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

My Favorite Yeast Protein:

AUS1 & YOR012W

                                                                                                                                                                                                                               

AUS1

 

SGD:  (SGD, 2002, <http://genome-www.stanford.edu/Saccharomyces/>)

Protein Sequence:

>YOR011W  Chr 15  
MSISKYFTPVADGSLTFNGANIQFGADAQGESKKSYDAEDSMPNPANQLNDITFQAEAGE
MVLVLGYPTSTLFKTLFHGKTSLSYSPPGSIKFKNNEFKSFSEKCPHQIIYNNEQDVHFP
FLTVEQTIDFALSCKFDIPKGERDQIRNELLREFGLSHVLKTIVGNDFFRGVSGGERKRI
SIIETFIANGSVYLWDNSTKGLDSATALDFLEILRKMAKATRSVNLVRISQASDKIVDKF
DKILMLSDSYQLFYGTVDECLTYFRDTLGIEKDPNDCIIEYLTSILNFQFKNKNLGNLSN
SSSASVLKTATGEVTKYTYNSDFDLYDQWKHSSYYRNIKQQIQGSSIDDSIKEVDPSDVS
PIFNIPLKKQLLFCTKRAFQRSLGDKAYMTAQFISVVIQSLVIGSLFYEIPLTTIGSYSR
GSLTFFSILFFTFLSLADMPIAFQRQPVVKKQSQLHFYTNWVETLSTTVFDYCFKLCLVI
VFSIILYFLAHLQYKAARFFIFLLFLSFYNFCMVSLFALTTLVAPTISVANLFAGILLLA
IAMYASYVIYLKNMHPWFVWIAYLNPAMYAMEAILSNELYNLKLDCSETIVPRGPTYNDV
PFSHKACAWQGATLGNDYVRGRDYLKQGLSYTYHHVWRNFGIIIGFLVFFIACTLFASQY
IKPYFNKDEIERNNSRLTRWLPFLNKKRGTRSSARNDSKYVGIPKSHSVSSSSSSLSAVP
YQISPSNKEMALNDYNEQPITETVETQKHIISWKNINYTVGTKKLINNASGFISSGLTAL
MGESGAGKTTLLNVLSQRVETGVVSGEILIDGHPLTDEDAFKRSIGFVQQQDLHLDLLSV
KESLEISCLLRGDGDRAYLDTVSNLLKLPSDILVADLNPTQRKLLSIGVELVTKPSLLLF
LDEPTSGLDAEAALTIVKFLKQLSLQGQAIFCTIHQPSKSVISHFDNIFLLKRGGECVFF
GPMDDACGYFMSHDNTLVYDKEHDNPADFVIDAVGNSNSSAGKDTAEEALTLNKEAIDWS
ALWESSVEKKLVKKETARLEDDARASGVDYTTSLWKQPSYLQQLALITRRQYICTKRDMT
YVMAKYCLNGGAGLFIGFSFWHIKHNIIGLQDSIFFCFMALCVSSPLINQIQDKALKTKE
VYVAREARSNTYHWTVLLLSQSIIELPLALTSSTLFFVCAFFSCGFNNAGWSAGVFFLNY
MLFAAYYSTLGLWLIYTAPNLQTAAVFVAFIYSFTASFCGVMQPYSLFPTFWKFMYRVSP
YTYFVETFVSILLHNWEIKCDMSEMVPGQPLTGQSCGQFMEAFIEEYGGYLHNKNTFTVC
AYCTYTVGDDFLKNENMSYDHVWRNFGIEWAFVGFNFFAMFAGYYLTYVARIWPKVFKII
TKVIPHRGKKPVQN

This database gave general information regarding the sequence of the AUS1 protein (See below). You can click on the link to view the protein sequence.

Protein Sequence Calculations
from Predicted Full length Translation

N-term

MSISKYF

C-term

GKKPVQN

Length(aa)

1,394

MW(Da)

157,750

pI

7.16

Amino Acid Composition (full length)

Retrieve Protein Sequence

 

Transcript Translation Calculations

Codon Bias

0.191  

Codon Adaptation Index

0.196  

equency of Optimal Codons

0.522  

Hydropathicity of Protein

0.019  

Aromaticity Score

0.137  

 

TRIPLES:  (TRIPLES, 2002, <http://ygac.med.yale.edu/triples/triples.htm>)

TRIPLES found no data on AUS1.   

 

The Grid:  (The Grid, 2002, <http://biodata.mshri.on.ca/grid/index.html>)

This database showed that YOR011W (AUS1) is an ABC transporter and is located in the membrane.  In addition, the database showed that AUS1 is associated with YIR009W.  This protein is involved in mRNA splicing in the snRNP U2.  More information can be found by clicking on the links below.

