This page is part of an undergraduate assignment at Davidson College


My Favorite Yeast Proteins: Understanding the Function of YEL068C and MATA1.

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The mysteries of a gene are not elucidated when only information about genesí nucleotide sequence has been obtained. The sequence can give clues to a genesí function, but it cannot reveal the full story. The protein products of gene can be post transcriptionally modified, which can change its function. Secrets of a proteins function are better understood by examining its amino acid sequence and by understanding the roles of the proteins that it with which it interacts. This final web project reports the results of database searches about the protein coded by the genes YEL068C and MATA1, and it includes a hypothetical experiment design that could be used to better understand the function of these proteins.

 


 

Stan Fields, Benno Schwikowski & Peter Uetz 2000: PDF files

 

Stan Fields, Benno Schwikowski, and Peter Uetz compiled 2709 interactions among 2039 yeast proteins to generate an integrated protein circuit of 1, 548 proteins.

 

YEL068C: http://www.bio.davidson.edu/courses/genomics/Benno/NB_Figure1color.pdf

This circuit is color coded by lines and boxes surrounding the proteins. The lines represent: red= cellular role and subcellular localization of interacting proteins are identical; blue=localizations are identical but function differ; green=cellular roles are identical but localizations differ; black=cellular role and localization are different or unknown; gray= not explained in paper. The boxes represent: blue= membrane fusion; gray=chromatin structure; green=cell structure; yellow=lipid metabolism; red=cytokinesis; butter color= not explained in paper.

 

YEL068C was located on a remote branch of the circuit but clusters with the proteins coded by DR183W, YDL071C, YGR269W, PRE10, and YNL155W. By using the SGD Full Search search engine, I was able to determine the role of the genes with which YEL068C clusters with in hopes of being able to make an inference about YEL068Cís role. YEL068C only directly interacts with YDL071C, but this gene is unannotated. The line indicated the interaction is gray, which is not explained in the table, so no information is revealed about the nature of the interaction. DR18W, YGR269W, and YNL115W are also unannotated. The SGD revealed that PRE10 is a multipcatalyitc endopepetidase involved in ubiqutin-dependent protein degradation (Hochstrasser 1996).Ubiquitin modification is related to cell cycle, class I antigene processing, signal transduction pathways, receptor mediated endocyctosis, and 26S proteasome degradation of bounded proteins (Hochstrasser 1996). Both YEL068C and PRE10 are connected through a distant circuit involving GNA1 (not pictured). Further investigation could explain YEL068C role by understanding the role of PRE10. YEL068C was in a butter colored box, which has no explanation associated with it, and thus no information on the protein could be derived through this option.

MATA1: http://www.bio.davidson.edu/courses/genomics/Benno/NB_Figure1color.pdf

This circuit is color coded by lines and boxes surrounding the proteins. The lines represent: red= cellular role and subcellular localization of interacting proteins are identical; blue=localizations are identical but function differ; green=cellular roles are identical but localizations differ; black=cellular role and localization are different or unknown; gray= not explained in paper. The boxes represent: blue= membrane fusion; gray=chromatin structure; green=cell structure; yellow=lipid metabolism; red=cytokinesis; butter color= not explained in paper.

 

A1 is in a butter-colored box and is connected to YIL113W by a gray line. Although it is difficult to determine from the picture, I believe that it may be connected to ALPHA1 too. By completing a SGD Full Search I was able characterize the function of some of the genes clustered around MATA1. MATA2, ALPHA1, and MCM1 are all involved in the mating process. This result supports the research on MATA1, which is included on my MFYG webpage that states that MATA1 is a translation factor that facilitates the switch of yeast mating type. YIL113 is unannotated (SGD 2000). It would be interesting to determine if this gene is involved in the mating type switch. SLT2 is a MAP kinase protein involved in protein amino acid phosphorylation and signal transduction pathways in the nucleus (Lee 1993). It is possible that this gene may be involved in signaling to insight the mating type switch, but that assumption is unclear. ANP1 is a protein amino acid glycosylation, which is located in the endoplasmic reticulum and aids in retention of glycosyltransferases in the Golgi as well as osmotic sensitivity (SGD 2000).†† I am not sure how this could relate to the mating type switch.

 

 

I also searched the several pdf files that are based on experiments surrounding the processes of aging, degradation, and membrane formation for the genes YEL068C and MATA1. YEL068C is on circuit for the aging, degradation, and membrane formation experiments. It clustered and interacted with the same proteins for all their targeted circuits.

