Tuesday, April 7, 2009
Galactose pathway
On page 130, Carroll mentions the fungus S. kudriavzevii. It is a prime example of the fossilization of genes. In this species, the galactose pathway is entirely fossilized. Please explain the role of galactose pathway in the organisms that utilize it. Include in your response an explanation of feedback mechanisms, proteins, and genes involved in the pathway. In other words, how does it work? Additionally, explain why this pathway is no longer under intense selection in S. kudriavzevii.
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The galactose pathway is used to “convert galactose into a usable form of glucose through series of enzymatic steps” (130). Barker’s yeast for example, can utilize the galactose as an alternative source of energy. The pathway requires four different enzymes that encode for four different genes. . After an increase in galactose concentration, galactose molecules bind onto Gal3p. This event leads via Gal80p to the activation of Gal4p, which then induces GAL3 and GAL80 gene transcription, There is a functional feedback loop that closes with the capture of activated Gal4p by newly synthesized Gal3p and Gal80p and decreases transcriptional activation and creating again the protein complex that can bind incoming galactose molecules. There are three other proteins involved to control the making of the enzymes and to make sure that the yeast makes enzymes only when they are needed and galactose is available.
ReplyDeleteThe only yeast that doesn’t utilize galactose is S. kudriavzevii. The reason for this is that “each of the seven genes had various-sized chunks of code missing that obliterated the integrity of their text” (131). The species adapted to living on other sugar sources and its galactose pathway was no longer needed and so it was no longer used. This example shows how specific fossilization of a gene is. This also relates to natural selection, and how it maintains what is needed but can’t maintain what is not needed anymore. However, the species inactivation can’t be easily reversed. Once a function is gone it most likely will not return, this is the rule of use it or lose it. Just like in the example of the ice fish they will never again use hemoglobin and the S kudriavzavii will not use galactose. The downside if this is that if for some reason the environment were to change again, the species will not have the genes available to them again and may not survive.
http://adsabs.harvard.edu/abs/2006q.bio.....4012S
http://www.crem.fct.unl.pt/Personal/Ze_Paulo/Saccharomyces/Saccharomyces.htm
As discussed in the earlier comment, the galactose pathway is a sequence to convert galactose into a form of glucose that is usable to brew alcohol. The pathway includes 7 genes that code for four different enzymes and three proteins that control the making of the enzymes. A feedback loop is created. When no galactose is present, the proteins stop the production of enzymes because they are not needed. However, when there is galactose, the proteins aid in the production of the enzymes needed.
ReplyDeleteIn the specific case of S. kudriavzevii, the DNA structure was a little different than that of normal baker’s yeast. This was found on leaves in Japan, rather than sugary plants, so it was of no use to brew alcohol. Therefore, the galactose pathway was not necessary to produce a usable form of glucose.
This resulted in significant changes in the 7 genes involved in the pathway; they were almost completely missing. The genes became fossilized over time because they were no longer a selective advantage. Evolution helps genes survive that are needed for the organism to survive, but unused genes are just left to die. In this case, the genes were not “immortal genes,” therefore, they were not safe over time by not being used by the species.
In a report done by the University of Wisconsin - Madison, where Carroll did much research, he was quoted saying “many people think evolution is always happening in a forward direction” (Bio-Medicine). However, evolution can actually get rid of genes from the past that are no longer an advantage. In the study done with S. kudriavzevii, the genes were found completely cut out of the sequence, with all genes around them fully intact.
When genes become fossilized, they are sometimes called relic genes or psuedo-genes. When observed, they look like “faded sign posts” that tell a past. Therefore, when researching ancient organisms, or even the Japanese yeast, stories can be told through the genes, even if they have evolved away.
