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My favorite yeast expressions
I started my search for SCYNL238W expression at the SGD expression connection. Given that Kex2 is involved in the processing of the sex pheromone µ-factor, I would have expected presence of µ-factor to induce transcription of Kex2. This was shown to not be the case however(see results here). Since expression levels were almost entirely unchanged, the gene clustering placed Kex2 among a somewhat diverse selection of genes that also did not respond to µ-factor. This is not an effective clustering pattern to determine related functions. With the exception of nitrogen depletion, which inhibited expression, environmental stresses failed to alter Kex2 expression levels. This surprised me, I would have expected any environmental stress to inhibit reproductive processes, in favor of conserving resources to be used instead in survival pathways. After this, I examined the results from the DNA damaging agents microarray, which also failed to produce any striking expression patterns. Again, clustering created a somewhat diverse group, though there were a surprisingly large number of transcription factors. Expression patterns from the Diauxic shift microarray also coupled Kex2 with a fairly large number of transcription factors, though as in the other cases, the expression pattern was a very moderate one, and therefore clustering will probably not give reliable functional relatives. Only two expression connection microarrays produced a recognizable expression pattern. Sporulation(see results here) induced Kex2 transcription in increasing amounts through 9 hrs. Clustering by this expression pattern related Kex2 to proteins involved in the sporulation process, which is not entirely surprising given that sexual reproduction would be expected under conditions favorable for budding. What was surprising was that no other sex genes clustered near Kex2. I hypothesized that this is due to the fact that the other sexual reproduction genes with which we are familiar are farther down in the pathway, and therefore display different expression patterns. I attempted clustering with different target genes, and found no noteworthy results. The other microarray that produced a recognizable pattern was varying zinc levels. What was noticeable was that when expression under excess zinc levels was plotted against deficient zinc levels, Kex2 was induced(see results here). Excess zinc vs. replete zinc did not alter expression, leaving us to conclude that deficient zinc inhibits Kex2 transcription. Once again, Kex2 did not cluster with any other sexual reproduction proteins, which makes any suggestion of functional relationships to clustering neighbors somewhat suspect. After expression connection, I searched the yeast microarray global viewer. This site searches numerous other microarray databases, but is limited in the fact that no gene clustering results are returned. The most striking expression pattern was from the Posas salt hog1 array, which indicated that Kex2 was induced under 4 out of the 6 saline stress conditions tested. I did not find any of the other expression patterns that were of particular notice, except for the few stress conditions in the Gasch stress array that induced expression of Kex2. But even these did not follow any pattern that I was able to ascertain. Overall, I did not find the microarray data publicly available to be particularly helpful in determining the function of Kex2, or in establishing functional relatives. I would suspect that this is due primarily to the fact that the factors that strongly affect Kex2 transcription were not tested in any of the microarrays accessible. Given that Kex2 lies early in the sexual reproduction pathway, the standard sex gene stimulator, µ-factor, fails to alter Kex2 expression.
Again, I started my search at expression connection, this time for my non-annotated gene SCYNL234W. As noted in my previous web page, it has been previously hypothesized that SCYNL234W is a previously unclassified heat shock protein due to sequence analysis data. The expression data do not support SCYNL234W as a global stress response gene. The gene may however be part of somewhat more specific shock responses. As would be expected for a potential shock protein, µ-factor has no apparent affect on SCYNL234W expression(see results here). The only real pattern from the DNA damaging agents array is that the mec1 mutant represses SCYNL234W in response to gamma irradiation, while the wild type does not. I’m not sure that much knowledge can be gleaned from this fact. The environmental changes microarray produced some very interesting results(seen here). Given the proposed role of YNL234W as a heat shock protein, I would have expected it to be induced universally in environmental stresses. Instead, it shows consistent strong induction under nitrogen depletion conditions, and mild induction in the presence of sorbitol. The Gasch stress microarray(seen here) displays quite similar results to the environmental stress array through Expression Connection(seen here). When clustered under the environmental stress array, SCYNL234W clustered mostly with a group of unknown ORFs, but interspersed were a few stress response transcription factors, and DNA repair enzymes supporting the model of SCYNL234W as a selective stress response(also called heat shock) protein. Oddly, anytime I reclustered the genes using even a very closely related new target, I found an almost entirely new set of clustered genes, suggesting that this is not a functional group. SCYNL234W also demonstrated a recognizable expression pattern during sporulation, and clustered with a number of DNA repair molecules, as well as some genes involved in meiosis. When I reclustered the genes using the meiosis gene SLK19, most of the same 20 genes clustered together once again, suggesting that this grouping may be legitimate(both clusters seen here). The only other microarray that demonstrated a noticeable expression pattern was the altered zinc level microarray. It seems that SCYNL234W is induced at low zinc levels, but that excess zinc has no effect(seen here). Once again, almost all of the clustered genes are non-annotated ORFs, and those that are annotated are of varying function, leaving us with little knowledge of functional relatives. With the presupposition that SCYNL234W may be a stress response protein, I would have expected to see more genes consistently clustering together, particularly in the environmental stress assay. In neither the sporulation nor the zinc microarrays, would I have expected to see much of a pattern, but in both of them, I got the same recurrent group of genes clustering upon multiple target changes, suggesting that these are in fact functional groups. I would suggest that SCYNL234W could possibly be a stress response protein, and one of the stresses to which it responds is reproduction, though this is merely a suggestion. The evidence supporting this is circumstantial at best, but this is the best prediction that I can make with the given data.
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Many thanks to Dr. A. Malcolm Campbell for his guidance in this endeavor as well as others.