Orf

Gene/s

Description

GO Annotations

Links

Function

Process

Component

YOR011W

·  AUS1

ABC ATP-binding cassette protein involved in Uptake of Sterols

·  ATP-binding cassette ABC transporter

·  sterol transport

·  membrane

AUS1 was identified in association with the following 1 proteins

Orf

Gene/s

Description

GO Annotations

System

Source/s

Pubmed

Links

Function

Process

Component

YIR009W

 MSL1

involved in splicing

RNA binding

 mRNA splicing

snRNP U2

Two Hybrid

MIPS

PubMed


 

DIP (Database of Interacting Proteins): (DIP, 2001, <http://dip.doe-mbi.ucla.edu/dip/Search.cgi?SM=3>)

This database show the interaction of AUS1 with YIR009W.  In this database, YIR009W is referred to as a “hypthetical protein.”  This is different than in The Grid site, where YIR009W is referred to as MSL1.  

DIP
994N


BROWSE LINKS

Protein: ATP-dependent transport protein homolog YOR011w

 

 

DIP

Cross Reference

Protein Name/Description

Interaction

Node

Links

PIR

SWISSPROT

GENBANK

DIP:989E

DIP:994N

S66876

---

gi:2131187

ATP-dependent transport protein homolog YOR011w

DIP:816N

S48353

YIS9_YEAST

gi:626287

hypothetical protein YIR009w

The graph below shows the interaction of AUS1 (YOR011W) with other proteins.  AUS1 is represented by the red dot, in the lower left hand side of the diagram.  YIR009W is represented by the dot that is directly in the middle. 

Figure courtesy of DIP.

 

MIPS: (MIPS, 2002. <http://mips.gsf.de/proj/yeast/CYGD/db/index.html>)

This database revealed that AUS1 is similar to ABC transport proteins.  This is expected because AUS1 is an ABC transport protein.

 

 

YRC Two-Hybrid Analysis &  Additional Y2H Results: 

Found no results for AUS1.

 

PDF maps: Aging, Membrane, Degration, Benno Figure 1:

No result for AUS1.

 

Function Junction: (Function Junction, 2002, < http://genome-www4.stanford.edu/cgi-bin/SGD/functionJunction>)

This database revealed that AUS1 is associated with proteins that serve as ABC transport proteins as well as proteins that are associated with RNA synthesis. This is similar to the data found previously.   

In addition, Pathcalling presented the following graph.  The graph shows the protein-protein interaction with regards to AUS1.  Once again, you can see that AUS1 (YOR011W) is associated with MSL1 (YIR009W).

Figure courtesy of Function Junction

 

Conclusions:

Although there is not much information regarding AUS1 in the databases searched, it is apparent that AUS1 indeed codes for a protein that is associated with ABC transport proteins.  In addition, from this search, as well as previous microarray and literature searches (see website 2 & 3), it seems as though this protein is associated with replication of DNA in the cell.

                                                                                                                                                                                                                               

YOR012W

 

SGD: (SGD, 2002, <http://genome-www.stanford.edu/Saccharomyces/>)

Protein sequence:

>YOR012W Chr 15 

MVASSINEESSLAVNLTSDVEKASKTLFKAFEKSYANDYLMKKFFHIPITEKVSRARINA MIHYYTTCYHDLDGEIAEANDFDAVAIWSRPGCHLPATLSDDESFNKIFFSRLDCEEARS HASGNGLLLPLCHRKRS

In addition, this database showed the general characteristics of the protein (See below). 

 

Protein Sequence Calculations
from Predicted Full length Translation

N-term

MVASSIN

C-term

LCHRKRS

Length(aa)

137

MW(Da)

15,482

pI

6.5

Amino Acid Composition (full length)

Retrieve Protein Sequence

 

Transcript Translation Calculations

Codon Bias

0.044

Codon Adaptation Index

0.123

Frequency of Optimal Codons

0.429

Hydropathicity of Protein

-0.310

Aromaticity Score

0.102


TRIPLES : (TRIPLES, 2002, <http://ygac.med.yale.edu/triples/triples.htm>)

No data was found for YOR012W.  

 

The Grid: (The Grid, 2002, <http://biodata.mshri.on.ca/grid/index.html>)

Returned no data for YOR012W

 

DIP:  (Database of Interacting Proteins): (DIP, 2001, <http://dip.doe-mbi.ucla.edu/dip/Search.cgi?SM=3>)

This database did not provide the names of any proteins that are similar to YOR012W.  In addition, DIP did not provide a protein interaction map for this protein.


NODE SEARCH RESULTS

DIP

Cross Reference

Protein Name/Description

Node

Links

PIR

SWISSPROT

GENBANK

DIP:8948N

Q12351

gi:

ORF YOR012W

 

MIPS: (MIPS, 2002. <http://mips.gsf.de/proj/yeast/CYGD/db/index.html>)

This database showed that YOR012W is related to YDR391C, which is a hypothetical protein.  Since the function of YDR391C is not known, this provides no information regarding the function of YOR012W.