Aging circuit: http://www.bio.davidson.edu/courses/genomics/Benno/aging.pdf

Membrane circuit: http://www.bio.davidson.edu/courses/genomics/Benno/membrane.pdf

Degradation circuit: http://www.bio.davidson.edu/courses/genomics/Benno/degradation.pdf

 

 

YEL068C

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This figure is color coded by the following: Aging: Gray, Pol-II-transcription: LightBlue, Protein-translocation: Yellow, Protein-synthesis: OrangeRed, Other: EmeraldGreen, Phosphate-metabolism: Black, Vesicular-transport: IndianRed, Cytokinesis: LightGray

 

YEL068C clustered with the same group of genes in each of the targeted circuits and was located in the same remote location. The color box surrounding provides no additional information about the protein. Thus, I do not believe that it has much to do with the aging, degradation, or membrane formation processes.

 

MATA1

This figure is color coded by the following: Aging: Gray, Pol-II-transcription: LightBlue, Protein-translocation: Yellow, Protein-synthesis: OrangeRed, Other: EmeraldGreen, Phosphate-metabolism: Black, Vesicular-transport: IndianRed, Cytokinesis: LightGray

 

MATA1 is located directly behind A2 (MATA2). Thus I am unable to determine the color of the box surrounding it and cannot use the color to make inferences about the protein function. I also was unable to determine which genes it directly interacted with as denoted by a line. I can tell that it is located near the center of the circuit and clusters with A2, ANP1, MCM1, YIL113, ALPHA1, SLT2.


Yeast Two Hybrid Database

 

The Yeast Two Hybrid Database was developed by Uetz et.al. MATA1 is not listed on this database, but YEL068C is a reported bait protein.

 

YEL068C (prey) interacts with YDL071C (bait).YDL071C is yet to be annotated (YPD 2000) so it is impossible to make any assumptions about the function of YEL068C based on this interaction.

 


Triples Database

 

The Triples Database is a database of TRansposon-Insertion Phenotypes, Locationization, and Expression in Saccharomyces. By utilizing a transposing based approach, researchers are able to develop three types of function data: 1) when a gene is expressed during the cell cycle, 2) disruption phenotypes, and 3)subcellular localization.

 

YEL068C and MATA1 are not in Triples Database.

 


Database for Interacting Proteins (DIP)

 

This database reveals protein-protein interaction for a queried gene. My search on DIP yielded no results for YEL068C and MATA1.

 


Enzymes and Metabolic Pathways Database (EMP)

 

This database allows you to enter a substrate and find out what metabolic pathway it is involved in. My search for YEL068C and MATA1 yield no results on EMP database.

 


WIT Database

 

WIT reveals protein function and the metabolic pathway it is involved with for multiple organisms. WIT did not produce any results for YEL068C and MATA1.

 


 

Snyder: Kinase Functionality

This database consists of data derived from protein chips of kinases. YEL068C and MATA1 are not included. It is not surprising MATA1 is not included because it is not a kinase. Just because YEL068C is not included on this database does not allow the assumption that YEL068C is not a kinase because YEL068C may not have been included on the protein chip.



Conclusions

 

The results produced for MATA1 from the Fields, Schwikowski, and Uetz PDF files are consistent with the expected function as a protein involved in the mating type switch. However, I was disappointed to discover that MATA1 was not included on many of the other databases.

 

The results produced for YEL068C by the Fields, Schwikowski, and Uetz PDF files and the Yeast Two Hybrids really revealed little about the function of the protein mainly because the only protein YEL068C interacts with is also unannotated.

 



Hypothetical Experiment to Better Understand the Protein Function of YEL068C

 

In order to understand the function of YEL068C, I would like to crystallize the protein. This process would be very difficult. First 1 milligram of YEL068C would need to be purified. To purify such a large quantity of the protein you would need to overproduce it, perhaps by cloning in an extra copy and growing large cultures. Then you would need to lyse the cells and purify. Then, I would use nuclear magnetic resonance (NMR) to determine the location of the atoms. From this model, I would look for unique folding patterns and molecules. Perhaps the conformation and unique folding patterns and/or molecules could suggest possible targets for the protein or it would resemble a class of proteins with a unique function.

 

 

References

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