This web page was produced as an assignment for an undergraduate course at Davidson College.
My Favorite Yeast Genes: OLE1and YGL052W
Ole1 and YGL052W are genes found in yeast Saccharomyces cerivisiae. This webpage provides details of both the annotated Ole1 gene and the non-annotated YGL052W gene.
The Annotated Gene: OLE1
Ole1 is located on Chromosome VII of the Watson strand in S. cerivisiae (SGD 2004). It has a coding sequence of 1500 base pairs as shown in Figure 1 (SGD 2004).
Ole1 is located on the Watson strand with coordinates 398631 to 400163 shown in Figure 2 (SGD 2004).
Figure 2. Map of Chromosome VII of S.cerivisiae showing genes ole1 (red) and its non-annotated neighbor YGL052W (red) on the Watson strand from Saccharomyces Genome Database (SGD).
Ole1 encodes the protein delta 9-desaturase (also called stearoyl-CoA desaturase, Acyl-CoA desaturase, fatty acid desaturase or stearoyl-CoA 9-desaturase) (Expasy 2004). It has a molecular weight of approximately125,704 kDa and a theoretical pI of 5.01 (Expasy 2004).
Delta-9 Desaturase is known to catalyze the formation of double bonds between C9 and C10 of palmitoyl and stearoyl CoA (Stukey et al. 1989). Introduction of the double bond in this locus involves the removal of two electrons and Hydrogen atoms from the saturated fatty acid chain thereby making it an unsaturated fatty acid. The two electrons are transferred from NADPH to an Oxygen molecule via cytochrome b5 and b5 reductase (Bossie et al. 1989).
Approximately 70% of the fatty acids in the cell membrane of S. cerivisiae consist of unsaturated fatty acids such as palmitoleic (16:1) and oleic (18:1) (Bossie et al., 1989). The remaining fatty acids are saturated, mostly palimitic (18:0), stearic (16:0) and myristic (14:0) (Bossie et al., 1989). With the action of delta 9-desaturase on these saturated precursors, the ratio of saturated to unsaturated increase over time (Bossie et al., 1989). The amino acid sequence for delta 9-desaturase is shown in Figure 3.
Figure 3. ORF translation of S. cerivisiae gene ole1 showing amino acid sequence of delta 9-desaturase from Saccharomyces Genome Database.
A BLASTn, Figure 3 and 4, for delta 9-desaturase showed high sequence homology with the following organisms such as Kluyveromyces lactis, Candida glabrata, Kluyveromyces thermotolerans and Sachharomyces kluyveri (NCBI 2004).
Figure 4.BLASTm Aligments of the query sequence with 78 BLAST hits i.e. organisms whose DNA sequence can be aligned with sequence of ole1 gene in S. cerivisiae.
Figure 5. Table showing list of some blast hits from BLASTn search of ole1 sequence from S. cerivisiae. Lower expect values indicate the extent to which the similarity between a certain species and S. cerivisiae at this locus is not due to chance.
Ole1 has homologous counterparts in organisms such as mice, rats, fruitflies, C. elegans and so on seen in Figure 6.
Figure 6. Homologous genes of ole1 in other organisms.
A PDB search for the structure of the product of ole1 gave no results (PDB 2004). The stucture of the protein delta-9 desaturase has probably not been determined.
The Non-Annotated Gene: YGL050W
YGL050W is located on the Watson strand of Chromosome VII between coordinates 405779 to 406600 (SGD 2004). It has a coding sequence of 306 base pairs shown in Figure 7 (SGD 2004). The translated amino acid sequence of YGL052W is shown in Figure 8 (SGD 2004).
Figure 7. Coding sequence of YGL050W obtained from Saccharomyces Genome Database. 1997. Homepage. < http://www.yeastgenome.org/> Accessed October 18, 2004.
Figure 8. ORF translation of S. cerivisiae gene ole1 showing amino acid sequence of delta 9-desaturase.
A BLASTn search showed alignments of YGL052W with 37 other sequences within the same and related organisms shown in Figure 9 and 10 (NCBI 2004). Moreover, the gene in the top few BLAST hits with low expect values (order of e-171) correspond to the Tandem VII locus in the same species. A PubMed search did not yield any relevant results for the Tandem VII locus and therefore, it is difficult to gain information on potential sequence matches of YGL052W with other gene sequences (PubMed 2004).
Swiss-Prot provides valuable information on the protein product of YGL050W (Expasy 2004). The theoretical pI calculated by from this site is 5.17 and the hypothetical molecular weight is 66383 kDa (Expasy 2004). Its molecular formula is C2485H4150N822O1032S135.
Ole1 produces delta-9-desaturase whose molecular function, biological process and cellular component are known and therefore, listed above. YGL052W is a non-annotated S. cerivisiae gene that possibly encodes a transmembrane protein but whose function it is difficult to predict given since I could find no homologs and, furthermore, could not find information on the BLAST hits from other organisms.
Bossie, M. A., and C. E. Martin. 1989. "Nutritional regulation of yeast delta-9 fatty acid desaturase activity." Journal of Bacteriology. 171(12): 6409-13.
Expasy. 2004. <http://www.expasy.org/>. Accessed 8 Oct, 2004.
Kyte-Doolittle Hydropathy Plot. 2004. <http://occawlonline.pearsoned.com/bookbind/pubbooks/bc_mcampbell_genomics_1/medialib/activities/kd/kyte-doolittle.htm>. Accessed 8 Oct, 2004.
NCBI (National Center for Biotechnology Information). 2004. <http://www.ncbi.nih.gov/> Accessed Oct. 8, 2004.
PDB (Protein Database). 2004. <http://www.rcsb.org/pdb/index.html>. Accessed 8 Oct, 2004.
PubMed. 2004. <http://www.pubmed.com/>. Accessed 8 Oct, 2004.
SGD (Saccharomyces Genome Database). 2004. <http//www.yeastgenome.org/>. Accessed 8 Oct, 2004.
Stukey, J. E., McDonough, V. M., and C. E. Martin. 1989. "Isolation and characterization of OLE1, a gene affecting fatty acid desaturation from Saccharomyces cerivisiae." Journal of Biological Chemistry. 264(28): 16537-44.
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