This web page was produced as an assignment for an undergraduate course at Davidson College.
MBP1 and YDL057W: Yeast Proteins
In this assignment I will analyze the protein products of the Saccharomyces cerevisiae genes MBP1 and YDL057W, which are annotated and non-annotated, respectively. Information about the genes MBP1 and YDL057W can be found here while information about the protein expression of MBP1 and YDL057W can be found here. Throughout this assignment, my own observations will be enclosed in purple-outlined boxes.
MBP1 is short for MluI-bow Binding Protein and it is a transcription factor composed of 833 amino acids. The transcription factor has a molecular weight of 93,907 Da and is involved in the regulation of the cell cycle as it progresses from the G1 phase to the S phase. It has an isoelectric point of 9.27 (MIPS).
Figure 1. Gene ontology information from NCBI Gene. Shows the molecular function, biological process, and cellular component of MBP1.
The structure of the protein can be visualized below (Figure 2).
Figure 2. The structure of MBP1 in both "protein" (A.) and "cartoon" (B.) forms, from the Protein Data Bank.
Now let's look at how MBP1 interacts with other proteins. The Database of Interacting Proteins (DIP) provides us with a circuit diagram of MBP1's interactions:
Figure 3. MBP1 protein interactions. A. A circuit diagram of MBP1's protein interactions. The two nodes connected to MBP1 are Swi6, with the thicker green line, and SKN7, with the thin green line. The red line shows the unverified results of high-throughput methods, linking MBP1 to FKH1. We will learn more about Swi6, SKN7, and FKH1 later. B. Legend for the circuit diagram. From DIP.
Figure 4. This chart, from the Saccharomyces Genome Database (SGD), shows all the known interactions of MBP1. MBP1 was used as the bait in Affinity Chromatography and Affinity Precipitation experiments 6 separate times (Koch et al. 1993, Siegmund and Nasmyth 1996, Winzeler et al. 1999, and Gavin et al. 2002). In all of these experiments, MBP1 attracted the protein Swi6p. In another study using Affinity Precipitation, a protein called FKH1P was used as the bait and attracted protein MBP1 (Ho et al. 2002). It is unclear why SKN7's interactions with MBP1, as found by DIP are not included in this table. There are no known genetic reactions.
Here is the basic information for the three proteins found to have physical interactions with MBP1. As mentioned in previous assignments, MBP1 and one of the genes it is found to interact with, Swi6, code for the proteins that make up what is called the "MCB-binding factor (MBF)." The MBF then "binds to [...] so-called MCB (MluI cell-cycle box) [...] and activates the transcription of [genes] at the G1--> S phase transition" (Xu et al. 1997).
Figure 5. Basic information for the protein Swi6, which forms a complex with MBP1 to regulate the G1 --> S progression in the cell cycle. From SGD.
Figure 6. Basic information for FKH1, which encodes forkhead protein. FKH1 physically interacts with MBP1 and is shown here to be involved in regulation of the cell cycle, as is MBP1. From SGD.
SKN7 is a transcription factor, like MBP1. It is involved in osmoregulation.
Figure 7. Basic information for Skn7p, From SGD.
According to the GO Term Finder, Swi6 is mapped to some of the same molecular functions, biological processes, and the same cellular component as MBP1 (Figure 6), as you would expect from their interactions. In addition, FKH1 is mapped to some of the same molecular functions, biological processes, and the same cellular component as MBP1 (Figure 6), indicating that it probably closely interacts with MBP1 as well.
Figure 9. The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides a circuit diagram of the cell cycle in S. cerevisiae. MBP1 is highlighted in red. In this diagram, its interaction with Swi6 to form the MBF is shown. The phase of the cell cycle is noted at the bottom of the diagram, and as aforementioned, MBP1 acts to transition the cell from the G1 phase to the S phase. While I searched for circuit diagrams that included FKH1 or Skn7p, the other proteins that physically interact with MBP1, I was unable to find any.
MBP1 appears in the document 'Degradation.pdf' that depicts a circuit diagram of proteins involved in degradation (Figure 9). It is colored yellow, indicating that it is involved in 'RNA-processing/modification."
Figure 10. One section of the degradation circuit diagram. A. Legend explaining the colors of the boxes. B. MBP1 appears in a light yellow (almost white in this image) box with the text highlighted in blue in the center of the image. From Degradation.pdf.
I also searched the TRIPLES (TRansposon Insertion Phenotypes, Localization and Expression in Saccharomyces) database for information on MBP1.
Figure 11. TRIPLES results for MBP1. As you can see, when a transposon interrupted the MBP1 gene, rendering it inactive, only two treatments showed growth different from that of the wild-type: 20Ben and HapTra. 20Ben is "Benomyl resistance as assayed by growth on YPD + 20mg/ml benomyl" and HapTra is "Cell inviability of haploid transformants." The list of assays has been abbreviated for space, but all assays that were omitted showed no significant change from the wild-type.
I also searched the PROWL database for information on MBP1, but it did not provide any new insights.
Finally, I searched Stan Fields' lab's yeast two-hybrid (Y2H -- method described below) results, but found no information on MBP1.
YDL057W is a non-annotated gene located right beside MBP1 on chromosome IV of the S. cerevisiae genome. It encodes a hypothetical protein, and hereafter "YDL057W" will refer to this hypothetical protein rather than the gene itself.
According to MIPS, the produced protein is 328 amino acids long with an isoelectric point of 7.14 and a molecular weight of 36,687 Da. The biological process, molecular function, and cellular component of YDL057W are currently unknown.
YDL057W yielded no results in the Protein Data Bank, which is to be expected, since it is not an annotated gene and therefore its protein product is unknown.
An SGD interactions search for YDL057W yielded no known physical or genetic interactions, indicating that research has not begun in earnest on this hypothetical protein. In addition, while DIP has YDL057W in its database, there is no graphic representation of any interactions.
I also searched the TRIPLES (TRansposon Insertion Phenotypes, Localization and Expression in Saccharomyces) database for information on YDL057W.
Figure 12. TRIPLES results for YDL057W. As you can see, when a transposon interrupted the YDL057W gene, rendering it inactive, none of the treatments showed growth different from that of the wild-type. The list of assays has been abbreviated for space, but all assays that were omitted showed no significant change from the wild-type.
I also searched the PROWL database for information on YDL057W, but it did not provide any new insights.
Finally, I searched Stan Fields' lab's Y2H results, but found no information on YDL057W.
DIP. Database of Interacting Proteins. <http://dip.doe-mbi.ucla.edu/dip>.
Expression Connection. <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl>.
KEGG. Kyoto Encyclopedia of Genes and Genomes. <http://www.genome.jp>.
MIPS. Munich Information Center for Protein Sequences. <http://mips.gsf.de/genre/proj/yeast/search_index.jsp>.
NCBI Gene. <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>.
PDB. Protein Data Bank. <http://www.rcsb.org/pdb>.
SGD. Saccharomyces Genome Database. <http://www.yeastgenome.org>.
SGD Gene Ontology Term Finder. <http://db.yeastgenome.org/cgi-bin/GO/goTermFinder>.
TRIPLES. TRansposon Insertion Phenotypes, Localization and Expression in Saccharomyces. <http://ygac.med.yale.edu/triples/triples.htm>.
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Please Contact Julie Ruble with any questions or comments.