March 26th Questions (p53)

1. Regulatory genes are those genes which control the transcription of other regulatory genes or structural genes. The method of this control can happen in a variety of ways including activating, suppressing, or enhancing the transcription of the structural genes. Structural genes are those that code for proteins that are expressed as part of the individual’s phenotype. Regulatory genes often control the expression of more than just one structural gene; also, because the regulatory genes can code for other regulatory genes, a cascade effect is created. The initial regulatory genes control many other genes down the chain. Thus, if there is a mutation in the DNA sequence of the regulatory gene, many subsequent genes will be affected.

The p53 gene is a regulatory gene. Specifically, it is a transcription factor that is activated when the cell experiences abnormal levels of stress. There are nine isoforms of this genes that work together to cause transcription genes to be activated. In the case of the p53 gene, activated transcription genes lead to a target cell beginning the process of apoptosis, or cellular suicide. If the first gene in this pathway (the transcription gene p53) is not allowed to do its job, then none of the subsequent genes in the cascade will be affected, and the overall result of apoptosis will not be achieved. This regulatory gene cascade is present in many genes other than p53. In all of these genes, inhibition of the first effecter prevents any other effects from being expressed. When the p53 gene is inhibited, the genes causing apoptosis are not expressed, thus the cell does not die and a tumor forms. Because there are nine isoforms that play a role in this activation, each of these must be expressed in a specific manner for the p53 gene to be fully functional, and if any of these isoforms is not expressed correctly, this can lead to tumor formation (Bourdon, 280). It is important, then, to study not only the p53 protein as a whole for cancer research, but more specifically how the expression of each of the isoforms is controlled as well as what misfoldings can cause errors.


2. In an evolutionary sense, why is it informative to study cancer and its implications in mice (see Lee and Bernstein, 1993 and Bourdon, 2007)?

Because we have learned that all diseases, cancer included, are subject to mutation, which could prove them even more deadly to all organisms across the world. At the same time all organisms may experience mutations in any part of their body that could potentially grant that organism immunity to a specific disease, virus, or specific kind of cancer. Through studying cancer’s implications in mice, it might be possible to draw helpful parallels from how mice evolve in response to the cancer and how the cancer evolves in response to the mice. These implications would be especially helpful if a mutation in hox/ regulatory genes yields immunity to a certain kind of cancer. This is important because that gene could be selected for and eventually become more abundant in mice populations on its own, but scientists could observe the properties of that mutation and work on researching a way to achieve the same properties in human regulatory genes, so that we may be closer to a cure for certain kinds of cancer.

Another reason that studying cancer and its implications in mice is beneficial is that there are fewer ethical issues associated with mice. In humans, cancer cells cannot be implanted to watch how the genes are expressed throughout the disease progression. In mice, however, this is a possibility. Furthermore, this can be done with many mice which allows researchers to identify if there is more than one misfolding that causes irregular expression of the p53 gene or any of its isoforms. Mice are preferable to any other animal for diseases such as this because their physiology is closely related to that of humans. The way the disease progresses and the mice’s response to drugs will closely parallel the response in humans. Thus, any discoveries that arise in the lab with the mice can be more easily transitioned into a human context.


3. Bourdon discusses the sequence similarity in portions of p53, p63 and p73, and refers to them as a gene family. How do you think these genes arose? Are they paralogs or orthologs of one another? By what mechanism might they have gained new functions?

A gene family is one in which the genes share a known homolog and they also tend to be biochemically similar. The p53, p63, and p73 genes all have a high level of sequence similarity in the DNA-binding domain. This allows the p63 and p73 to transactivate p53-responsive genes causing cell-cycle arrest and ultimately apoptosis. There have also been studies showing that the p53 gene family has a dual gene structure found in Drosophila, zebrafish, and humans. It has also been shown that the human p53 gene has a dual gene structure similar to p73 and p63 genes(Bourdon 277). Due to the similarity in structure and sequence between both p53 genes in other species as well as the similarity between p53 genes and p63 and p73 genes within the same species it is likely that this gene family arose a result of duplication. Gene duplication happens when there is an error in mitosis leading to the duplication of certain gene sequence. These duplications can then grow larger and replicate again through subsequent cell division, which is likely the case with the p53 gene family. If this is the case, these genes are likely paralogs that resulted from a gene duplication event. This is when a gene in an organism is duplicated to occupy two different positions in the same genome. However, as Bourdon mentions, the members of the p53 gene family all have different biological functions. If they all originated from the same duplicated sequence one may wonder how this could be. The duplicated gene sequences, once a part of the genome, are free to mutate and gain new function just as any other gene. Also, if one sequence mutates it will not necessarily affect the others. If the mutation to one of these paralogs is advantageous it may be selected for and become more abundant in the population. It is likely that the p53 gene family originated in a manner similar to this.


4. In the Bourdon paper, the author discusses how changes in expression of the 9 different p53 isoforms (proteins) can cause “genome instability, cancer and other pathologies.” Why then is it important to study protein folding and misfolding in these isoforms?

As we mentioned before, the nine isoforms need to be expressed in a specific manner to allow a stressed cell to enter apoptosis. If any of these isoforms are expressed in an inappropriate amount, the transcription of structural genes that initiate apoptosis will not occur and tumor formation can result. It is important, then, to study these folding and misfoldings to isolate the specific causes of misexpression of the isoforms of p53. If the folding program can predict which misfoldings will lead to the most prevalent mutation that causes the isoforms to lose functionality, then appropriate treatments that prevent or target these misfoldings can be researched. Attacking a cancer that is promoted by a protein, but not knowing any of the properties of this protein can be a fruitless fight. If researchers can determine exactly how the mutation occurs, then a treatment that prevents this mutation could possibly be created. In addition, if this mutation has already occurred in a person, perhaps a treatment could be developed that eradicates this specific protein from the body and other treatment could allow the protein to be folded correctly and prevent tumor formation. In our opinion, these treatments are quite possible in the future if the exact cause of the misfolding is pinpointed through programs such as Folding@Home.


5. Typically, p53 is a “tumor-suppressor gene,” which indicates that if it loses function, tumors will result. However, expression of some of the isoforms of p53 can actually contribute to tumor formation. Further, not all mutations in p53 result in a loss of function. This makes it difficult to understand the clinical role of p53. Considering people like Debbie, why is it so vital to determine the status of p53 in each patient?

It is so vital to determine that status of p53 in each patient because the expression of p53 isoforms can drastically change how cancer behaves and develops. At the same time, knowing the status of p53 in each patient could lend helpful insight that could show a growth that was originally thought to be cancerous, is actually not, since certain types of p53 genes will suppress cancerous tumors. In the case of Debbie, the doctors were not 100% positive that the tumor was cancerous until they had performed an operation, so it is in a case exactly like that in which determining the status of the p53 gene would be vital. With so many isoforms contributing to a variety of different functions, behaviors, and characteristics, knowledge on a patient to patient basis will always serve helpful in treating each patient to the fullest potential of our twenty first century biological and technological advances.