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

Microarray Analysis:

                           AUS1 & YOR012W

Microarrays can be used for a number of purposes, though is most commonly used to analyze expressions of various proteins.  Microarrays show how proteins are expressed at various conditions.  Analyzation of this data may give insight as to the function of the protein.

                                                                                                                                                                                                                                                                                                                                                                                                                                                              

  AUS 1

            As previously determined, AUS 1 is a protein found in yeast.  It codes for an ATP-Binding Cassette transporter (ABC transporter) that transports sterols from the endoplasmic reticulum to the plasma membrane.  Below you will find an analyzation of microarray data for this protein:

All the following microarrays use the following scale (Courtesy of ExpressionConnection <http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>):

 

Click on a color strip to see data for that gene.

 

Expression at Different Alpha Factor Concentrations:

Orf Gene Process Function Component
YOR011W   AUS1     sterol transport   ATP-binding cassette (ABC) transporter   membrane
YIL116W   HIS5     histidine biosynthesis   histidinol-phosphate aminotransferase   cell
YGR143W   SKN1     cell wall organization and biogenesis*   not yet annotated   integral membrane protein
YOR014W   RTS1     protein biosynthesis   protein phosphatase type 2A   cytoplasm*
YHL011C   PRS3     histidine biosynthesis*   ribose-phosphate pyrophosphokinase   cytoplasm
YBR284W         biological_process unknown   molecular_function unknown   not yet annotated
YJR004C   SAG1     agglutination (sensu Saccharomyces)   cell adhesion receptor   cell wall (sensu Fungi)*
YGR059W   SPR3     cell wall organization and biogenesis*   structural constituent of cytoskeleton   prospore membrane*
YNL261W   ORC5     DNA replication initiation*   adenosinetriphosphatase*   origin recognition complex
YBR074W         biological_process unknown   molecular_function unknown   not yet annotated
YNR043W   MVD1     ergosterol biosynthesis*   diphosphomevalonate decarboxylase   cytosol
YOR229W   WTM2     transcription   not yet annotated   not yet annotated
YGR068C         biological_process unknown   molecular_function unknown   not yet annotated
YLR445W         biological_process unknown   molecular_function unknown   not yet annotated
YGR065C   VHT1     biotin transport   biotin transporter   plasma membrane
YJR028W         Ty element transposition   not yet annotated   not yet annotated
YAL065C-A            
YKL197C   PEX1     peroxisome organization and biogenesis   adenosinetriphosphatase   cellular_component unknown
YIL162W   SUC2     sucrose catabolism   beta-fructofuranosidase   cytoplasm*
YJL044C   GYP6     intracellular protein transport   GTPase activator   cellular_component unknown
YIL168W   SDL1     serine family amino acid metabolism   N-acetyl-gamma-glutamyl-phosphate reductase   cellular_component unknown

Figure 1: Microarray data of various proteins’ expression levels with regards to changes of concentration in the alpha factor. (Courtesy of Expression Connection)

What is an alpha factor?

            The alpha factor causes arrests the cell in the G1 phase.  This allows the cell to make proteins associated with mating (Zymor,2001, <http://www.zymor.com/y1001-frame.html>).   Thus, it is expected that proteins that are associated with the preparation of reproduction are induced when the alpha factor is present.

What does this data show?

    By looking at the microarray data above, it is shown that AUS1 is induced at the different levels of alpha factors.  This expression is similar to the expression of proteins associated with DNA replication as well as cellular organization.  Both of these process require ATP, and thus it makes sense that an ABC transport protein would be expressed similarly to ATP dependent proteins.  It also makes sense that proteins associated with reproduction would be induced in the presence of the alpha factor because the cells are preparing for reproduction.

                                                                                                                                                                             

 

Expression in Response to Alpha-Factor:

Orf Gene Process Function Component
YOR011W   AUS1     sterol transport   ATP-binding cassette (ABC) transporter   membrane
YPR022C         biological_process unknown   molecular_function unknown   not yet annotated
YMR309C   NIP1     translational initiation   translation initiation factor   cytoplasm*
YER048C   CAJ1     biological_process unknown   chaperone regulator   cellular_component unknown
YLR285W         biological_process unknown   molecular_function unknown   not yet annotated
YDL229W   SSB1     protein biosynthesis   chaperone   polysome
YBR129C   OPY1     mating (sensu Saccharomyces)   molecular_function unknown   not yet annotated
YCR029C         not yet annotated   not yet annotated   not yet annotated
YML052W   SUR7     sporulation (sensu Saccharomyces)   molecular_function unknown   integral membrane protein*
YPR113W   PIS1     phosphatidylinositol biosynthesis   CDP-diacylglycerol-inositol 3-phosphatidyltransferase   endoplasmic reticulum
YDR172W   SUP35     translational termination   translation release factor   cytosol
YBL007C   SLA1     cell wall organization and biogenesis*   cytoskeletal protein binding   actin cortical patch (sensu Saccharomyces)
YOR361C   PRT1     translational initiation   translation initiation factor   cytoplasm*
YNL311C         biological_process unknown   molecular_function unknown   not yet annotated
YOR087W   YVC1     cation homeostasis   calcium channel*   vacuole (sensu Fungi)
YNR067C   DSE4     cytokinesis, completion of separation   glucan 1,3-beta-glucosidase   extracellular
YGL238W   CSE1     protein-nucleus export   importin-alpha export receptor   nuclear membrane
YPR147C         biological_process unknown   molecular_function unknown   not yet annotated
YBR154C   RPB5     transcription from Pol II promoter*   DNA-directed RNA polymerase III*   DNA-directed RNA polymerase III complex*
YML125C         biological_process unknown   molecular_function unknown   not yet annotated
YCR075C   ERS1     cystine transport   cystine transporter   integral membrane protein

