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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.
1http://genome-www4.stanford.edu/cgi-bin/SGD/protein/protein?sgdid=S0005182
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
6 http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=kex2
7 http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=7443
8 http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=8020
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
Send comments, questions and suggestions to edhaas@davidson.edu
Many thanks to Dr. A. Malcolm Campbell for his guidance in this endeavor as well as others.