This web page was produced as an assignment for an undergraduate course at Davidson College.

My Favorite Yeast Proteins!

Annotated Gene: CCL1/YPR025C    (YPD Protein Report)    Brief report of YPR025C        Microarray data for YPR025C

Non-Annotated Gene:  YHR078W   (YPD Protein Report)     Brief report of YHR078W     Microarray data for YHR078W

Annotated Gene: CCL1/YPR025C    (YPD Protein Report)     

Saccharomyces cerevisiae  Chromosome XVI      

SGD: 50006229        Genbank: CAA89279.1         MIPS (PIR): 539383        SWISS-PROT: P37366  

        While the microarray data for CCL1 shows this gene clustering with many varied annotated and non-annotated genes under several different experimental conditions, the field of proteomics has also been making its contribution to the discovery and annotation of the way cells work.  Although disjointed, the various protein databases have expanded upon the information gathered by microarrays.  For example, the Database of Interacting Proteins shows six other proteins that interact with the protein cyclin CCL1, most of which did not appear linked in previously data:

Retrieves information about a particular interaction
Retrieves 1 level of interaction links.

CENTERED ON
Links	Interaction information	PIR	SWISSPROT	GENBANK	NAME
	-	S39383	CCL1_YEAST	481786	cyclin CCL1
INTERACTS WITH 6 PROTEINS
		A25698	KI28_YEAST	83397	probable protein kinase KIN28
		S38164	PR16_YEAST	539085	ATP-binding protein PRP16
		S69628		2131508	hypothetical protein YDR460w TFB3
		S51391		1077361	probable membrane protein YLR373c
		S69566	GNP1_YEAST	2119772	glutamine transport protein, high affinity
		OKBY85	PH85_YEAST	2144418	protein kinase PHO85

(table courtesy of DIP, permission requested)

 The Yeast Protein Database agrees with the table above that KIN28 and TFB3 are both linked to CCL1, but also relates VID22.  A yeast integration circuit showing protein interactions published by Schwikowski, Fields, and Uetz (shown below) also connects CCL1 with KIN28, but also shows lines to RAD59 and SNZ3, which are linked by YPD to each other but not to CCL1 or KIN28.  

KIN28, as a subcomponent of the kinase sub complex TFIIK of TFIIH along with CCL1, has been a known interaction.  The red line above indicates that their cellular and subcellular localizations are identical.  Most of the other proteins are involved with DNA repair with the exception of VID22, which is only known to be in the plasma membrane, and SNZ3, which is connected to metabolism and cell stress, as well as involved with the biosynthetic enzyme vitamin B6.  Ito et al. (1), who are cited by the YPD, used the two-hybrid method and compared their results with Uetz et al. (2) and found that not much overlap occurred, resulting in greater knowledge of the yeast proteome interactions.   

This membrane protein interaction map shows CCL1 connected with the same proteins as the larger scale one, with RAD59 color-coded as a cell cycle control protein, which makes sense as one of its roles is in meiosis.  The black box represents KIN28, which is coded for RNA turnover.  The aging map codes both CCL1 and KIN28 as pol-II transcription factors, which they have been identified as by the YPD as well.  The degredation map shows no particular color distinction for any of these proteins. 

        The Yeast Resource Center links CCL1 with PRP16, as the table above does; PRP16 is an RNA binding protein that also plays a role in RNA splicing.  The PathCalling Yeast Interaction Database claims no interactions for CCL1.  The Triples database (3, 4) disrupted a CCL1 clone with the mTn transposon and the protein was still expressed, which means that the insertion randomly landed downstream of the promotor.  The subcellular location was unable to be determined by this database because it failed to stain above a background level.  

Databases consulted with no significant results for CCL1:

What is There?  (WIT)

Enzymes and Metabolic Pathways Database

Gerstein's Lab

Non-Annotated Gene:  YHR078W   (YPD Protein Report)     Brief report of YHR078W

S. cerevisiae  Chromosome VIII

SGD: S0001120    Genbank: AAB68887.1    MIPS (PIR): S46809        SWISS-PROT: P38799

        Besides the microarray data for this gene, not much information exists even in protein databases.  WIT links YHR078W with integral nuclear envelope protein NDC1, which is an annotated gene.  Badcock and Churcher say here that this protein (assumably NDC1) is essential for mitotic viability as it is required for spindle pole body duplication in G1 and may insert the spindle pole body into the nuclear envelope.  They also posit the ER as a possible localization (5). NDC1 functions as a nuclear export/import protein, which correlates with the previous microarray data found.  

        In light of this data, a possible experiment to find out more information and see if YHR078W is actually involved in transport as predicted would be the yeast-two hybrid method.  Since no other genes have been linked to this one besides the one that codes for NDC1, it would be a logical choice as prey.  Other possibilities include the products of the genes from the microarray data that clustered with YHR078W and were involved in transport, such as BOS1, GEA1, FTR1, MSP1, and AGP3.  Depending on what it linked with, it would be possible both to verify YHR078W function and to solidify its subcellular localization.  Since so little information about this particular gene and resulting protein actually exists, any positive results with this experiment could possibly result in a breakthrough for YHR078W.

Databases consulted with no significant results for YHR078W:

Database of Interacting Proteins

Schwikowski, Fields, and Uetz PDF Files:

       NB_Figure1         Membrane        Aging        Degredation

Yeast Resource Center

PathCalling Yeast Interaction Database

TRIPLES

Gerstein's Lab

References

1.    Ito, Takashi, Tomoko Chiba, et al.  10 April, 2001.  A comprehensive two-hybrid analysis to explore the yeast protein interactome.  Proc. Natl. Acad. Sci. USA, Vol. 98(8):4569-4574.  8 November, 2001.  http://www.pnas.org/cgi/content/full/98/8/4569

2.    Uetz, P., L. Giot, et al.  10 February, 2000.  A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.  Nature, Vol.403(6770): 623-7.  8 November, 2001.   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10688190&dopt=Abstract

4.    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 and gene disruption. Nature 402, 413-418. Nature 402, 413-418.

5.    Badcock, K., C. Churcher, et al.  Submitted (Nov 1994) to EMBL/Genbank/DDBJ Data Banks.  http://wit.mcs.anl.gov/WIT2/CGI/prot.cgi?user=&org=SC&prot=sp|P32500

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