Figure 2.  Expression of AUS1 in response to the alpha factor.  (Courtesy of Expression Connection )

            In this set of data, the expression of AUS1 is analyzed with regards to long-term exposure to the alpha factor.  In this case, AUS1 is repressed only after its been exposed to the alpha-factor for about two hours.  This may be because after two hours of exposure to the alpha factor, the cell continues with the replication process, and thus these proteins are not needed, and are repressed.

 

                                                                                                                                                               

 

Expression during the diauxic shift

rf Gene Process Function Component
YOR011W   AUS1     sterol transport   ATP-binding cassette (ABC) transporter   membrane
YJL011C   RPC17     transcription initiation from Pol III promoter   DNA-directed RNA polymerase III   DNA-directed RNA polymerase III complex
YER076C         biological_process unknown   molecular_function unknown   not yet annotated
YCR098C   GIT1     phospholipid transport   phospholipid transporter   plasma membrane
YCL048W         biological_process unknown   molecular_function unknown   not yet annotated
YIL154C   IMP2'     DNA repair*   transcription factor   cellular_component unknown
YBL031W   SHE1     biological_process unknown   molecular_function unknown   cellular_component unknown
YBR030W         biological_process unknown   molecular_function unknown   not yet annotated
YMR048W   CSM3     meiotic chromosome segregation   molecular_function unknown   cellular_component unknown
YKL220C   FRE2     iron transport*   ferric-chelate reductase   plasma membrane
YAR047C         biological_process unknown   molecular_function unknown   not yet annotated
YCL023C         biological_process unknown   molecular_function unknown   not yet annotated
YAL013W   DEP1     phospholipid metabolism   not yet annotated   not yet annotated
YPL121C   MEI5     biological_process unknown   molecular_function unknown   cellular_component unknown
YDR228C   PCF11     mRNA polyadenylation*   cleavage/polyadenylation specificity factor   mRNA cleavage factor complex
YDL187C         biological_process unknown   molecular_function unknown   not yet annotated
YBR182C   SMP1     transcription   transcription factor*   nucleus
YNR060W   FRE4     iron-siderochrome transport   ferric-chelate reductase   plasma membrane
YMR082C         biological_process unknown   molecular_function unknown   not yet annotated
YCR052W   RSC6     chromatin modeling   molecular_function unknown   nucleosome remodeling complex
YIR025W   MND2     meiotic recombination   molecular_function unknown   cellular_component unknown

Figure 3.  This figure shows how the expression of AUS1 changes with the diauxic shift. Courtesy of ExpressionConnection.

What is the diauxic shift?

            Diauxic shift refers to the change between anaerobic to aerobic respiration.  This time period is typically associated with vast number of changes in protein expression (European Bioinformatics Institute  <http://industry.ebi.ac.uk/~alan/MicroArray/IntroMicroArrayTalk/tsld015.htm>).

What does this data show?

            AUS1, along with many proteins involved with reproduction and transport are repressed during this change.  This makes sense because a cell will not be “concerned” with reproduction while trying to acclimate to a different type of respiration. 

 

                                                                                                                                                                                

Expression Regulated by the PHO pathway:

