Chemical Genetics
This page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
This page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
What is chemical genetics?
Chemical genetics is the use of small molecules to investigate proteins and biochemical pathways. Some small molecules have the ability to bind to proteins in a very specific way, and can alter the way that protein functions for a given period of time. For example, if you have ever taken ibuprofen for a headache, you have exposed your body to chemical genetics. Ibuprofen inhibits a pathway that produces prostaglandins (compounds that cause inflammation and pain). When the body is exposed to ibuprofen, the pathway is shut down, and you will not feel the discomfort from a headache. [1]
Do any chemicals inhibit the XPA protein?
When a chemical is known to affect a specific gene or protein, it is registered PubChem and similar databases. PubChem can be searched by bioassay, compound, or substance to help identify these particular chemicals. A PubChem search for XPA returned the chemical sulforaphane as a potential inhibitor of XPA. |
Sulforaphane is a natural dietary isothiocyanate that is normally found in broccoli and other cruciferous vegetables. There are many types of isothiocyanates, and are found in a wide variety of vegetables, but they are all defined by the presence of the -N=C=S group (Figure 1). Sulforaphane contributes to many biological processes in the body and is highly recommended in the diet for its chemopreventive properties. [2] Although sulforaphane is active in many pathways, sulforaphane plays a key role in the oxidative stress pathway. [3] Sulforaphane is directly involved with two oxidative stress proteins called Keap1 and Nrf2. In the cell, Nrf2 is normally repressed by Keap1, and chemopreventive agents allow Nrf2 to function and continue in the oxidative stress pathway. [4] Sulforaphane is one of the chemopreventive agents that allows this release. |
Sulforaphane releases Nrf2 from Keap1 by modifying specific Keap1 residues. Specifically, sulforaphane is known to react with Keap1 cysteine residues, which disrupts Nrf2 binding and allows Nrf2 to accumulate in the nucleus. [5] Without this release, Nrf2 would not be functional in the oxidative stress pathway, and oxidative stress would accumulate to unhealthy levels.
So how does this oxidative stress pathway relate to XPA? Structurally, there is one very important similarity between Keap1 and XPA: the presence of zinc in the protein. Keap1 has 0.9 zinc atoms per monomer and is known as a zinc metalloprotein. [6] This means that zinc is largely incorporated into the structure and functional roles of Keap1. In fact, the release of zinc from Keap1 is the process that allows the disruption of binding between Keap1 and Nrf2. This release occurs as a result of sulforaphane disrupting cysteine residues in Keap1.
The XPA protein relies on the presence of zinc as well; the ability of XPA to bind to other proteins is dependent on a zinc finger motif (See the Motifs page for background on a zinc finger motif.) Within the zinc finger motif, there are four cysteine residues that, if mutated, will inhibit the function of XPA. [7] These residues coordinate the zinc molecule that allows the protein to function. A recent study showed that when stem cells were exposed to sulforaphane, DNA repair was inhibited. [8] The study suggested that XPA shares the zinc-release mechanism, which would result in zinc release by sulforaphane to inhibit the XPA protein. This was the first study to research the effects of sulforaphane on XPA and more research is needed for more conclusive evidence.
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Discussion
Although oxidative stress, sulforaphane, and XPA have many known mechanistic properties, there are many more properties that are unknown. In addition to the unknown mechanisms, it is also unknown how these different pathways interact with each other in the body. An interesting path for research would be to analyze how these different DNA repair pathways are affected simultaneously by an increase or decrease of this drug. However, because the potential relationship between sulforaphane and XPA has only been recently discovered, it is also important that future research is conducted to investigate the mechanisms further.
The application of chemical genetics in relation to XPA can be found in my Future Research and Specific Aims.
References
1. The Royal Society of Chemistry. Chemistry In Your Cupboard. http://www.rsc.org/learn-chemistry/resources/chemistry-in-your-cupboard/nurofen/2
2. Gupta, P., Kim, B., Kim SH., Srivastava, SK. (2014) Molecular targets of isothiocyanates in cancer: Recent advances. Molecular Nutrition and Food Research 2014: 00, 1–23. doi: 10.1002/mnfr.201300684. Available from http://www.ncbi.nlm.nih.gov/pubmed/24510468.
3. Guerrero-Beltrán C., Calderón-Oliver M., Pedraza-Chaverri J., Chirino Y. (2012) Protective effect of sulforaphane against oxidative stress: recent advances. Experimental and Toxicologic Pathology, 64(5), 503-508. doi: 10.1016/j.etp.2010.11.005. Available from http://www.ncbi.nlm.nih.gov/pubmed/21129940.
