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My favorite yeast genes
For my favorite annotated yeast gene, I chose SCYNL238W, or kex2. Kex2, also called qds1, vma45, and srb1, is a 2445 bp gene encoding an 814 aa protein called KEX2.1 KEX2 was the first protein to be discovered in a family of enzymes known as the kexin-like proprotein convertases. These enzymes are interesting in that they are all translated with an extended N-terminal sequence that acts as an intramoleclar chaperone, and then cleaves itself from the mature protein.2 The absence of this chaperone region disallows proper folding of the enzyme, and results in the localization of the misfolded protein in the ER. This chaperone region has been shown to be sufficient for proper folding of the protein, even when not covalently bonded to the translation product.3 The mature KEX2 protein catalyzes the processing of the sex pheromone µ-factor, and killer protoxin by cleaving the Arg-Xaa bond in Lys-Arg-Xaa and Arg-Arg-Xaa.4 SGD lists the biological process of KEX2 as under pheromone processing. KEX2 is a membrane bound protein localized to the trans face of the golgi apparatus.5 The KEX2 deletion mutant has been shown to be viable, but does not properly express killer.6 A BLAST search using the DNA sequence demonstrated very little homology to proteins in other species. I knew from my pubmed readings that this was not true, so I performed a BLASTp using the translation sequence. This search produced impressive results. There are numerous homologues in a wide variety of species. A conserved domain search demonstrated two conserved domains, both from the subtilase family of proteins.7,8
For my non-annotated gene, I chose a neighbor of kex2, SCYNL234W. I performed a Kyte-Doolittle hydropathy plot, which predicted that the translation would have no transmembrane domains. While attempting to search in NCBI for the sequence to BLAST, I accidentally searched the locus under PubMed instead of nucleotide. I was surprised to find three articles mentioning the region. One of them simply stated that upon deletion of the region, no phenotype was noticed.9 The other two however, characterized the gene product as a novel heme containing shock protein.10,11 A BLAST search using the DNA sequence showed some sequence similarity with a few other yeast proteins, but none outside the species. The primary protein showing sequence similarity is the yeast global transcription regulator SIN4, which was also listed as TSF3. Intersetingly, SIN4 only shows similarity in the regions away from the heme group. A BLASTp search using the translation sequence showed very little sequence similarity to other proteins, except in a short segment towards the center. This segment showed homology to a vast range of globins, particularly neuroglobin, in a variety of species. A conserved domain search identified this region as a globin domain. These data appear to support the conclusions of the two papers identifying this protein as a novel heme containing shock protein.
2Lesage G, et al. (2000) The Kex2p proregion is essential for the biosynthesis of an active enzyme and requires a C-terminal basic residue for its function. Mol Biol Cell 11(6):1947-57http://genome-www4.stanford.edu/cgi-bin/SGD/reference/geneinfo.pl?locus=KEX2
3Lesage G, et al. (2000) The Kex2p proregion is essential for the biosynthesis of an active enzyme and requires a C-terminal basic residue for its function. Mol Biol Cell 11(6):1947-57http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10848621&dopt=Abstract
4Fuller RS, et al. (1989) Yeast prohormone processing enzyme (KEX2 gene product) is a Ca2+-dependent serine protease. Proc Natl Acad Sci U S A 86(5):1434-8http://genome-www4.stanford.edu/cgi-bin/SGD/GO/go.pl?goid=4290
5Bryant NJ and Boyd A (1993) Immunoisolation of Kex2p-containing organelles from yeast demonstrates colocalisation of three processing proteinases to a single Golgi compartment. J Cell Sci 106 ( Pt 3)():815-22http://genome-www4.stanford.edu/cgi-bin/SGD/GO/go.pl?goid=5802
9 Sartori G, Mazzotta G, Stocchetto S, Pavanello A, Carignani G (2000) Inactivation of six genes from chromosomes VII and XIV of Saccharomyces cerevisiae and basic phenotypic analysis of the mutant strains. Yeast. 2000 Feb;16(3):255-65. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10649454&dopt=Abstract
10 Sartori G, Aldegheri L, Mazzotta G, Lanfranchi G, Tournu H, Brown AJ, Carignani G.(1999) Characterization of a new hemoprotein in the yeast Saccharomyces cerevisiae. J Biol Chem 1999 Feb 19;274(8):5032-7 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9988749&dopt=Abstract
11 Liu Y, Vidanes G, Lin YC, Mori S, Siede W (2000) Characterization of a Saccharomyces cerevisiae homologue of Schizosaccharomyces pombe Chk1 involved in DNA-damage-induced M-phase arrest. Mol Gen Genet 2000 Jan;262(6):1132-46 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10660074&dopt=Abstract
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Many thanks to Dr. A. Malcolm Campbell for his guidance in this endeavor as well as others.