Closer research of the missing genes in S. kudriavzevii showed a mutation in the DNA replication. Scientists studied the mechanism that binds the ssDN
A and initiated the replication process. During this experiment, a mutation was found within the ssDNA-binding protein. Therefore, the protein wasn’t binding to the DNA to be copied or repaired. This lead to the gradual disappearance and decay of the 7 genes that coded for the galactose pathway in this Japanese yeast.
http://www.hhmi.org/bulletin/spring2005/pdf/Yeast.pdf
http://www.vetscite.org/publish/items/001888/index.html
http://news.bio-medicine.org/biology-news-2/Fossil-genes-reveal-how-life-sheds-form-and-function-153-1/
Galactose is a hexose sugar, similar to glucose, differing only in the stereochemistry of C4. Stereochemistry relates to the special arrangements of molecules. Galactose is part of the disaccharide lactose. Unpon entering the cell, galactose is phosphorylated by glactokinase. Then a UDP glucose group (a nucleotide sugar) exchanges its glucose for galactose. The enzyme UDP glucose
ReplyDelete-> galactose 1 phosphate uridylyltransferase governs this reaction. An empirase then changes the stereochemistry of the C4 on the galactose, turning the galactose into glucose. The glucose is then released as glucose-1-phosphate. The glucose -1-phosphate undergoes structural changes, making it glucose-6-phosphate. This glucose molecule is then capable of entering glycolisis. There is a negative feedback loop in this reaction as excessive glucose binds to the necessary enzymes for the reaction. This is meant to prevent the energy expenditure needed to turn galactose into glucose when there is already a lot of glucose available. Also the Galactose pathway is activated by the presence of galactose.
The genes coding for the enzymes at work in this process are no longer under intense selection by S. kudriavzevii Due to the simple fact that galactose was became scarce in there environment, and was no longer a usable source of energy. The protist turned to other sources of energy and this metabolic pathway was no longer necessary.
chemistry.umeche.maine.edu/CHY251/Terms4.html
en.wikipedia.org/wiki/Udp-glucose
http://www.biocarta.com/pathfiles/m_g1pPathway.asp
Galactose is a monosaccharide that undergoes dehydration synthesis with glucose to form lactose. In galactose metabolism, galactose undergoes enzymatic reactions to form glucose. The first step in this process involved the phosphorylating-action of galactokinase, converting galactose into galactose 1-phosphate. Galactose 1-phosphate is then exchanged with the glucose group in UDP-glucose by means of galactose 1-phosphate uridyltransferase, resulting in UDP-galactose and release glucose-1-phosphate. The glucose 1-phosphate is then converted into glucose 6-phosphate by phosphoglucomutase. The final product is now able to undergo glycolysis. Galactose is used as fuel for glycolysis when glucose is not present. The GAL genes responsible for the break down of galactose are switched off by the presence of glucose, acting as means of negative feedback.
ReplyDeleteAccording to an article about Chimeric genomes of Natural hybrids of Saccharomyces, the similarities between S. cerevisiae and S. kudriavxevii indicate that derivation “…from a single hybridization event”, after which “the hybrid genome underwent extensive chromosomal rearrangements, including chromosome losses and the generation of chimeric chromosomes by the nonreciprocal recombination between homeologous chromosomes.” In part to selective pressures on fermentation, “hybrid genomes maintained the S. cerevisiae genome but reduced the S. kudriavzevii fraction”, which resulted in S. kudriavzevii’s inability to utilize the galactose pathway.
Chris Todd Hittinger, who worked with Carroll on a PNAS article about the fossilized genes in S. kudriavzevii, said that “…numerous DNA bases…have been edited out through mutation to terminate the physiological message they were responsible for transmitting along the pathway”, suggesting a mutation, perhaps during hybridization of the Saccharomyces genome caused S. kudriavzevii to lose the GAL genes. Antonis Rokas, another of Carroll’s colleagues, also mentions that genes are fossilized if they are no longer used. This statement suggests that S. kudriavzevii lived in an environment with high levels of glucose, getting rid of the need to metabolize galactose.
http://ethesis.helsinki.fi/julkaisut/laa/biola/vk/peuhkuri/fig2_3.gifhttp://www.biocarta.com/pathfiles/m_g1pPathway.asphttp://74.125.95.132/search?q=cache:9Kp6eZ4b2qcJ:biochemie.web.med.uni-muenchen.de/Yeast_Biol/03%2520Yeast%2520Metabolism.pdf+galactose+metabolism+in+yeast&cd=2&hl=en&ct=clnk&gl=us&client=firefox-ahttp://aem.asm.org/cgi/content/abstract/75/8/2534http://www.vetscite.org/publish/items/001888/index.html