MY FAVORITE YEAST GENES
Figure 1. These budding yeast cells have been tagged using GFP (Green Fluorescent Protein) and are visualized using fluorescence microscopy (http://www.unige.ch/sciences/biologie/bimol/htmls/gasser-f.html). Permission requested from Susan Gasser.
is located in the genome of Saccharomyces cerevisiae commonly known
as baker's or budding yeast (SGD, 2001; http://genome-www.stanford.edu/Saccharomyces/).
This gene is situated on chromosome X and is called such because it is
a "Factor ARrest" gene (YPD, 2001; http://www.proteome.com/databases/YPD/reports/FAR1.html).
FAR1 is a cyclin-dependent protein kinase inhibitor involved in cell-cycle arrest (SGD, 2001; http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=FAR1). This arrest in the G1 phase is important because it allows for cell-cycle synchronization between two haploid cells with opposite mating types. The cell-cycle arrest begins with the secretion of peptide pheromones a and alpha by haploid yeast cells. This secretion induces conjugation between cells of opposite mating types along with morphological changes within the cells when the pheromones bind to their receptors. This binding initiates a signal transduction pathway since the receptor is coupled with a heterotrimeric guanosine triphosphate-binding protein (G protein) in both haploid yeast cells. A mitogen-activated protein (MAP) kinase cascade is stimulated and Cdc28 protein kinase is inactivated (Leeuw et al. 1210). The cell cycle is halted since Cdc28p is essential for the G1 phase to end and the S phase to begin. Far1p inactivates the Cdc28 protein kinase of the Cdc28p-Clnp complex. The transcription of FAR1 is actually induced by the secreted mating pheromone (Peter and Herskowitz 1230). FAR1 may also play a role in the polarized orientation of growth during mating (Butty et al. 1511).
A FAR1 mutant has a viable phenotype. Two substitutions in FAR1 lead to the far1-D1 mutation--glycine 646 and proline 671 are replaced by aspartic acid and leucine, respectively (Figure 3). This null mutant can still induce the signal transduction pathway as in the wild-type, but is unable to halt the cell-cycle at the G1 phase when exposed to mating pheromone. Far1-D1 mutant exposure to mating pheromone can also lead to unusual cell morphology. However when these mutants are not affected by mating pheromone, they have normal cell growth, budding, size, and pheromone production. A second FAR1 mutant (far1-22p) results from the replacement of serine 87 with proline (Figure 3). This mutant can induce a G1 arrest in the absence of a mating pheromone by altering the phosphorylation by the Cdc28p-Cln2p kinase complex. There are six other null mutants including FAR1-22,nls1; FAR1-22deltaNES, far1-s, Far1-60F3p, farc1-c, and far1-H7 at the FAR1 locus (YPD, 2001; http://www.proteome.com/databases/YPD/reports/FAR1.html).
Yeast Proteome Database Protein Report for FAR1- This site is a wealth of knowledge--it describes FAR1's function, pathway, mutant phenotype, genetic interactions, etc.
SGD- This site provides a summary of FAR1.
Annotated Yeast Gene: CDC28- A fellow student's web page describing CDC28, a cyclin-dependent kinase. This page describes the cell cycle and the role of cyclin-dependent kinases.
The unannotated gene YBR293W is an ORF (open reading frame) since only
physical properties are known.
It is located on the long arm of chromosome 2 in the genome of Saccharomyces cerevisiae.
Figure 4. Physical map of chromosome 2 illustrating the unannotated gene, YBR293W.
