Purpose of this Page
The purpose of this page is to investigate the purpose and function that the unannotated ORF YOL058C serves in Saccharomyces cerevisiae. To accomplish this task I will analyze and discuss DNA microarray data. I will be investigating multiple experimental conditions that yeast cells are put under and looking at the microarray data to see if YOL085C is a significantly induced or repressed along with any other known genes to try and identify YOL085C's purpose by the "guilt by association" analyzing technique.
Databases Searched and Found Significant Results for YOL085C
Low concentrations of alpha factor has very interesting effects on the expression of YOL085C. There are very drastic changes of induction and repression between low level concentrations of alpha factor in the presence of yeast. Two other ORFs show similar patterns of induction but not repression. This data has two interesting points to be observed. First, is the high level of fluctuation at low levels of alpha factor and second is the drastic switch of induction to repression and back to induction of YOL085C in a matter of 1.35nM of alpha factor. This may indicate that YOL085C is involved in some process of shmooing when only low level of alpha factor are available. It would be best if the other two ORFS, YOR156C and YCL048W, were annotated genes with a known function so that a hypothesis could be form through "guilt by association" technique. Unfortunately the two ORFs do not have a known function, however this data is promising and shows potentially that YOL085C does have a specific role in yeast metabolism.
From the data shown in this microarray it is very clear that YOL085C is very sensitive to large changes in temperature. Increases in heat cause a 3 fold induction of YOL085C at almost all the various heat increases conducted in this experiment. The reverse affect is also true, decreases in heat had a 3 fold repressive effect on YOl085C expression. The gray squares indicate that not data was able to be collected for a particular interval of an experiment, like in the first heat shock test. I have no doubt that if data were collected at the gray intervals for the first heat shock test there would be a 3 fold induction. The only other condition of interest for this experiment is the amino acid starvation condition. There was significant repression of YOL085C during the amino acid starvation test, but this is to be expected because most expression is repressed when yeast is starved. It is reasonable to say after looking at this microarray data YOL085C is probably involved in some sort of temperature regulation process or a process that is governed by the temperature of the environment where yeast are located.
There is not much data to show that YOL085C plays any role in the yeast cell cycle, but there is one point worth noting, at point cdc15 10 minutes there is 3 fold repression. The CLN2 gene and HTA1 gene are also repressed 3 fold at cdc15 10 minutes. The two annotated genes CLN2 and HTA1 are involved in the start of the G1 cycle and chromatin assembly respectively. YOL085C may play a minor part at this stage of the cell cycle with CLN2 and HTA1.
The histone depletion test caused initial induction which was then slightly repressed and at the 6 hour mark there was a sudden 3 fold induction. This pattern coincides with the behavior of ORF YFR057W, but to a lesser degree. The gene RPS26A shows similar induction at the 6 hour mark, but it does not mimic YOL085C's early behavior in the experiment. There is some affect on YOL085C expression by histone depletion which indicates that YOL085C may be involved in collaboration with RPS26A and YFR057W in conditions of extreme histone depletion.
The data recorded for the zinc experiment show that zinc depletion results in the overall repression of YOL085C. The condition involving the Zap1 mutant causes a high repression of YOL085C which suggests that the repression of YOL085C is a component of zinc homeostasis in yeast cells. Other genes which have known functions that acted similarly to YOL085C in this experiment are primarily genes that are involved in meiosis. This data implies that zinc deficiency causes a halt to cellular processes involved in meiosis. It could be possible that YOL085C is a gene that is involved in meiosis along with the other unannotated genes that act similarly to zinc depletion.
Microarray data on YOL085C offered some revealing data on a ORF that has no known function. It is fairly clear that YOL085C expression is very sensitive to temperature fluctuations and that it is is directly repressed in the Zap1 mutant when there is a zinc deficiency. The databases on variable alpha factor concentrations and histone depletion had interesting results for YOL085C, although there were not many genes with known functions that were compared to YOL085C in these tests, so it is difficult to say what the function of YOL085C is under those conditions. Nonetheless, it is worth noting that there was clear similarity between YOL085C and multiple ORFs in these databases which shows that YOL085C does serve a function (at least in the scope of the databases shown here).
Lyons TJ, et al. (2000) Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc Natl Acad Sci U S A 97(14):7957-62
Wyrick JJ, et al. (1999) Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402(6760):418-21