This web page was produced as an assignment for an undergraduate course at Davidson College.

MY FAVORITE YEAST PROTEINS

Known: AUS 1

Unknown: YOR012W

 

Fig. 1 Picture of Chromosome XV.  Both AUS 1 and YOR012W are closely located on this chromosome of Saccharomyces Cerevisiae. (Permission pending from SGD, <http://genome-www4.stanford.edu/cgi-bin/SGD/ORFMAP/ORFmap?sgdid=S0005537> )

                                                                                                                                                                                                                                                        

The Known Gene: AUS1/ YORO11 W

 

Where is AUS 1 located on the chromosome?

            AUS 1 is located on Chromosome 15 between 349678 and 353862.  It is part of the first exon (SGD, <http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?featureName=YOR011W>). 

 

What is the DNA and protein sequence of AUS 1?

The genomic DNA sequence for AUS 1 can be viewed at the SGD site (<http://genome-www4.stanford.edu/cgi-bin/SGD/getSeq?seq=YOR011W&flankl=0&flankr=0&map=a3map>).  

The protein sequence for AUS1 can be viewed at the SGD site (<http://genome-www4.stanford.edu/cgi-bin/SGD/getSeq?seq=YOR011W&flankl=0&flankr=0&map=p3map >).

 

Where in the cell is this protein expressed?

        This protein is expressed in the cellular membrane (SGD, <http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?featureName=YOR011W>) .

 

What is the Biological Function & Process of the AUS 1 gene?

            AUS 1 is a protein found in yeast that serves as an ATP- Binding Cassette transporter (ABC transporter).  ABC proteins are the largest family of proteins.  Its primary function is to transport sterols from the endoplasmic reticulum to the plasma membrane.  Since the concentration of sterols is the highest in the plasma membrane, this protein works against the concentration gradient (Menon, 2002, <http://www.biochem.wisc.edu/menon/>).  In order to pump these proteins against the gradient, the transporter must bind ATP (Locer, 2002, <http://www-ssrl.slac.stanford.edu/research/highlights_archive/Rees_ABC.html >).

    For more information regarding sterols, check out these websites:

     At the present time, scientists are unsure of the exact mechanism of how this process works, though there are many laboratories that are currently investigating this question.

 

What happens if there is a mutation in AUS 1?

            A cell with a mutated AUS 1 gene is still viable.  The only observed phenotype difference between a mutated and wild type cell is that the mutated cell does not show as high cholesterol accumulation as the wild type (SGD, <http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?featureName=YOR011W> and Wilcox et al, 2002). 

 

Are there any orthologs of this gene? 

            The SGD (<http://genome-www.stanford.edu/cgi-bin/SGD/Sacch3D/getblast?name=YOR011W&db=mammal>) revealed similarities to proteins found in humans, mice, rats, and sheep.  Entrez protein (<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein>) showed many similarities in a wide variety of bacteria.    

                

Why do we want to learn about this gene?

Yeast are being used in order to better understand the mechanics of cholesterol transfer in humans.  Thus, by understanding the cellular processes in yeast, scientists may be able to understand this process in humans.  Perhaps such knowledge would lead to a better understanding of the effects of sterols in human cells.

 

                                                                                                                                                                                                                               

The Unknown Gene: YOR012W

 

Where is this gene found?

            The YOR012W gene is found on Chromosome 15 in Saccharomyces Cerevisiae between 356542 and 356955.  It is located in the first exon (SGD, <http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?featureName=YOR012W>). 

 

What is the structure of this protein?

            Predator (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_preda.html) predicts that the structure of the protein is 42.34% Alpha helix, 9.49% extended strand and 48.18% random coil.

 

Where is the protein located in the cell?

            The location of the protein is dependent upon a number of factors. First, the function of the protein may help to determine where the protein is located.  Since the function of this protein is unknown, it cannot be used to determine its location.

            Another factor that plays a role in the location of a protein depends on the proteins relation to water- if it is hydropathic or hydrophilic.  A good way to determine the hydropathy rating for a protein is to use a Kyte-Doolitte hydropathy plot (http://occawlonline.pearsoned.com/bookbind/pubbooks/bc_mcampbell_genomics_1/medialib/activities/kd/kyte-doolittle.htm).  The plot for this protein is shown below in figure 2:

           

                   

            Figure 2.  This Kyte-Doolitte plot shows a red line at 1.8.  This protein does not cross the red line at any point in the graph. (Permission pending)

            Because the plot of the YOR012W protein remains below 1.8, it is safe to assume that the protein is not a transmembrane protein.  Thus, it is possible that this protein is located in the cytoplasm. 

 

Are there any orthologs of this protein in other animals?

            BLAST found no similarities in any yeast or worm proteins  (BLAST, <http://genome-www.stanford.edu/cgi-bin/SGD/worm/getblast2.pl?name=YOR012W&db=worm>). 

            BLAST found that the YOR012W protein is similar to Mouse proliferin (p= 0.52), Human proliferin (0.64), and Human prolactin (0.996). 

            In humans, the proliferin protein is related in sequence to the hormone prolactin.  These proteins are regulated by growth factors and typically secreted by fetal and adult cells.  The proteins are thought to be involved with message carrying between the fetus and the mother during pregnancy.  Typically, these messages would stimulate uterine growth, though scientists are not exactly sure of the mechanics of this process (Nielson-Hamilton, http://www.bb.iastate.edu/faculty/nilsham.html)

 

What could be the function of this protein?

Before hypothesizing the function of the protein, the YOR012W gene must be proven to be in a coding region of the genome. Further analysis of this sequence would have to be performed before such conclusions can be drawn.  For now, lets assume that it is in a coding region.  

Though this proteinís sequence is similar to proteins associated with uterine growth during pregnancy in mammals, there is no such process in yeast.  Thus, this is probably not the proteinís exact function.  The protein may still be associated with growth and reproduction and perhaps is used to trigger cell division during replication. 

                                                                                                                                                                                                                               

 

References:

Locher, K; Douglas, A.; Caltech R. 2002.  ABC Transporter Aritchture and Mechanism. http://www-ssrl.slac.stanford.edu/research/highlights_archive/Rees_ABC.html  Accessed 10-3-02

Menon, A. 2002. Department of Biochem at UW-Madison.  Membrane biogenesis; biosynthesis of glycosyl-phosphatidylinositol anchored membrane proteins; transbilayer movement of phospholipids; intracellular sterol transport.  http://www.biochem.wisc.edu/menon/ Accessed 10-3-02.

Phillips, T.; Brinen, L.  X-Ray Crystal Structure ofA Bacterial ATP-Binding Cassette Transporter Determined at 4.5 A.  http://www-ssrl.slac.stanford.edu/research/highlights_archive/g_chang.html  Accessed 10-3-02.  

  Wilcox, L.; Balderes, D.; Wharton B.; Tinkelenberg, A.; Rao, G.; Sturley, S. 2002. Transcriptional Profiling Identifies Two Members of the ATP-binding Cassette Transporter Superfamily Required for Sterol Uptake in Yeast.  J Biol Chem. Vol 277 No. 36.  pp. 32466-32472.  

-----.  Margaret Nilsen-Hamilton: Professor of Biochemsitry and Molecular Biology. Iowa State University.  http://www.bb.iastate.edu/faculty/nilsham.html Accessed 10/4/02.

 


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