Orf Gene Process Function Component
YOR011W   AUS1     sterol transport   ATP-binding cassette (ABC) transporter   membrane
YJL175W         biological_process unknown   molecular_function unknown   not yet annotated
YOR144C   ELG1     negative regulation of DNA transposition*   molecular_function unknown   cellular_component unknown
YGR102C         biological_process unknown   molecular_function unknown   not yet annotated
YKL072W   STB6     biological_process unknown   not yet annotated   not yet annotated
YFR032C         biological_process unknown   molecular_function unknown   not yet annotated
YDR419W   RAD30     DNA repair   eta DNA polymerase   replication fork
YDR108W   GSG1     ER to Golgi transport*   molecular_function unknown   TRAPP
YCL024W   KCC4     protein amino acid phosphorylation*   transcription factor*   bud neck
YLR035C   MLH2     DNA repair   not yet annotated   not yet annotated
YER151C   UBP3     deubiquitination   ubiquitin-specific protease   cytoplasm
YJL102W   MEF2     translational elongation   translation elongation factor   mitochondrion
YOL006C   TOP1     regulation of transcription from Pol II promoter*   DNA topoisomerase I   nucleus
YOL081W   IRA2     RAS protein signal transduction   RAS GTPase activator   cellular_component unknown
YIL038C   NOT3     regulation of transcription from Pol II promoter*   3'-5' exoribonuclease   cytoplasm*
YDR325W   YCG1     mitotic chromosome condensation   molecular_function unknown   condensin
YGL217C         biological_process unknown   molecular_function unknown   not yet annotated
YNL240C   NAR1     biological_process unknown   iron hydrogenase   cellular_component unknown
YLL054C         biological_process unknown   molecular_function unknown   not yet annotated
YIL159W   BNR1     response to osmotic stress*   molecular_function unknown   contractile ring (sensu Saccharomyces)
YGL176C         biological_process unknown   molecular_function unknown   not yet annotated

Figure 4.  Expression of AUS1 with regards to the PHO pathway. (Courtesy of Expression Connection.)  

    The PHO pathway is initiated when the levels of phosphate decrease.  This pathway increases the availability of phosphate to be used in cellular metabolism (Thomas, 2001, <http://www.ucsf.edu/ekolab/people/melissa.html>).  Thus, process that deal with DNA replication and reproduction will most likely be repressed because the cell does not need to use energy to perform these tasks.  The data above supports this hypothesis.  AUS1, as well as proteins associated with DNA repair, amino acid phosphorylation, translational elongation, etc, are repressed in these conditions.  

                                                                                                                                                                        

 

Yeast Cell Cycle Analysis Project:   

Name Score Peak
AUS1 0.153
Reference Genes
CLN2 10.9 G1
HTA1 10.68 S
CLB4 3.08 G2
SWI5 6.726 M
ASH1 11.8 M/G1
Plot of AUS1 (YOR011W)

Figure 5.  This figure shows the expression of AUS1 throughout the yeast cell cycle. (Courtesy of ExpressionConnection.)

    This figure shows that AUS1 does not show a very distinct pattern during the cell cycle.  Thus, it probably does not regulate the cell cycle, but is needed at various phases during the cycle (in areas where the protein is highly induced: cdc15 240 min).

                                                                                                                                                                        

 

 

Expression in response to histone depletion:

Orf Gene Process Function Component
YOR011W   AUS1     sterol transport   ATP-binding cassette (ABC) transporter   membrane
YNR033W   ABZ1     ribosomal large subunit nucleus export   para-aminobenzoic acid (PABA) synthase   cellular_component unknown
YMR017W   SPO20     non-selective vesicle fusion*   v-SNARE   prospore membrane
YER150W   SPI1     biological_process unknown   molecular_function unknown   cell wall
YBL064C         regulation of redox homeostasis   thioredoxin peroxidase   mitochondrion
YEL023C         biological_process unknown   molecular_function unknown   not yet annotated
YER081W   SER3     serine biosynthesis   phosphoglycerate dehydrogenase   cellular_component unknown
YMR113W   FOL3     folic acid and derivative biosynthesis   dihydrofolate synthase   cellular_component unknown
YDR350C   TCM10     biological_process unknown   molecular_function unknown   not yet annotated
YLR216C   CPR6     protein folding   peptidyl-prolyl cis-trans isomerase   cytoplasm
YGR286C   BIO2     biotin biosynthesis   biotin synthase   not yet annotated
YEL070W         biological_process unknown   molecular_function unknown   not yet annotated
YPL147W   PXA1     fatty acid transport   ATP-binding cassette (ABC) transporter   integral peroxisomal membrane
YHR126C         biological_process unknown   molecular_function unknown   not yet annotated
YDR021W   FAL1     mRNA splicing*   ATP dependent RNA helicase   nucleolus
YLL026W   HSP104     response to stress*   heat shock protein*   cytoplasm
YFL059W   SNZ3     pyridoxine metabolism   molecular_function unknown   not yet annotated
YJR158W   HXT16     hexose transport   glucose transporter*   plasma membrane
YPL240C   HSP82     response to stress*   heat shock protein*   cytoplasm
YDL077C   VAM6     homotypic vacuole fusion (non-autophagic)*   not yet annotated   vacuole (sensu Fungi)*
YMR171C         biological_process unknown   molecular_function unknown   not yet annotated

Figure 6. Expression of Aus1 with response to histone deletion.  (Courtesy of Expression Connection.)

