As discussed in a previous web assignment (click here to view), SNF3 is found on the fourth chromosome of Saccharomyces cerevisiae. It is located in the plasma membrane and encodes for a glucose sensor protein. It is involved in glucose binding and glucose transporter and receptor activity. This web assignment will examine the role of SNF3 using microarray data from various experiments. For each experiment, a scale (Figure 1) will be used to determine the extent of the induction and repression of the gene.
Figure 1. The color scale expression levels of genes as determined by microarrays. The more intense red color indicates a strongly induced gene, while the intense green color indicates a strongly repressed gene. The black in the middle indicates a 1:1 ratio with the control (Image from Expression Connection 2004).
Evolution of expression during glucose limitation (Ferea, T.L., et al. 1999). click here to read abstract of this article
This experiment used evolved strains from three independent cultures after continuous aerobic growth that had been limited to glucose for more than 250 generations. Many genes had significantly altered expression, and these genes were "involved in glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolite transport" (Ferea, T.L., et al. 1999).
SNF3 was both reduced and induced under the experimental conditions of glucose limitation (Figure 2). Since the SNF3 gene is involved in glucose binding and glucose transporter and receptor activity, I expected the gene to be repressed. If there is no glucose present, I expected this gene to be expressed a lot less than when there was an abundance of glucose.
Figure 2. SNF2 gene expression during glucose limitation. When compared to the control, one evolved strain showed a 1:1 ratio with the control, one evolved strain showed slight reduction, and one showed slight induction (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl>).
Figure 3. Gene expression of SNF3 during glucose limitation and 20 genes with similar expression levels. (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YDL194W&dataset=evolution&type=similar>)
In Figure 3, the gene expression of SNF3 is compared with 20 genes that have the most similar expression to SNF3 in the experimental condition of glucose limitation. None of these genes shares the same biological function or process, but a few are located in the plasma membrane with SNF3, possibly exhibiting a correlation between the location of the gene and its expression during glucose limitation; however, there is not clear enough evidence to make any conclusions from this data. The majority of the genes with similar expressions do not have a known biological process or molecular function. Guilt by association may be able to associate some of the unknown functions, processes, and components with those of SNF3.
Expression during the diauxic shift (DeRisi, J.L., et al. 1997) click here to read abstract of this article
The diauxic shift refers to the metabolic shift from fermentation to respiration. This experiment investigated the temporal program of gene expression that occurred with the diauxic shift which indicates the role of the gene in this shift (DeRisi, J.L., et al. 1997). Figure 4 shows the pattern of SNF3's gene expression as a result of time. The gene begins repressed and rises gradually until about the tenth hour. At this point, the gene is reduced and raises sharply at about the sixteenth hour. Figure 5 compares the expression of SNF3 with the 20 most similar gene expressions during the diauxic shift. Again, many of these genes do not seem to have similar processes, functions, or locations. However, AZR1 is located in the plasma membrane with SNF3 and seems to have a similar function as SNF3 as AZR1 transports azol and SNF3 transports glucose.
Figure 4. Expression levels of SNF3 during the diauxic shift. Gene expression of SNF3 varies as a result of the diauxic shift and increasing time (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl>).
Figure 5. Gene expression of SNF3 during a diauxic shift and 20 genes with similar expression levels (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YDL194W&dataset=diauxic&type=similar>).
Expression in response to histone depletion (Wyrick, J.J., et al. 1999) click here to read the abstract of this article
Genes are usually repressed by the eukaryotic genome containing nucleosomes, DNA wrapped around histone proteins. This experiment investigated how nucleosomes influence global gene expression by depleting the histones. The depletion of histone H4 caused 15% of the genes to have induced expression, 10% of the genes to have reduced expression, and 75% to have no significant change of expression (Wyrick, J.J., et al. 1999). SNF3, after a little more than an hour, is one of the genes that is induced in response to the histone depletion as shown by Figure 6. One of the genes with a similar gene expression in this experimental condition, MEP1, has the same cellular component as SNF3 and transports ammonium instead of glucose (Figure 7). These similarities explain why these genes have similar expressions in the same environment.
Figure 6. Expression levels of SNF3 in a response to histone depletion. Gene expression of SNF3 varies as a result of histone depletion and increasing time (Image from <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl>).
Figure 7. Gene expression of SNF3 during histone depletion and 20 genes with similar expression levels (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?id=23660&dataset=histone&type=graph>).
Evolution of expression during glucose limitation (Ferea, T.L. et al. 1999). click here to read abstract of this article
For details of this experiment, see previous section about glucose limitation. Figure 8 shows that all three evolved strains were reduced about the same amount. This is what I expected because I had hypothesized in an earlier web assignment (click here to view that assignment) that this gene was involved in the signal transduction of glucose. Since the amount of glucose was decreased, I assume that there is some pathway in which the presence of glucose signals the production of YDL199C and the lack of glucose resulted in less expression of YDL199C.
