MY FAVORITE ANNOTATED AND UNANNOTATED YEAST PROTEIN
WHEN AND WHERE IS IT EXPRESSED AND WHAT DOES IT DO?
This page was created as an assignment for an undergraduate genomics course at Davidson College.

UNANNOTATED YEAST PROTEIN-YJU3

SUMMARY OF INFO FROM THE PREVIOUS TWO WEB SITES
    Analysis of YJU3ís conserved domains suggest that it is a lysophospholipase.  Lysophospholipases remove the second fatty acid from a phospholipid after the first fatty acid is removed by a phospholipase (Cox, 2000).  Microarray data indicate that the YJU3 gene is strongly induced during a diauxic shift (SGD, 2001). Specifically YJU3 is not induced until glucose levels nearly reach zero.  The data suggest that YJU3 may be involved in the breakdown of phospholipids to produce energy when glucose is not available.

NEW EXPERIMENTS
    The Yale Gerstein Lab used protein macroarrays to discover what proteins bound phospholipids (http://spine.mbb.yale.edu/protein_chips/).  YJU3 was not found to bind to any of the phospholipids tested in this experiment.  Considering YJU3 has highly conserved domains with lysophospholipases, one would have expected that YJU3 would interact with phospholipids.  However, since lysophospholipases cleave the second fatty acid from phospholipids only after the first fatty acid is removed, it would be interesting to redo this experiment using phospholipids that have had the first fatty acid removed.  YJU3 may be found to interact with these modified phospholipids.
    In another experiment, Snyder and his team (2000) created a unique transposon that allowed them to observe when a gene was expressed using a lacZ gene, and where the gene was expressed using an epitope tag.  Among the strains Snyderís lab produced, three strains containing the transposon in the YJU3 gene were created.  The targeted YJU3 genes showed light expression during sporulation and vegetative growth.   No significant phenotype disruptions were observed under the environmental conditions tested by Snyderís lab.  There was also no staining above background levels when grown in YPD medium. http://ygac.med.yale.edu/triples/basic_search.asp
    Considering the microarray data, it may prove advantageous to observe YJU3 transposon mutants undergoing a diauxic shift.  The YJU3 transposon mutants may exhibit abnormal growth and phenotypes when the cell is exposed to these conditions if the YJU3 protein is responsible for providing energy from the breakdown of phospholipids when glucose is depleted.  If YJU3 mutants respond under these conditions, the phenotypes that result may help elucidate the functions of the YJU3 protein.  Also the localization of the YJU3 protein when it is active may be discovered.
    Using a technique developed by Brian Chaitís lab (1999), protein levels of the YJU3 protein between yeast undergoing a diauxic shift and yeast growing in normal conditions could be compared.   For example yeast undergoing a diauxic shift could be grown in a media containing heavy nitrogen and yeast growing under normal conditions could be grown in a media containing light nitrogen.  Then the levels of the YJU3 protein could be evaluated using mass spectroscopy.  If YJU3 is actively translated during a diauxic shift then there should be a significant difference in the amount of YJU3 protein observed between these two conditions.
    Brian Chaitís lab at the Rockefeller University in NYC (1999) also used stable isotopes to observe differences in phosphorylation of a protein between two conditions. This method could be used to discover if the YJU3 protein is phophorylated during a diauxic shift.  If YJU3 is regulated by phosphorylation then there should be a reciprocal change in  the amount of YJU3 protein that is phosphorylated during a diauxic shift.
    If the YJU3 protein is regulated by phosphorylation then it would be useful to use a protein chip to discover what kinase does the phosphorylation using the technique developed by Mike Snyderís lab (2000).  Specifically the YJU3 gene could be spotted in all of the wells on a chip.   Then a different kinase plus radioactive ATP could be added to each well.  A resulting dark spot would suggest that the kinase may be involved in the regulation of the YJU3 protein through phosphorylation. http://bioinfo.mbb.yale.edu/genome/yeast/chip/


 

NO USEFUL INFO FOUND YET

DIP
No information about YJU3 was found.
http://dip.doe-mbi.ucla.edu/dip/Search_DIP.cgi

Two Hybrid
YJU3 was not in the Fieldís lab database for yeast two hybrid experiments.
http://depts.washington.edu/sfields/yplm/data/index.html

Path Calling Interaction Database
A search for YJU3 produced no protein interactions.
http://portal.curagen.com/extpc/com.curagen.portal.servlet.PortalYeastList