            Though the exact role of histones may not be known, they are thought to be associated with chromatin and cellular organization.  In the past, it has been found that large portions of the “histone molecule may be deleted without significantly affecting the viability of the organism” (Access Research Network, 1997, <http://www.arn.org/docs/reviews/rev009.htm>).  Thus, the change in expression for these proteins must assist the cell in adapting to the depletion.  In this case, AUS1 is highly induced.  Perhaps ABC transport proteins are necessary when adjusting to histone depletion. 

                                                                                                                                                                        

Expression during Sporulation:

Orf Gene Process Function Component
YOR011W   AUS1     sterol transport   ATP-binding cassette (ABC) transporter   membrane
YER176W   ECM32     regulation of translational termination   RNA helicase*   polysome
YNL146W         biological_process unknown   molecular_function unknown   not yet annotated
YJR140C   HIR3     G1/S-specific transcription in mitotic cell cycle   transcription co-repressor   nucleus
YIL060W         biological_process unknown   molecular_function unknown   not yet annotated
YNL137C   NAM9     protein biosynthesis   structural constituent of ribosome   mitochondrial small ribosomal subunit
YLR326W         biological_process unknown   molecular_function unknown   not yet annotated
YGR050C         biological_process unknown   molecular_function unknown   not yet annotated
YKL058W   TOA2     transcription initiation from Pol II promoter   general RNA polymerase II transcription factor   transcription factor TFIIA
YLR037C   DAN2     biological_process unknown   molecular_function unknown   cell wall (sensu Fungi)
YJL199C         biological_process unknown   molecular_function unknown   not yet annotated
YNL305C         biological_process unknown   molecular_function unknown   not yet annotated
YIL113W   SDP1     MAPKKK cascade (cell wall biogenesis)   MAP kinase phosphatase   cytoplasm*
YJL099W   CHS6     Golgi to plasma membrane transport*   molecular_function unknown   cellular_component unknown
YHR130C         biological_process unknown   molecular_function unknown   not yet annotated
YNL267W   PIK1     cytokinesis*   1-phosphatidylinositol 4-kinase   nucleus*
YJL105W   SET4     biological_process unknown   molecular_function unknown   not yet annotated
YPR004C         biological_process unknown   molecular_function unknown   not yet annotated
YHR181W         biological_process unknown   molecular_function unknown   not yet annotated
YPL187W   MF(ALPHA)1     pheromone response (sensu Saccharomyces)   pheromone   extracellular
YKL147C         biological_process unknown   molecular_function unknown   not yet annotated

Figure 7. This figure shows the expression of AUS1 with regards to sporulation. (Courtesy of Expression Connection.)

During sporulation, AUS1 is first repressed then slightly induced.  This may be because ABC transporters are not needed in the very beginning of the sporulation cycle, but then are needed between 7-9 hours into the cycle (when AUS1 is induced). 

                                                                                                                                                            

Varying Zinc Levels:

Orf Gene Process Function Component
YOR011W   AUS1     sterol transport   ATP-binding cassette (ABC) transporter   membrane
YDR069C   DOA4     deubiquitination*   ubiquitin-specific protease   26S proteasome
YJR119C         biological_process unknown   molecular_function unknown   not yet annotated
YDL207W   GLE1     poly(A)+ mRNA-nucleus export   molecular_function unknown   nuclear pore
YDR005C   MAF1     negative regulation of transcription from Pol III promoter   molecular_function unknown   nucleus
YJL079C   PRY1     biological_process unknown   molecular_function unknown   endoplasmic reticulum*
YDL217C   TIM22     mitochondrial translocation   protein transporter   mitochondrial inner membrane translocase complex
YDR430C   CYM1     biological_process unknown   molecular_function unknown   cellular_component unknown
YML002W         biological_process unknown   molecular_function unknown   not yet annotated
YJL073W   JEM1     protein folding*   co-chaperone   endoplasmic reticulum*
YOL044W   PEX15     peroxisome organization and biogenesis*   molecular_function unknown   peroxisomal membrane
YER013W   PRP22     lariat formation, 5'-splice site cleavage   pre-mRNA splicing factor*   spliceosome complex
YPL077C         biological_process unknown   molecular_function unknown   not yet annotated
YGL228W   SHE10     biological_process unknown   not yet annotated   not yet annotated
YOR325W         biological_process unknown   molecular_function unknown   not yet annotated
YDR518W   EUG1     protein folding*   protein disulfide isomerase   endoplasmic reticulum
YGR009C   SEC9     non-selective vesicle fusion*   v-SNARE   membrane
YGR032W   GSC2     cell wall organization and biogenesis*   1,3-beta-glucan synthase   actin cap (sensu Saccharomyces)*
YNR065C   YSN1     biological_process unknown   molecular_function unknown   not yet annotated
YIL040W   APQ12     biological_process unknown   molecular_function unknown   cellular_component unknown
YKL165C   MCD4     GPI anchor biosynthesis   not yet annotated   cell wall (sensu Fungi

Figure 8.  Expression of AUS1, and related proteins, with response to various zinc levels.(Courtesy of Expression Connection.)  

