.

Question 5

The CEN.PK2-1C need four compounds in the growth media which wild-type yeast does not. Which are these four compounds?

Use what you learned about yeast gene nomenclature and how to find phenotype information.

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Using the link Retrieve Sequences on the right side, you can obtain sequences associated with the gene. Scroll down the page for view the sequence (below).

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Question 6:

The partial seguid for the LEU2 ORF is ldseguid=88shvf and the length is 1095 bp. What is the complete checksum?

Click on the “Protein” tab in order to find out information regarding the protein encoded by the gene.

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Question 5:

What is the EC Number of the protein? EC stands for Enzyme commission, and the EC number is a classification of enzymes by the reaction they catalyze.

Question 6:

What is the molecular weight (Da) of the protein encoded by LEU2. Tip! Search the page (Ctrl-F) for “weight” and you will quickly find what you are looking for.

Question 7

This is an individual question for each student. Go the the Google Spreadsheet for this exersice. Find your name in the "Name" column. The column called Standard gene name contains a standard name for a yeast gene. Your task is to download the coding sequence for this gene from SGD (http://www.yeastgenome.org) and calculate the ldseguid checksum for this sequence. Please answer with seguid checksum as indicated for the first example student “Max Maximus”.

© Björn Johansson 2013 - 2025