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


My Favorite Non-Annotated Yeast Gene: YGR058W
 

GENERAL INFORMATION AND LOCATION





My favorite non-annotated yeast gene is also located on chromosome 7 between bases 596137 and 617144 (as seen on the map below provided by yeastgenome.org. ).  An open reading frame in this region codes for a unknown protein product.  This 335 amino acid protein is found in several species of yeast.  The Molecular, biological, and cellular mechanisms for this protein have not been discovered.  Swiss Prot merely labels this proteins as žhypothetical 38.4 kDa protein in MUP1-SPR3 intergenic regionÓ. (Swiss Prot)
 

FIGURE 1 - This image from yeasstgenome.org shows the chromosomal location of YGR058W


 
 
 
 
 
 

Amino Acid Sequence for YGR058W:
 

MCAKKLKYAAGDDFVRYATPKEAMEETRREFEKEKQRQQQIKVTQAQTPNTRVHSAPIPLQTQYNKNRAE
NGHHSYGSPQSYSPRHTKTPVDPRYNVIAQKPAGRPIPPAPTHYNNLNTSAQRIASSPPPLIHNQAVPAQ
LLKKVAPASFDSREDVRDMQVATQLFHNHDVKGKNRLTAEELQNLLQNDDNSHFCISSVDALINLFGASR
FGTVNQAEFIALYKRVKSWRKVYVDNDINGSLTISVSEFHNSLQELGYLIPFEVSEKTFDQYAEFINRNG
TGKELKFDKFVEALVWLMRLTKLFRKFDTNQEGIATIQYKDFIYATLYLGRFLPH


STRUCTURE







To predict the structure of this nonannotated protein I visited the PREDATOR site.  Using the amino acid sequence I found through NCBI, PREDATOR predicted the protein's secondary structure to contain 40% alpha helices, 51% random coils and 7.76% extended strands.
 

FIGURE 2 - This figure shows the PREDATOR predicted secondary structure of the unknown protein.
 
 



 
 
 
 

 
To get a better sense of this protein's 3D structure and possible cellular location, I used the Kyte-Doolittle site to predict possible transmembrane regions in the unknown protein's sequence.  According to the Kyte-Doolittle Hydropathy plot this protein appears to have one definite transmembrane region and one possible transmembrane region.  Thus, it is possible that this protein is a membrane protein of some sort.
FIGURE 3 - This image from the Kyte-Doolittle site predicts from an amino acid sequence the potential for transmembrane regions within the protein.  A score about 1.8 indicates a likely transmembrane spanning region.  The unknown protein YGR058W has two such regions

 
 

FUNCTION

To ascertain the function of this protein I searched for similar homologous proteins that could possibly reveal the biological and molecular function of this unknown protein.  Using Blastp and the amino acid sequence, I searched for similar proteins within the NCBI database.  Unfortunately, there were no homologous proteins found. (Blastp results) I then attempted to find any conserved domains for this unnamed protein, hoping this would reveal a possible family of proteins to which the unknown protein belongs.  While there was one region conserved with another gene (called COG5126) it had a poor e-value (Conserved Domain Search).  Finally, I ran the amino acid sequence on NCBI's tBlastn search.  This search resulted in more promising results.  The amino acid sequence had high similarity (e-127) to a gene called žSaccharomyces cerevisiae sporulation-specific septin (SPR3) geneÓ.(NCBI Nucleotide page for this gene) This 2965 base pair gene is also located on chromosome 7 and produces a 512 amino acid protein called sporulation specific septin. NCBI notes that this gene belongs to a family of bud neck microfilaments found in yeast.  Thus, this gene is involved in the structural formation of budding yeast cells.  From this limited information the relationship between this protein and the unknownYGR058W is difficult to determine.   Yet, this finding brings this protein one step closer to characterization.


CITATIONS
Swiss Prot Homepage http://us.expasy.org/sprot/
yeastgenome.org http://db.yeastgenome.org/
NCBI Nucleotide/Protein Databases http://www.ncbi.nlm.nih.gov/
PREDATOR http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_preda.html
Kyte-Doolittle Hydropathy Plot http://occawlonline.pearsoned.com/bookbind/pubbooks/bc_mcampbell_genomics_1/medialib/activities/kd/kyte-doolittle.htm
 


GENOMICS HOMEPAGE

Contact: altrzebucki@davidson.edu