    Zinc is associated with good health.  It is thought to be needed to repair wounds, assist in cellular reproduction, boost immunity, along with many more functions (VirtualHealthInfo, 1999, <http://www.virtualhealthinfo.com/supp/zinc.htm>).  AUS1 wild type cells, and zap1 mutants are repressed when there is deficient levels of zinc.  This trend is also observed in some of the proteins involved in protein folding as well as regulation of DNA replication. 

                                                                                                                                                                        

 

Conclusions:

    By looking at the mircroarray data, AUS1 is expressed differently depending on the situation.  At times when ABC transporters are needed, AUS1 is induced, and at times when ABC transporters are not needed, the protein is repressed.  AUS1 tends to show similar expression patterns with those proteins that are involved with cellular reproduction.  Thus, ABC transporters must play some role in the reproductive cycle of yeast.   

 

                                                                                                                                                                                                                                                                                                                                                                                                                                                               

YOR012W

            As previously discussed, YOR012W is an unannotated yeast protein, thus no one understands the function of the protein.  On this page, microanalysis is used to analyze the possible functions of this protein.

All the following analyzations use the following scale (Courtesy of Expression Connection):

Click on a color strip to see data for that gene.

 

Expression at Different Alpha Factor Concentrations:

Gene Process Function Component
YOR012W         biological_process unknown   molecular_function unknown   not yet annotated
YDR095C         biological_process unknown   molecular_function unknown   not yet annotated
YFL032W         biological_process unknown   molecular_function unknown   not yet annotated
YLL020C         biological_process unknown   molecular_function unknown   not yet annotated
YOL143C   RIB4     vitamin B2 biosynthesis   riboflavin synthase   cellular_component unknown
YLR264W   RPS28B     protein biosynthesis   structural constituent of ribosome   cytosolic small ribosomal subunit (sensu Eukarya)
YBR254C   TRS20     ER to Golgi transport   molecular_function unknown   TRAPP
YHR093W   AHT1     biological_process unknown   molecular_function unknown   cellular_component unknown
YDR232W   HEM1     heme biosynthesis   actin cross-linking*   mitochondrial matrix
YMR151W   YIM2     biological_process unknown   molecular_function unknown   not yet annotated
YOR180C   DCI1     fatty acid beta-oxidation   dodecenoyl-CoA delta-isomerase   peroxisomal matrix
YMR194W   RPL36A     protein biosynthesis   structural constituent of ribosome*   cytosolic large ribosomal subunit (sensu Eukarya)
YGL173C   KEM1     35S primary transcript processing*   5'-3' exoribonuclease   cytoplasm
YOL099C         biological_process unknown   molecular_function unknown   not yet annotated
YER183C   FAU1     folic acid and derivative biosynthesis   5-formyltetrahydrofolate cyclo-ligase   cellular_component unknown
YGR165W         aerobic respiration   molecular_function unknown   cellular_component unknown
YER085C         biological_process unknown   molecular_function unknown   not yet annotated
YEL035C   UTR5     biological_process unknown   molecular_function unknown   cellular_component unknown
YHR021C   RPS27B     protein biosynthesis   structural constituent of ribosome   cytosolic small ribosomal subunit (sensu Eukarya)
YDL114W         biological_process unknown   molecular_function unknown   not yet annotated
YNL249C   MPA43     biological_process unknown   molecular_function unknown   cellular_component unknown

Figure 9.  The expression of YOR012W with regards to different concentrations of the alpha factor.  (Courtesy of Expression Connection.)

The alpha factor arrests the cell in the G1 phase.  When the alpha factor is present in low concentrations, YOR012W is very slightly induced.  Other proteins, mostly ones associated with protein biosynthesis and aerobic respiration, show similar patterns of expression.  Perhaps YOR012W shows similar functions as these proteins. 

                                                                                                                   

 

Expression in Response to Alpha-Factor:

