This web page was produced as an assignment for an undergraduate course at Davidson College.
MY FAVORITE YEAST GENES
Figure1. Section of S. cerevisiae chromosome 7 showing the location of both Msp1 and YGR031W.
Msp1 is a Saccharomyces cerevisiae gene located on the seventh chromosome from base pairs 542204 – 543292. The gene consists of one exon that is 1089 base pairs and 362 amino acids in length (SGD, accessed October 7, 2003; http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=msp1). Nakai et al (1993) first reported msp1 in a paper published in The Journal of Biological Chemistry. They found that MSP1, although important, was not essential for either cell growth or mitochondrial functions in yeast because the homozygous null mutant is viable (Nakai et al 1993).
Figure 2. Picture from Nakai et al (1993) showing the sequence of MSP1 and the subsequent amino acid sequence. In addition, the restriction enzyme sites, the putative membrane spanning domain and the putative nucleotide binding domain are shown. (permission pending)
Msp1 is an ATPase of the putative AAA ATPase family. Figure 3 shows the physical structure of 1e32, a member of the ATPase family whose structure is similar to that of MSP1.
Figure 3. Physical structure of 1e32, a gene that encodes an ATPase similar to MSP1. (picture from PDB)
Msp1 is responsible for the translocation of proteins into the mitochondria. In the presence of a translocating chain, the outer membrane import machinery (MOM complex) and the inner membrane import machinery (MIM complex) form translocation contact sites as a part of the membrane preprotein import machinery (Gene Ontology, accessed on October 7, 2003; http://db.yeastgenome.org/cgi-bin/SGD/GO/go.pl?goid=6628). Therefore, Msp1 functions as part of a chain across the mitochondrial membrane to import proteins (see Figure 4).
Figure 4. Hydropathy plot for MSP1 using the amino acid sequence, showing the transmembrane domain at the beginning of the protein. (image from Kyte-Doolittle)
Msp1 is localized to the outer mitochondrial membrane. MSP1 interacts with the cytoplasm to allow the preproteins from the cytoplasm to be translocated (as mentioned above) into the mitochondria. MSP1 is an integral membrane protein with one membrane spanning domain towards the beginning of the protein (see Figure 2).
Since there is nothing known about this gene yet, I started with the nucleotide sequence (see Figure 5) and the amino acid sequence.
Figure 5. The nucleotide sequence for YGR031W. (picture from SGD)
Using the amino acid sequence, I did a conserved domain search (NCBI) and found that YGR031W has several conserved domains (see Figure 6).
Figure 6. Results from a conserved domain search with the amino acid sequence of YGR031W. (picture from NCBI's conserved domain database)
The domain 'abhydrolase' is a very common domain among a wide range of proteins, an alpha/beta hydrolase fold. The abhydrolase is a catalytic domain. The 'MhpC' domain is for the hydrolase superfamily, and corresponds to the abhydrolase domain. The 'pldB' indicates a lysophospholipase domain. A lysophospholipase is an enzyme that catalyses the hydrolysis of a single fatty acid ester bond in lysoglycerophosphatidates with the formation of glyceryl phosphatidates and a fatty acid (Medical dictionary search engine).
In addition, I performed a Kyte-Doolittle Hydropathy Plot with the amino acid sequence (see Figure 7). The Hydropathy plot shows predicted transmembrane domains within the protein sequence. From the hydropathy plot, there are four potential transmembrane domains in YGR031W.
Figure 7. Kyte-Doolittle Hydropathy Plot for YGR031W. The green line shows the hydropathy of the protein; the red line indicates the threshold for transmembrane domains. there are 5 potential transmembrane domains for this protein. (picture from Kyte-Doolittle)
Figure 7. Predator image of YGR031W. The purple shows random coils, the blue shows alpha helicies, and the red shows extended strands. (image from Predator)
Looking at the Predator image there are seven sections of alpha helicies in this protein and ten clumps of extended strands. According to SCOP (structural classification of proteins), the family of lypophospholipases have common core that is decorated with many additional structures and mixed beta-sheet of 9 strands, with strands 4, 6 and 8 are antiparallel to the rest. The extended strands in the Predator image may correspond to beta-sheets in this case, lending strength to the idea that YGR031W belongs to the lysophospholipase family.
Based on the conserved domain and the predator image, I propose that YGR031W is a lysophospholipase embedded across a membrane in the cell, perhaps the Golgi or the ER.
Protein Data Base, <www.pdb.org>
Nakai, M, E Toshiya, H Toshiharu, H Matsubara. 1993. Intramitochondrial protein sorting: isolation and characterization of the yeast MSP1 gene which belongs to a novel family of putative ATPases. Journal of Biological Chemistry 268(32):24262-24269.
SGD (Saccharomyces Genome Database), <http://www.yeastgenome.org>
Questions or comments?: e-mail Sarah Baxley