 

YRC Two-Hybrid Analysis & Additional Y2H Results: 

Produced no results.

 

PDF maps: Aging, Membrane, Degration, Benno Figure 1:

No result for YOR012W.

 

Function Junction: (Function Junction, 2002, < http://genome-www4.stanford.edu/cgi-bin/SGD/functionJunction>)

No information was gained from Function Junction.

 

Yale Gernstein Lab: (Yale Gerstein Lab, 2001, < http://bioinfo.mbb.yale.edu/genome/yeast/search.cgi?orf=YOR012W>)

This database stated that the protein of YOR012W is located in the cytoplasm. 

 

Possible Experiments:

 Although this page did not reveal any new information regarding YOR012W, the information that was found on previous pages can be used to hypothesize the function of the protein.  Past pages have suggested that YOR012W is associated with DNA replication, specifically either with  transcription factors or with DNA repair.  

Experiment 1:  Proteins involved with transcription factors or with DNA repair are typically located in the nucleus.  This contradicts the information found by the Yale Gernstein Lab.  This lab found that YOR012W is located in the cytoplasm (see above).  Thus, it is important to test to see where the protein is actually located.  One way to do this would be to use a fluorescently labeled probe.  The probe would contain the complementary sequence of  YOR012W, and would move into the cell via a virus or an injection of antibodies.  The probe would bind to the YOR012W sequence.  After binding, scientists could look at the cell under a microscope and determine where the YOR012W protein is located (in the cytoplasm or the nucleus) by viewing the labeled probe.  Thus, the location of YOR012W would be determined. 

Although the Gerstein lab believes that YOR012W is found in the cytoplasm,  YOR012W typically clusters with genes associated with transcription and DNA repair.  Thus, it is likely that this protein is associated with these processes and is found inside the nucleus of the cell.  Determining the location of this protein may lead to a better understanding of its function.  

 

Experiment 2:  The microarray website showed that YOR012W is associated with either transcription or DNA repair.  In order to determine which process it is associated with, an experiment that involves a modified version of the bar code method by Winzeler (Campbell & Heyer, 166) could be used.  In this method, the YOR012W gene is deleted and then replaced by a specific marker.  This marker will be easily identifiable, and will function as a sort of bar code later in the experiment.   Other bar coded mutants will also be created.  These mutants will lack proteins that are known to be associated with replication, such as transcription factors and DNA repair proteins.  The mutants would then be spotted out on a microarray chip. 

The mutants that lacked transcription factors would not replicate and grow.  Eventually, these mutants would die.  Mutants that lacked DNA repair proteins would still grow and replicate, though perhaps at altered rates (depending on the mutation).  By comparing the expression (color) of the YOR012W mutants to those of transcription factors and DNA repair proteins, it may be possible to determine in which process YOR012W is involved.  Thus, this experiment may clarify the function of YOR012W.  

                                                                                                                                                                              

 

References:

Campbell, AM and Heyer, LJ.  Genomics, Proteomics, & Bioinformatics 2003.  San Francisco, CA: Pearson Education, Inc.

Database of Interacting Proteins (DIP), 2001, <http://dip.doe-mbi.ucla.edu/dip/Search.cgi?SM=3> Accessed 11/11/02

Function Junction, 2002, < http://genome-www4.stanford.edu/cgi-bin/SGD/functionJunction> Accessed 11/15/02

MIPS Comprehensive Yeast Genome Database (CYGD), 2002, <http://mips.gsf.de/proj/yeast/CYGD/db/index.html>

 

Saccharomyces Genome Database (SGD), 2002, <http://genome-www.stanford.edu/Saccharomyces/> Accessed 11/13/02

 

Schwikowski, Benno; Uetz, Fields. 2000.  A network of protein-protein interactions in yeast. Nature Biotechnology. 18:1257-1261. (PDF files)

The Grid, 2002, <http://biodata.mshri.on.ca/grid/index.html>.  Accessed 11/14/02

TRIPLES, 2002, <http://ygac.med.yale.edu/triples/triples.htm>. Accessed 11/11/02

Yale Gerstein Lab, , 2001, < http://bioinfo.mbb.yale.edu/genome/yeast/search.cgi?orf=YOR012W> Accessed 11/15/02

YRC Two-Hybrid Analysis, 2000, <http://depts.washington.edu/%7Eyeastrc/th_11.htm> Accessed 11/11/02.

YRC Two-Hybrid Analysis’ Additional YRH Results, 2000, <http://depts.washington.edu/%7Eyeastrc/th_12.htm> Accessed 11/11/02

   


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