Orf Gene Process Function Component
YOR012W         biological_process unknown   molecular_function unknown   not yet annotated
YCL026C         not yet annotated   not yet annotated   not yet annotated
YOL024W         biological_process unknown   molecular_function unknown   not yet annotated
YCL026C-A   FRM2     negative regulation of fatty acid metabolism   molecular_function unknown   cellular_component unknown
YNR073C         biological_process unknown   molecular_function unknown   not yet annotated
YHR157W   REC104     meiotic recombination*   molecular_function unknown   cellular_component unknown
YLL052C   AQY2     water transport   water channel   cellular_component unknown
YHR160C   PEX18     protein-peroxisome targeting   protein binding   cytosol*
YOR380W   RDR1     response to xenobiotic stimulus   transcription factor   nucleus
YGL089C   MF(ALPHA)2     pheromone response (sensu Saccharomyces)   pheromone   extracellular
YGR016W         biological_process unknown   molecular_function unknown   not yet annotated
YKR015C         biological_process unknown   molecular_function unknown   not yet annotated
YPR025C   CCL1     transcription initiation from Pol II promoter*   general RNA polymerase II transcription factor*   transcription factor TFIIH
YNR069C         biological_process unknown   molecular_function unknown   not yet annotated
YLR302C         biological_process unknown   molecular_function unknown   not yet annotated
YPL065W   VPS28     protein-vacuolar targeting*   molecular_function unknown   not yet annotated
YER137C         biological_process unknown   molecular_function unknown   not yet annotated
YGR219W         biological_process unknown   molecular_function unknown   not yet annotated
YIL028W         biological_process unknown   molecular_function unknown   not yet annotated
YOL053W         biological_process unknown   molecular_function unknown   not yet annotated
YFR035C         biological_process unknown   molecular_function unknown   not yet annotated

Figure 10.  Expression of YOR012W in response to the alpha-factor. (Courtesy of Expression Connection.)

 

            This data shows that between 25-30 mins of exposure to the alpha factor, YOR012W is slightly repressed.  Then, this protein is highly induced at 60 mins, then returns back to being repressed at around 90 mins.  This pattern of expression is also viewed in proteins that transport water, serve as transcription initiator factors, meiotic recombination proteins, etc.  Perhaps YOR012W is associated with factors that are not needed when the alpha factor is first present, but are needed once the alpha factor has been present for a period of time (approx. one hour).  Thus, its function could be similar to that of a transcription initiation factor. 

                                                                                                             

 

 

Expression during the diauxic shift:

Orf Gene Process Function Component
YOR012W         biological_process unknown   molecular_function unknown   not yet annotated
YOR016C   ERP4     secretory pathway   molecular_function unknown   integral membrane protein
YIL055C         biological_process unknown   molecular_function unknown   not yet annotated
YJL220W         biological_process unknown   molecular_function unknown   not yet annotated
YLR007W   NSE1     DNA repair*   molecular_function unknown   nucleus
YGL141W   HUL5     polyubiquitination*   ubiquitin-protein ligase   cellular_component unknown
YJR126C   VPS70     protein-vacuolar targeting   molecular_function unknown   cellular_component unknown
YOL051W   GAL11     transcription from Pol II promoter   RNA polymerase II transcription mediator   mediator complex
YMR189W   GCV2     one-carbon compound metabolism   glycine dehydrogenase (decarboxylating)   not yet annotated
YOL001W   PHO80     regulation of phosphate metabolism   cyclin-dependent protein kinase, regulator   cyclin-dependent protein kinase holoenzyme
YNL278W   CAF120     regulation of transcription from Pol II promoter   molecular_function unknown   CCR4-NOT complex
YDL138W   RGT2     glucose transport*   glucose transporter   plasma membrane
YOR290C   SNF2     chromatin modeling   general RNA polymerase II transcription factor   nucleosome remodeling complex
YMR165C   SMP2     aerobic respiration*   molecular_function unknown   cellular_component unknown
YIL019W         biological_process unknown   molecular_function unknown   not yet annotated
YNR031C   SSK2     protein amino acid phosphorylation*   MAP kinase kinase kinase   cellular_component unknown
YOR154W         biological_process unknown   molecular_function unknown   not yet annotated
YOR110W   TFC7     transcription initiation from Pol III promoter   RNA polymerase III transcription factor   transcription factor TFIIIC
YNL337W         biological_process unknown   molecular_function unknown   not yet annotated
YDR431W         biological_process unknown   molecular_function unknown   not yet annotated
YNR070W   PDR18     biological_process unknown   molecular_function unknown   cellular_component unknown

Figure 11.  This figure shows the expression of YOR012W, and other similar proteins, during the diauxic shift. (Courtesy of Expression Connection.)

            As stated previously, diauxic shift refers to the change between aerobic and anaerobic respiration.  In these conditions, the cell will not use energy in order to replicate, but instead will use its energy in adjusting to the new environment.  In this situation, YOR012W becomes more and more repressed the longer the cell is in this environment.  This pattern is similar to the proteins associated with DNA repair and and transcription promoters.  Thus, it seems possible that this protein is somehow associated with DNA replication. 