4. Zhang D, Hannink M. (2003) Distinct Cysteine Residues in Keap1 Are Required for Keap1-Dependent Ubiquitination of Nrf2 and for Stabilization of Nrf2 by Chemopreventive Agents and Oxidative Stress. Molecular and Cellular Biology, 23(22), 8137-8151. Available from http://www.ncbi.nlm.nih.gov/pubmed/14585973.
5. Eggler AL., Liu G., Pezzuto JM., van Breemen RB., Mesecar AD. (2005) Modifying specific cysteines of the electrophile-sensing human Keap1 protein is insufficient to disrupt binding to the Nrf2 domain Neh2. Proceedings of the National Academy of Sciences of the United States of America, 102(29), 10070-5. doi: 10.1073/pnas.0502402102. Available from http://www.ncbi.nlm.nih.gov/pubmed/16006525.
6. Dinkova-Kostova A., Holtzclaw W., Wakabayashi N. (2005) Keap1, the sensor for electrophiles and oxidants that regulates the phase 2 response, is a zinc metalloprotein. Biochemistry, 44(18), 6889-99. Available from http://www.ncbi.nlm.nih.gov/pubmed/15865434.
7. Morita, et al. Implications of the zinc-finger motif found in the DNA-binding domain of the human XPA protein. Genes to Cells. 1996. 1, 437–442. Available from http://www.ncbi.nlm.nih.gov/pubmed/9078375.
8. Piberger, Koberle, & Hartwig. (2014) The broccoli-born isothiocyanate sulforaphane impairs nucleotide excision repair: XPA as one potential target. Molecular Toxicology, 88, 647-658. Available from http://www.ncbi.nlm.nih.gov/pubmed/24352536.
1. The Royal Society of Chemistry. Chemistry In Your Cupboard. http://www.rsc.org/learn-chemistry/resources/chemistry-in-your-cupboard/nurofen/2
2. Gupta, P., Kim, B., Kim SH., Srivastava, SK. (2014) Molecular targets of isothiocyanates in cancer: Recent advances. Molecular Nutrition and Food Research 2014: 00, 1–23. doi: 10.1002/mnfr.201300684. Available from http://www.ncbi.nlm.nih.gov/pubmed/24510468.
3. Guerrero-Beltrán C., Calderón-Oliver M., Pedraza-Chaverri J., Chirino Y. (2012) Protective effect of sulforaphane against oxidative stress: recent advances. Experimental and Toxicologic Pathology, 64(5), 503-508. doi: 10.1016/j.etp.2010.11.005. Available from http://www.ncbi.nlm.nih.gov/pubmed/21129940.
4. Zhang D, Hannink M. (2003) Distinct Cysteine Residues in Keap1 Are Required for Keap1-Dependent Ubiquitination of Nrf2 and for Stabilization of Nrf2 by Chemopreventive Agents and Oxidative Stress. Molecular and Cellular Biology, 23(22), 8137-8151. Available from http://www.ncbi.nlm.nih.gov/pubmed/14585973.
5. Eggler AL., Liu G., Pezzuto JM., van Breemen RB., Mesecar AD. (2005) Modifying specific cysteines of the electrophile-sensing human Keap1 protein is insufficient to disrupt binding to the Nrf2 domain Neh2. Proceedings of the National Academy of Sciences of the United States of America, 102(29), 10070-5. doi: 10.1073/pnas.0502402102. Available from http://www.ncbi.nlm.nih.gov/pubmed/16006525.
6. Dinkova-Kostova A., Holtzclaw W., Wakabayashi N. (2005) Keap1, the sensor for electrophiles and oxidants that regulates the phase 2 response, is a zinc metalloprotein. Biochemistry, 44(18), 6889-99. Available from http://www.ncbi.nlm.nih.gov/pubmed/15865434.
7. Morita, et al. Implications of the zinc-finger motif found in the DNA-binding domain of the human XPA protein. Genes to Cells. 1996. 1, 437–442. Available from http://www.ncbi.nlm.nih.gov/pubmed/9078375.
8. Piberger, Koberle, & Hartwig. (2014) The broccoli-born isothiocyanate sulforaphane impairs nucleotide excision repair: XPA as one potential target. Molecular Toxicology, 88, 647-658. Available from http://www.ncbi.nlm.nih.gov/pubmed/24352536.
Site Created By: Sarah Drewes
Contact: [email protected]
Last Modified: 05/18/14
University of Wisconsin-Madison
Contact: [email protected]
Last Modified: 05/18/14
University of Wisconsin-Madison