ANNOTATED YEAST PROTEIN-SGS1

SUMMARY OF INFO FROM PREVIOUS WEB SITES
    SGS1 is a DNA helicase involved in transcription of rRNA and replication (SGD, 2001). SGS1 is thought to suppress illegitimate recombination and interact with RNA polymerase II during rRNA transcription (SGD, 2001).  SGS1 interacts with Top3, Top2, (YPD protein report, 2001) and srs1 proteins (Lee, 1999) to perform these functions.  SGS1 is also thought to play a role in cell cycle checkpoints (Frei, 2000; McVey, 2001).  SGS 1 is interesting because it is a homologue to the gene that causes Wernerís and Bloomís syndrome in humans (YPD protein report, 2001).  Bloomís syndrome results in increased incidences of cancer, genomic instability, and growth retardation (Watt, 1996).  Wernerís syndrome results in premature aging (Guarente, 1997).  SGS1 in yeast is being used a model for these to diseases.

The Hrdc domain of the SGS1 protein has been crystalized.

From PDB database at http://www.rcsb.org/pdb/cgi/explore.cgi?pid=225481005252650&pdbId=1D8B

NEW INFO
Protein Interaction Map
    In the protein interaction map, SGS1 interacts with TOP3 and AUT7 and AUT7 in turn interacts with TOP2 (Schwikowski, 2000).  AUT7 attaches autophagosomes to microtubules (SGD, 2001).  TOP2 is involved in meiotic recombination and DNA elongation (SGD, 2001).  TOP3 is a topoisomerase that works with the SGS1 helicase to regulate meiotic recombination (SGD, 2001).
In the main protein interaction map, SGS1 and TOP3 are said to have similar roles but different locations and SGS1 and AUT 7 are said to have the same location but different functions.  In the other protein interaction maps SGS1 is classified as being involved in meiosis, aging, and RNA processing and modification.  AUT7 is grouped with proteins involved with protein degradation, vesicular transport, RNA turnover, and meiosis.  TOP3 is categorized as being involved in chromosome structure, meiosis, and recombination.
Protein interaction maps can be found at this web site: http://depts.washington.edu/sfields/yplm/data/index.html

NEW EXPERIMENTS
     Since SGS1 is involved in meiosis, transcription, and cell cycle check points, the SGS1 protein is probably regulated in some fashion.  To discover whether phosphorylation plays a role in the regulation of SGS1, the SGS1 protein could be analyzed using a protein chip technique developed by Snyderís lab and a stable isotope method developed by Brian Chiatís lab.  In Snyderís method SGS1 protein would be spotted in every well of a protein chip.  Then a different kinase and radioactive ATP would be added to each well.  If the kinase phosphorylated SGS1 then a dark spot would appearl.  In the stable isotope method developed by Chiatís lab, cells could be stalled at different stages in growth in a media containing normal nitrogen.  When the cells were allowed to proceed with normal growth heavy nitrogen could be introduced to the medium.  Observing the rations of heavy to light nitrogen may elucidate the time and stage that the SGS1 protein is being phosphorylated.
     There  is not a lot of evidence supporting the AUT7 SGS1 interaction predicted by the protein interaction map developed by Schwikowski (2000).  AUT7 and SGS1 are predicted to be a link between Top3 and Top2 proteins.  This suggests that the AUT7 SGS1 interaction takes place during meiosis.  It would be interesting to observe the protein levels of these two proteins at different stages in a cell's life using the stable isotope method developed by Brian Chiatís lab (1999).  It would also be interesting to see if the two proteins are phosphorylated at the same times or reciprocally phosphorylated using Brian Chiatís stable isotope method (1999).  Any correlation between the two proteins may help elucidate when the two proteins are working together.

NO USEFUL INFO FOUND YET
Two Hybrid
Stan Fieldís Lab has no data regarding SGS1.
http://depts.washington.edu/sfields/yplm/data/index.html
Since SGS1 interacts with DNA it is a good candidate for the yeast two hybrid approach.

Path Calling Interaction Database
SGS1 was not found to interact with any proteins.
http://portal.curagen.com/extpc/com.curagen.portal.servlet.PortalYeastList

DIP database
The DIP database shows SGS1 interacting with Top3.
http://dip.doe-mbi.ucla.edu/dip/Search_DIP.cgi
 



REFERENCES

CHAITíS LAB
    Oda, Y., K. Huang, F.R. Cross, D. Cowburn, and Brian T. Chait. 1999. PNAS. Vol. 96:
            6591-6596.

