My Favorite Yeast Expression(s):

Ste2 (annotated) and YFL030W (unannotated)

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

My Favorite Annotated Yeast Gene's Expression: Ste2

By mining the databases available, the protein expression given by the function of the gene Ste2 may be further analyzed. Function Junction and Expression Connection, searches of many different databases performed on the SGD database, initiates the discovery of information about this gene.

The Function Junction website's use of the Yeast Microarray Global Viewer (provided by the Laboratoire de genetique moleculaire, Paris, France) is an excellent starting place for exploring this gene's expression. A couple experiments found here are of note:

Screen shots from the Function Junction website. Click on each to see an enlarged, more detailed view.

First, the Yale experiment shows some interesting findings. Of the three different types of conditions the yeast were grown (1M NaCl for 10, 30, and 90 minutes) the Ste2 gene was induced greatly during the the 30 minute condition. This would imply that there is some optimal time for the presence of salt that somehow causes the type a yeast cell to increase its production of Ste2 (encoding alpha pheromone receptor), presumably for reproduction.

The Hardwick rapamycin experiment also provides some interesting information. When rapamycin is added to the yeast cell, induction of Ste2 occurs. Even more interestingly, when amino acid starvation and addition of rapamycin is the experimental condition, induction of the Ste2 gene increases dramatically. This can be interpretated as the cell's attempt to reproduce at times of high stress, which may be counterintuitive.

Unfortunately, no genes were found to have strong interactions with STE2, as is indicated on this rather depressing Function Junction graphic:

Screen shots from the Function Junction website. Courtesy SGD (2003).

The Expression Connection yielded some important hits, which show genes with similar expression patterns, therby making them "guilty by association" and, thus, related to one another. The most obvious experimental scenario where one would expect an induction of the alpha pheromone receptor would be when alpha factor is introduced to the cell. Indeed, this is the case:

Expression at different alpha-factor concentrations for STE2

Screen shots from the Expression Connection website. Courtesy SGD (2003).

As expected, Ste2 is induced when alpha factor is added to the yeast cell. Interestingly enough, however, it doesn't really matter how much alpha factor is added after 1.5 nM. This search also shows several other yeast genes associated with mating: FUS1, FUS3, GPA1, and AXL1. Although Function Junction didn't find these genes directly interacting with STE2, it would not be surprising if these genes were found in to be in some connection, remote though it may be.

Expression in time response to alpha-factor for STE2

Screen shots from the Expression Connection website. Courtesy SGD.

An experiment taking the yeast genomes at different times after the alpha factor was added yielded similar results. Again, production of alpha pheromone receptors when alpha pheromone is present is expected, but this data also suggests that there may be some upper limit (120 minutes?) when the cell may acclimate itself to the condition of extra alpha factor availability or the cell may not have the available material to produce more alpha pheromone receptors.

Expression in response to environmental changes for STE2

Screen shots from the Expression Connection website. Courtesy SGD.

Also notable are those experiments that related the activity of Ste2 to environmental factors, like those that yeast cells may encounter outside of the laboratory. As would be expected, mating factor receptors is repressed when the cell is under large environmental stress. This is the case above, when the cell is attempting to grow in an environment that is depleted of nitrogen. Also, repression of Ste2 can be seen when the cell is in the stationary phase upwards of 6 hours. Again, this is expected, as pheromone receptors are not needed when there is no pheromone for the cell to uptake to initiate reproduction. As would be expected a gene under a similar name (Ste6) is very similar in expression to Ste2. This gene is involved in a factor transport, which is why one would name it in connection with its cousin, Ste2. a factor is produced in greater amounts in the cell when other cells are present to begin sexual reproduction. This makes sense here -- both the genes for alpha factor receptors and a factor transporters are induced when alpha factor is present in the cells.

The other experiments that the Expression Connection website looks for (response to DNA-damaging agents, expression during the diauxic shift, evolution of expression during glucose limitation, regulation by the PHO pathway, expression during the cell cycle, response to histone depletion, expression during sporulation, and response to varying zinc levels) yielded fairly uninteresting results. Overall, the gene Ste2 seems fairly cut and dried. The cell cycle view confirms that the seven-transmembrane region protein is being made constantly for use in the membrane of the Sacchromyces cell. This production increases when the factor that binds to it (alpha pheromone) is present. The yeast cell halts this process when it is under heavy stress and is more concerned with survival than reproduction, or is in a stationary phase until it comes into contact with another yeast cell to mate with.