1 ATGAGTATTT CAAATTGGAT CACCACTGCG TATTTAATTA CATCAACATC
51 TTTTCAACCT CTTTATGGGT CATTTTCTGA TGCACTTGGT CGAAGAAACT
101 GCCTTTTCTT TGCTAATGGG GCTTTTACCA TTGGATGTCT AGCCTGTGGT
151 TTCTCGAAAA ACATCTACAT GCTTAGTTTT ATGAGAGCAT TGACAGGCAT
201 AGGAGGTGGT GGCTTGATCA CACTTTCTAC AATCGTAAAT TCAGACGTTA
251 TTCCAAGTTC GAAAAGAGGA ATTTTTCAAG CGTTTCAGAA TTTACTTTTG
301 GGATTTGGTG CCATATGTGG AGCGTCTTTC GGTGGCACAA TAGCGTCGAG
351 CATTGGTTGG AGGTGGTGTT TTCTCATCCA AGTACCCATA TCTGTGATTA
401 GTTCCATATT AATGAATTAT TATGTACCTA ATCAGAAAGA ATATAATCGT
451 CAAAATTCTA GCATATTCCA AAATCCCGGA AAAATACTCA GGGACATAGA
501 TGTTATGGGC TCAATTCTTA TTATAACTGG TCTCACACTA CAGCTTCTTT
551 ACCTGAGCCT GGGGTGTTCT ACTTCTAAAT TATCATGGAC CAGCCCTTCT
601 GTGCTACTGC TATTAGTTGG GAGTGTAATA ATCCTCTTAC TGTTCATATT
651 GCACGAAAGG AAAACAAGTG CTAGAGCGAT TATTCCTATG GAGCTGGTCA
701 ATTCCTCCTA CAGTGTCGTT GTACTTTCGA TAAGTATACT TGTTGGTTTT
751 GCCAGCTACG CGTATCTTTT TACTTTACCA TTATTCTTTC AGATTGTACT
801 TGGAGATTCC ACTGCAAAAG CAGGATTACG TCTTACGATT CCTTCCCTAT
851 TTACTCCGGT AGGCAGTCTC ATAACAGGAT TTTCCATGAG CAAGTACAAC
901 TGTCTAAGAT TATTACTCTA CATTGGTATT TCTTTGATGT TTTTGGGTAA
951 CTTTTTATTC CTGTTTATTG AAAAAACTTC TCCGAACTGG TTGATTGGTC
1001 TATTTTTGAT ACCTGCAAAT CTAGGACAAG GTATCACTTT TCCTACGACC
1051 TTGTTTACTT TCATATTTAT GTTCTCTAAG AGTGACCAAG CTACTGCGAC
1101 ATCAACTTTA TATTTATTCC GTAGTATTGG ATCTGTATGG GGTGTTGCAA
1151 TTTCAGCTGG CGTCATTCAA TTATCTTTCG CAGGTTTATT GCGTAGTAAT
1201 TTGAAAGGTC TACTGGATGA AAACAAGATA AAGAAACTTA TTGTTCAGCT
1251 TAGTGCAAAC TCCTCATATA TTGGATCTTT ACATGGCGAA GTTAAAAACA
1301 CAGTCATAAA GAGTTTTGAT GAGGCAACAA AGAGGGCTCA TCTAATGTCT
1351 ACATTACTCT CTTCATTGGC CCTGATACTC TGCATCCTTA AAGACAATCT
1401 GGCGAAACCT AAAACAAGAA GATAA
species: Saccahromyces cervisiae
definition: chromosome II reading frame
E=0.0, excellent match
nucleotide length: 4160 bp
accession number: Z36162 Y13134
amino acid sequence: MSISNWITTAYLITSTSFQPLYGSFSDALGRRNCLFFANGAFTI
(predicts secondary structure of a protein)
51.05% random coil
22.78% extended strand
The reliability plot did not indicate that this was a correct prediction since very little of it was above 0.8.
Analysis (predicts whether protein is an integral membrane protein)
This ORF most likely codes for an integral membrane protein since the hydropathy plot peaks above 2.0.
There was only 30.4% alignment with a sugar transporter with an E-value of 1x10-4. This must not be a very highly conserved sequence.
YBR293W most likely codes for an integral membrane protein, but I could not ascertain the function of this gene. The only prediction I can make regarding the role of this gene in the life of yeast would be that it is involved in budding since genes that regulate budding are not highly conserved.
Kyte J, Doolittle
RF. 1982. J. Mol. Biol. 157:105-132.
Leeuw T, et al. 1995. Pheromone Response in Yeast: Association of Bem1p with Proteins of the MAP Kinase Cascade and Actin. Science 270:1210-1213.
Peter M, Herskowitz I. 1994. Direct Inhibition of the Yeast Cyclin-Dependent Kinase Cdc28-Cln by Far1. Science 265:1228-1231.
NCBI. BLASTn Results. http://www.ncbi.nlm.nih.gov/blast/Blast.cgi#536749 Accessed 2001 Sept 30.
NCBI. Conserved Domain Database. http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi Accessed 2001 Sept 30.
PREDATOR. PREDATOR result for UNK_2789840. http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa-predator.html Accessed 2001
SGD. FAR1/YJL157C. http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=FAR1 Accessed 2001 Sept 28.
YPD. YPD Protein Report for FAR1. http://www.proteome.com/databases/YPD/reports/FAR1.html Accessed 2001 Sept 28.