Cox, Michael and David Nelson. 2000.Lehninger Principles of Biochemistry.  Worth Publishers.
       New York. 363-384.

FIELDíS LAB
     http://depts.washington.edu/sfields/

    YEAST TWO HYBRID
        Uetz P et al. (2000) A comprehensive analysis of protein-protein interactions in
            Saccharomyces cerevisiae [PDF; 480 KB!]. Nature, Feb 10, 403 (6770): 623-627.

    PROTIEN INTERACTION MAPS
        Schwikowski B et al. (2000) A network of protein interactions in yeast. Nature Biotechnology
        Dec. 2000, in press.
        http://depts.washington.edu/sfields/yplm/data/index.html

Frei, Christian and Susan M. Gasser. January 2000. The yeast Sgs1p helicase acts upstream of
    Rad53p in the DNA replication checkpoint and colocalizes with Rad53p in S-phase-specific
    foci. Genes and Dev. 14(1): 81-96.http://www.genesdev.org/cgi/content/full/14/1/81

Guarente, Leonard. October 1997. Link between aging and the nucleolus. Genes and Dev. 11(19):
    2449-2455. http://www.genesdev.org/cgi/content/full/11/19/2449

Lee, S. K. , Johnson, R. E. , Yu, S. L. , Prakash, L. & Prakash, S. 1999. Requirement of Yeast
    SGS1 and SRS2 genes for replication and transcription. Science 286: 2339-2342.
    http://www.sciencemag.org/cgi/content/full/286/5448/2339?ijkey=bWVP.CI6.mh6A

McVey, M. , Kaeberlein, M. , Tissenbaum, H. A. & Guarente, L. 2001. The short life span of
    Saccharomyces servisiae sgs1 and srs2 mutants is a composite of normal aging processes and
    mitotic arrest due to defective recombination. Genetics 157: 1531-1542.
    http://www.genetics.org/cgi/content/full/157/4/1531

PATH CALLING INTERACTION DATABASE
    02/10/00 - A collaboration between Stanley Fields' Lab at the University of Washington, Dept.
        of Genetics & Howard Hughes Medical Institute and CuraGen Corporation has completed
        a genome-wide analysis of the protein-coding genes of the yeast genome. This analysis
        identifies  proteins which are likely to form stable complexes with other proteins.
        http://portal.curagen.com/extpc/com.curagen.portal.servlet.PortalYeastList

SNYDERíS LAB

http://ygac.med.yale.edu/default.stm

    TRIPLES DATA BASE
        http://ygac.med.yale.edu/triples/triples.htm

            Kumar, A., Cheung, K.-H., Ross-Macdonald, P., Coelho, P.S.R., Miller, P., and Snyder,
            M. (2000). TRIPLES: a Database of Gene Function in S. cerevisiae. Nucleic Acids Res.
            28, 81-84. (Full-text in PDF reproduced with permission from NAR Online
           http://www.oup.co.uk/nar )

           Ross-Macdonald, P., Coelho, P.S.R., Roemer, T., Agarwal, S., Kumar, A., Jansen,
            R., Cheung, K.-H., Sheehan, A., Symoniatis, D., Umansky, L., Heidtman, M., Nelson,
            K., Iwasaki, H., Hager, K., Gerstein, M., Miller, P., Roeder, G.S., and Snyder, M.
            (1999).  Large-scale analysis of the yeast genome by transposon tagging gene
            disruption.Nature 402, 413-418.

    PROTEIN-KINASE INTERACTION

        http://bioinfo.mbb.yale.edu/genome/yeast/chip/

            H Zhu, J Klemic, S Chang, P Bertone, A Casamayor, K Klemic, D Smith, M Gerstein, M
           Reed, & M Snyder (2000). Analysis of yeast protein kinases using protein chips. Nature
            Genetics 26: 283-289.

SGD database. 2001.Stanford.
         http://genome-www.stanford.edu/Saccharomyces/

Watt, Paul M. and Ian D. Hickson. 1996. Failure to unwind causes cancer. Current Biology.
   6:265-267. http://journals.bmn.com/journals/list/browse?uid=JCUB.bb6308&rendertype=text

YPD database. 2001. Proteome, Inc.
          http://www.proteome.com/databases/index.html

Yale Gernstien Lab
    http://spine.mbb.yale.edu/protein_chips/
 
 

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