My Favorite Unannotated Yeast Gene's Expression: YFL030W

The expression of the unannotated yeast gene is more intriguing, as its function is unknown according to the SGD database. Unfortunately, but as expected, no genes were found to be connected with the unannotated gene:

Screen shots from the Function Junction website. Courtesy SGD (2003).

Again, simarly to the Ste2 gene's hits on the Function Junction database, there were some experiments involving YFL030W that stuck out:

Screen shots from the Function Junction website. Click on each to see an enlarged, more detailed view.

Several predictions about the function of the unannotated gene can be made from the preceding experiments. First, according to the Yale salt experiment, it appears NaCl, after a long period of time (90 minutes), induces the production of this gene (graph above goes from 90 to 30 to 10 minutes, left to right). Whether this is due to experimental error or is an actual effect of the gene product is uncertain, however. Also, many different processes could be affected by salt, so the interpretations from this data are boundless. The second experimental condition (Linde anaerobic) was growing the cell in anaerobic conditions. This produced repressed expression of the gene. A hypothesis can be made that this gene is only produced in aerobic conditions or has is a gene where oxygen is necessary to complete its function. Finally, the Jelinsky experiment added MMS, an alkylating agent, to the yeast cells. In our gene, this produced a large induction of the gene product, maybe indicating that the product is needed to help repair the cell when DNA-damaging agents are added.

The Expression Connection webpages also yielded some interesting findings, although many of the experimental conditions produced no change in the expression of YFL030W:

Expression during the diauxic shift for YFL030W

Screen shots from the Expression Connection website. Courtesy SGD (2003).

There is a fairly interesting pattern here, where immediate repression eventually yields to induction in an almost exponential fashion. This experiment indicates again that this gene may be involved in anaerobic respiration, as diauxic shift is a change from anaerobic to aerobic respiration. In addition, this appears to be in conjunction with the Linde article -- anaerobic conditions caused a repression of YFL030W. In the experiment above, anaerobic conditions show repression. However, as aerobic respiration becomes available, induction of the YFL030W gene is seen. The genes that were found to be similar to our unannotated gene are fairly vaired. SFC1 is of particular note, as it is also found in a different experiment, further connecting it with YFL030W. This gene's biological process is fumarate transportation, which is essential for growth on ethanol or acetate (SGD). How this connects with the oxygen dependancy of this gene remains to be seen.

Expression in response to environmental changes for YFL030W

Screen shots from the Expression Connection website. Courtesy SGD (2003).

The results of the environmental changes experiment is very informative, as the outcomes are very strong (both induction and repression), and since it involves so many conditions, those genes that "fit" well are more likely to make the gene in question "guilty by association". YFL030W is induced during heat shock, during the yeast cell's stationary phase (especially after half a day), and when ethanol is added to the media. When sugars are added (glucose, mannose, and sucrose especially) the gene is dramatically repressed. Again, these data indicate YFL030W's importance during aerobic cellular activity. The repression in the presence of sugars in perplexing, however, as it is hard to see a connection between sugar addition and respiration.

Screen shots from the Expression Connection website. Courtesy SGD (2003).

The genes listed above identify with YFL030W most uniquely. This is again a variety of gene products, but fumarate transport (SFC1), acetate metabolism (ACH1), and aerobic respiration (RIP1) all seem like viable options for this gene product of the unannotated ORF. The other experiments weren't extremely helpful. The cell cycle analysis, for example, showed that the gene is held fairly constant throughout the cell cycle. It is fairly clear that the gene comes to play in extreme conditions. In any case, it is almost certain that anaerobic and aerobic conditions hold the key to the product of the unannotated gene on chromosome 6.

The data gleaned from the original look at YFL030W (without microarray data) was not very informative, and not much could be hypothesized. However, this data surely preliminarily confines the unannotated gene to a more selective group.

References:

Jelinsky, Scott A. and Leona D. Samson. Global response of Saccharomyces cerevisiae to an alkylating agent. PNAS, Vol. 96, Issue 4, 1486-1491, February 16, 1999

Linde, J. J. M. ter. Genome-Wide Transcriptional Analysis of Aerobic and Anaerobic Chemostat Cultures of Saccharomyces cerevisiae. Journal of Bacteriology, December 1999, p. 7409-7413, Vol. 181, No. 24.

Palmieri L, et al. (1997) Identification of the yeast ACR1 gene product as a succinate-fumarate transporter essential for growth on ethanol or acetate. FEBS Lett 417(1):114-8

Saccharomyces Genome Database

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