                                                                                                                                                                       

Expression regulated in the PHO Pathway:

Orf Gene Process Function Component
YOR012W         biological_process unknown   molecular_function unknown   not yet annotated
YIL165C         biological_process unknown   molecular_function unknown   not yet annotated
YMR165C   SMP2     aerobic respiration*   molecular_function unknown   cellular_component unknown
YOL110W   SHR5     RAS protein signal transduction*   molecular_function unknown   cellular_component unknown
YOR394W         biological_process unknown   molecular_function unknown   not yet annotated
YER153C   PET122     protein biosynthesis   molecular_function unknown   mitochondrial inner membrane
YDR123C   INO2     positive regulation of transcription from Pol II promoter*   specific RNA polymerase II transcription factor   nucleus
YOR336W   KRE5     beta-1,6 glucan biosynthesis   UDP-glucose:glycoprotein glucosyltransferase   endoplasmic reticulum
YGL150C   INO80     DNA repair*   ATPase   chromatin remodeling complex
YIL174W         biological_process unknown   molecular_function unknown   not yet annotated
YLR422W         biological_process unknown   molecular_function unknown   not yet annotated
YDR423C   CAD1     transcription   not yet annotated   not yet annotated
YHL005C         biological_process unknown   molecular_function unknown   not yet annotated
YIL013C   PDR11     sterol transport   ATP-binding cassette (ABC) transporter   membrane
YDR125C   ECM18     cell wall organization and biogenesis   molecular_function unknown   cellular_component unknown
YDL014W   NOP1     rRNA modification*   snoRNA binding   nucleolus*
YDR314C         biological_process unknown   molecular_function unknown   not yet annotated
YFR051C   RET2     ER to Golgi transport*   protein binding   COPI vesicle coat
YGL128C   CWC23     biological_process unknown   molecular_function unknown   cellular_component unknown
YIL086C         biological_process unknown   molecular_function unknown   not yet annotated
YEL045C         biological_process unknown   molecular_function unknown   not yet annotated

Figure 12. Expression of YOR012W with regards to the PHO pathway. (Courtesy of Expression Connection.)  

    As stated previous, the PHO pathway is initiated when phosphate levels decrease. The pathway makes phosphate available for cellular metabolism.  Also stated above, it is expected that proteins associated with cellular reproduction be repressed in such conditions because the cell does not want to "waste" energy on reproduction.  YOR012W is repressed during these conditions, as shown above.  In addition, this protein shows similar expression patterns to proteins that are involved with DNA repair, transcription, and other functions associated with reproduction.

                                                                                                                                                                       

Yeast Cycle Analysis Project:

Name Score Peak
YOR012W 0.01
Reference Genes
CLN2 10.9 G1
HTA1 10.68 S
CLB4 3.08 G2
SWI5 6.726 M
ASH1 11.8 M/G1
Plot of YOR012W

Figure 13. Expression of YOR012W in the yeast cell cycle. (Courtesy of Expression Connection.)  

    This figure shows the expression of YOR012W through the cell cycle of yeast. This protein does not show a very specific pattern through the cell cycle, but instead fluctuates between being induced and repressed.  It seems that  this protein is needed at points throughout the cell cycle, but is induced at specific times and repressed at other time points.  Perhaps this protein has a very specific function in the reproductive cycle, and is expressed only when this function is needed.

                                                                                                                                                                        

 

Expression in response to histone depletion:

Orf Gene Process Function Component
YOR012W         biological_process unknown   molecular_function unknown   not yet annotated
YOR282W         biological_process unknown   molecular_function unknown   not yet annotated
YOR368W   RAD17     meiotic recombination*   not yet annotated   not yet annotated
YPR071W         biological_process unknown   molecular_function unknown   not yet annotated
YBR293W         biological_process unknown   not yet annotated   not yet annotated
YOR069W   VPS5     Golgi retention*   molecular_function unknown   endosome
YFR012W         biological_process unknown   molecular_function unknown   not yet annotated
YNL171C         biological_process unknown   molecular_function unknown   not yet annotated
YER179W   DMC1     meiosis*   single-stranded DNA binding*   nucleus*
YLL007C         biological_process unknown   molecular_function unknown   not yet annotated
YBL048W         biological_process unknown   molecular_function unknown   not yet annotated
YNL181W         biological_process unknown   molecular_function unknown   not yet annotated
YOL118C         biological_process unknown   molecular_function unknown   not yet annotated
YNL076W   MKS1     regulation of nitrogen utilization   molecular_function unknown   cellular_component unknown
YOR070C   GYP1     vesicle-mediated transport   RAB GTPase activator   Golgi apparatus
YPR167C   MET16     methionine metabolism*   phosphoadenylyl-sulfate reductase (thioredoxin)   cellular_component unknown
YOR383C   FIT3     biological_process unknown   molecular_function unknown   cell wall (sensu Fungi)
YGL214W         biological_process unknown   molecular_function unknown   not yet annotated
YMR155W         biological_process unknown   molecular_function unknown   not yet annotated
YLR467W   YRF1-5     biological_process unknown   not yet annotated   not yet annotated
YLR123C         biological_process unknown   molecular_function unknown   not yet annotated

Figure 14.  Expression of YOR012W and other similar proteins with regards to histone depletion. (Courtesy of Expression Connection.)

