TP08_Saccharomyces_Genome_Database\TP08_Saccharomyces_Genome_Database
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.
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 ? (chromosome number, etc…). Use the same reasoning as for YAR002 above.
Many yeast genes (but not all) have a standard name as well. 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 (Fig 2).
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 shown in (Fig 3)
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.
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 in Fig 4.
Question 4:
The deletion of the gene YCL018W also produces a phenotype. This phenotype is auxotrophy for a certain compound, which one? The leu2 mutant is auxotrophic for which compound?
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 additions to the media which wild-type yeast does not. Which are these four compounds?
Use what you know about yeast gene nomenclature (Fig 3) and how to find phenotype information (Fig 4)
Using the link Retrieve Sequences on the right side, you can obtain sequences associated with the gene.
Select the “Sequence Details” link as shown in Fig 6. Scroll down the page for view the sequence (Fig 7).
Question 6:
Verify the SEGUID for the LEU2 open reading frame (ORF). The first five characters are ezpMk, what are the last five?
Click on the “Protein” tab in order to find out information regarding the
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 “Molecular Weight” and you will quickly find what you are looking for.
Question 7:
This is an individual question for each student. Follow this link that points to a Google Spreadsheet. You should find your name in the leftmost 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 SEGUID for this sequence. Please answer with SEGUID checksum as indicated for the first example student “Max Maximus”.
© Björn Johansson 2020