Figure 8. SNF2 gene expression during glucose limitation. When compared to the control, all three evolved strains were repressed about the same amount (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl>).
Figure 9 can be used to help associate a biological process, molecular function, and cellular component with the unknown YDL199C through the guilt by associated method. Since YDL199C and these genes have similar gene expression, there is a possibility that they will also have similar processes, functions, and cellular components. The 20 genes with similar gene expression during glucose limitation do not have similar processes or cellular components connected with them. Some processes include transcription regulation, protein catabolism, and chromatin remodeling and some possible cellular components include the ER, nucleus, transport vehicle and the mitochondrion. Although these are some possibilities, it is difficult to determine whether or not these will actually have the same characteristics or if they exhibit similar gene expression for some unrelated reasons.
Figure 9. Gene expression of SNF3 during glucose limitation and 20 genes with similar expression levels (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YDL199C&dataset=evolution&type=similar>).
Expression during the diauxic shift (Derisi, J.L., et al. 1997) click here to read abstract of this article
For details of this experiment, see previous section about the diauxic shift. Figure 10 indicates that YDL199C is induced for almost the entire time, except for a drop off around the sixteenth hour. This suggests that the gene YDL199C may be involved in the metabolic shift from fermentation to respiration.
Figure 10. Expression levels of SNF3 during the diauxic shift. Gene expression of SNF3 varies as a result of the diauxic shift and increasing time (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl>).
Using the guilt by associated method, it can be hypothesized that YDL199C may be involved in ethanol fermentation or aerobic respiration (Figure 11), which would confirm the results from Figure 10. There is no definite way to determine whether these genes are in fact related or if they simply have similar gene expression during the diauxic shift, but this figure does present possible new processes of YDL199C.
Figure 11. Gene expression of SNF3 during the diauxic shift and 20 genes with similar expression levels (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YDL199C&dataset=diauxic&type=similar>).
Expression in response to histone depletion (Wyrick, J.J., et al. 1999) click here to read the abstract of this article
For details of this experiment, see previous section about histone depletion. Figure 12 shows that YDL199C is induced at a fairly constant slope during the time of the experiment with a jump at about 1.5 hours and its highest induction at the final time of 6 hours. Figure 13 indicates that, by guilt through association, YDL199C may be involved in amino acid phosphorylation, cellular fission, or DNA replication. Many processes, functions, and components are unknown in this figure which may just mean that these genes have not been researched extensively. One cellular component of a similarly expressed gene that catches my eye is that of YHR140W. This gene is expressed as integral to a membrane, and the YDL199C, from my earlier web assignment, is probably found in a membrane as well. This is an interesting similarity, but since the process or function of YHR140W is not known, I can not associate any process or function with YDL199c.
Figure 12. Expression levels of SNF3 during the histone depletion. Gene expression of SNF3 varies as a result of histone depletion and increasing time (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl>).
Figure 13. Gene expression of SNF3 during histone depletion and 20 genes with similar expression levels (Image from Expression Connection <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YDL199C&dataset=histone&type=similar>).
Conclusion
The abundance of microarray information seems to affirm some presumptions of the function of YDL199C and sheds light on some other possible functions. The glucose limitation experimental data confirms that there is probably a relationship between glucose and the YDL199C gene. When there was a limited amount of glucose present, gene expression of this gene was reduced. The information from the diauxic shift experiment proposed that this gene may be involved in the metabolic shift from fermentation to respiration. Guilt by association does not provide a clear associated process or function because there is no clear pattern of function or process of the genes with similar gene expression under the same experimental conditions.
DeRisi, J.L., Iyer, V.R., and Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale [abstract]. Science, Oct 1997; 278: 680 - 686. <http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000045635>. Accessed 2004 Oct 21.
Expression Connection Database. 2004. <http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl> Accessed 21 October 2004.
Ferea, T.L., Bostein, D, Brown, P.O., and Rosenzweig, R.F. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast [abstract]. PNAS, Aug 1999; 96: 9721 - 9726. <http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000060077>. Accessed 2004 Oct 21.
Wyrick, J.J., Holstege, F.C., Jennings, E.G., Causton, H.C., Shore, D, Grunstein, M, Lander, E.S., and Young, R.A. 1999. Chromosomal landscape of nucleosome-dependent gene expression and silencing yeast. Nature. 1999 Nov 25;402(6760):418-21. <http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000055640>. Accessed 2004 Oct 21.
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