This data shows that YOR012W is induced until 1.5 hours, when the protein becomes slightly repressed.  After this point, the protein becomes induced again.  Perhaps the expression of this protein fluctuates with the cell cycle. This pattern is similar to that found in meiotic division, golgi retention, meiosis, etc.  Once again, YOR012W shows similar expression patterns as that of proteins associated with reproduction in yeast cells.  

                                                                                                             

 

Expression for Varying Zinc Levels:

Orf Gene Process Function Component
YOR012W         biological_process unknown   molecular_function unknown   not yet annotated
YIL086C         biological_process unknown   molecular_function unknown   not yet annotated
YIL099W   SGA1     sporulation (sensu Saccharomyces)   glucan 1,4-alpha-glucosidase   vacuole (sensu Fungi)
YDL109C         biological_process unknown   molecular_function unknown   not yet annotated
YLR280C         biological_process unknown   molecular_function unknown   not yet annotated
YPL046C   ELC1     RNA elongation from Pol II promoter   transcription elongation factor   transcription elongation factor complex
YIR036C         biological_process unknown   molecular_function unknown   not yet annotated
YIR016W         biological_process unknown   molecular_function unknown   not yet annotated
YOR318C         biological_process unknown   molecular_function unknown   not yet annotated
YPR039W         biological_process unknown   molecular_function unknown   not yet annotated
YHR149C         biological_process unknown   molecular_function unknown   not yet annotated
YPR092W         biological_process unknown   molecular_function unknown   not yet annotated
YBR214W   SDS24     meiosis*   molecular_function unknown   cellular_component unknown*
YCL034W   LSB5     actin filament organization   molecular_function unknown   cellular_component unknown
YLR279W         biological_process unknown   molecular_function unknown   not yet annotated
YGR069W         biological_process unknown   molecular_function unknown   not yet annotated
YJR038C         biological_process unknown   molecular_function unknown   not yet annotated
YFR012W         biological_process unknown   molecular_function unknown   not yet annotated
YJR128W         biological_process unknown   molecular_function unknown   not yet annotated
YDR406W   PDR15     transport   ATP-binding cassette (ABC) transporter   integral membrane protein
YGR067C         biological_process unknown   molecular_function unknown   not yet annotated

Figure 15.  Expression of YOR012W, and related proteins in varying zinc levels. (Courtesy of Expression Connection.)

           In these conditions, YOR012W is repressed.  This patter is similar to proteins that are associated with sporulation, RNA elongation, meiosis, etc.  This unannotated protein shows similar expression to proteins known to be associated with replication.

                                                                                                                                                                                                                       

Conclusion:

To summarize, YOR012W was found to:

Based on these observations, it seems very likely that YOR012W is associated with reproduction of the yeast cells, perhaps with transcription or repair of DNA.   This hypothesis is consistent with the hypothesis derived from analyzing orthologs and hydropathy plots on the previous website (Favorite Proteins).  Thus, it seems very likely that YOR012W is important in reproduction.

*: indicates that more than one annotation exists for the gene.

 

                                                                                                                                                                                 

** Function Junction also provides analysis of microarray data, though did not have any different data for AUS1 and YOR012W than that shown above.  Thus, this data  was not analyzed in this web page. **  

 

References:

Behe, MJ. 1990. Histone Deletion Mutant Challenge the Molecular Clock Hypothesis.” Trend in Biochemical Science.  Vol. 15 Pp. 374-376.

Robinson, A.  An Introduction to DNA Microarray Technology.  European Bioinformatics Institute. <http://industry.ebi.ac.uk/~alan/MicroArray/IntroMicroArrayTalk/sld001.htm> Accessed 10/20/02.  

Thomas, M. 2001. Perturbing Signal Transduction in the Pho Pathway.  University of California. <http://www.ucsf.edu/ekolab/people/melissa.html> Accessed 10/24/02.

----.  1997.  Book Reviews: Histone Deletion Mutant Challenge the Molecular Clock Hypothesis.  Access Research Network. <http://www.arn.org/docs/reviews/rev009.htm> Accessed 10/20/02.

----.  2002.  Expression Connection. <http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl> Accessed 10/25/02.  

----.  2002.  Function Junction.  <http://genome-www4.stanford.edu/cgi-bin/SGD/functionJunction> Accessed 10/25/02.

----. 1999.  Zinc.  Virtual Health.  <http://www.virtualhealthinfo.com/supp/zinc.htm> Accessed 10/24/02.

Megan's Home Page

Genomics Web Tools

Genomic Front Page

Return To Biology Course Materials

Davidson College Biology Department

© Copyright 2002 Department of Biology, Davidson College, Davidson, NC 28036 Send comments, questions, and suggestions to: Meshafer@davidson.edu