|
|
| (6 intermediate revisions not shown) |
| Line 1: |
Line 1: |
| | {{Team:Purdue/header}} | | {{Team:Purdue/header}} |
| | | | |
| | + | ====Project: Hypoxia-Sensitive Circuits==== |
| | | | |
| - | '''OUR PROJECT'''
| + | Low oxygen level, or hypoxic, environments are issues in both plant and mammalian systems. From water-logged soils to overpopulated regions of tumors, hypoxic regions provide a niche for novel technologies to be put into place to exploit this condition. |
| | | | |
| - | Design of Promoter for Analyzing Hypoxic Response in Arabidopis
| + | Plants in areas with improper levels of oxygen will have to switch from aerobic respiration to lactic and then alcohol fermentation in order to sustain their metabolic processes. Unfortunately this switch to alcohol fermentation will lead to the accumulation of byproducts that are detrimental to a plant’s life. So a synthetic biological circuit centering on the Adh promoter has been developed to indicate when these low oxygen levels (less than 5% oxygen) are present. |
| | | | |
| | + | Hypoxia is also very prevalent in densely populated regions of tumors. It is believed that these areas may initiate hypoxia-driven angiogenesis, a process which aides greatly in tumor proliferation. Accordingly, an additional circuit has been created that will highlight the areas where hypoxic regions (less than 1% oxygen) have arisen during tumor development. The development and characterization of these novel circuits will help to lay down foundation for potential remedies to these consequences of hypoxia in both mammalian and plant systems. |
| | | | |
| | | | |
| - | '''OLD IDEAS'''
| |
| | | | |
| - | ==Oxygen Sequestration to Inhibit Photorespiration in C3 Plants==
| |
| | | | |
| - | ===The problem=== | + | <html> |
| - | Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen. While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species. Photorespiration occurs when O2 concentrations increase relative to CO2. In relatively dry conditions, the stomata of plants close to preserve moisture. Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2. When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue. The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P). The key enzyme in the carbon-fixation process is RuBisCO. Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P. However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead. This generates less G3P and produces a toxic intermediate. Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.
| + | <object id="prezi_a20ce800a98ca3f62c38bf71b009608497e0306d" name="prezi_a20ce800a98ca3f62c38bf71b009608497e0306d" classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" width="550" height="400"><param name="movie" value="http://prezi.com/bin/preziloader.swf"/><param name="allowfullscreen" value="true"/><param name="allowscriptaccess" value="always"/><param name="bgcolor" value="#ffffff"/><param name="flashvars" value="prezi_id=a20ce800a98ca3f62c38bf71b009608497e0306d&lock_to_path=0&color=ffffff&autoplay=no"/><embed id="preziEmbed_a20ce800a98ca3f62c38bf71b009608497e0306d" name="preziEmbed_a20ce800a98ca3f62c38bf71b009608497e0306d" src="http://prezi.com/bin/preziloader.swf" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="550" height="400" bgcolor="#ffffff" flashvars="prezi_id=a20ce800a98ca3f62c38bf71b009608497e0306d&lock_to_path=0&color=ffffff&autoplay=no"></embed></object> |
| | + | </html> |
| | | | |
| - | ===The solution===
| |
| - | Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities. By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered. In theory, this would reduce oxygen concentrations and inhibit photorespiration. A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.
| |
| | | | |
| - | ====Arabidopsis Metabolism====
| |
| | | | |
| - | [http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=CALVIN-PWY The Calvin Cycle]
| |
| - |
| |
| - | [http://www.plantcyc.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-181 Photorespiration]
| |
| - |
| |
| - | ===Oxygen-Sensitive Promoters===
| |
| - |
| |
| - | ====In Arabidopsis====
| |
| - | *Whole-genome study to determine Arabidopsis response to hypoxic stress [http://www.plantphysiol.org/cgi/content/full/137/3/1115] --[[User:Jmason|Jmason]]
| |
| - | *Expression and evolution of functionally distinct haemoglobin genes in plants [http://www.springerlink.com/content/u7610835248t2021/]
| |
| - | **Also discusses growing and modifying Arabidopsis to test promoter regions for functionality --[[User:Jmason|Jmason]]
| |
| - | *Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development [http://www.ncbi.nlm.nih.gov/pubmed/19449151]
| |
| - | **Specifically, mentions a promoter region for an AAA-ATPase that is activated in the presence of reactive singlet O2 species. --[[User:Jmason|Jmason]]
| |
| - | *The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment. [http://www.ncbi.nlm.nih.gov/pubmed/19176720] --[[User:Jmason|Jmason]]
| |
| - |
| |
| - | ====In Saccharomyces====
| |
| - | *Ixr1p regulates oxygen-dependent HEM13 transcription [http://www3.interscience.wiley.com/cgi-bin/fulltext/123305985/HTMLSTART]
| |
| - | **Great article that analyzes the effects of different promoters during hypoxia, also explains how they generated hypoxic conditions in lab --[[User:Jmason|Jmason]]
| |
| - |
| |
| - | ====In Bacteria====
| |
| - | *Sinorhizobium meliloti, a nitrogen-fixing bacterium, forms a symbiotic relationship with legumes in the root nodules of the plant. Because these bacteria must produce enzymes to modify environmental nitrogen, they are also able to detect levels of oxygen using the FixL-FixJ two-component system. [http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(07)37010-9] --[[User:Skearney|Skearney]]
| |
| - | * The DosT/DevS system found in Mycobacterium tuberculosis has an analogous oxygen-sensing function.[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17600145] --[[User:Skearney|Skearney]]
| |
| - |
| |
| - | ===Resources===
| |
| - | ====Photorespiration and Calvin cycle review====
| |
| - | [http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]
| |
| - |
| |
| - | [[Team:Purdue/Collaboration|Potential Partners and Collaborators]]
| |
| - |
| |
| - | [[Team:Purdue/Arabidopsis Links|Arabidopsis Links]]
| |
| - |
| |
| - | ====Potentially useful articles====
| |
| - | [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.043008.091948?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov Processes Relevant to Photorespiration] - Addresses metabolic pathways associated to photorespriation
| |
| - |
| |
| - | [http://dx.doi.org/10.1016/j.copbio.2005.02.001 Great article on plant response to abiotic stress] - Discusses applications of genetic engineering to improving stress tolerance
| |
| - |
| |
| - | [http://www.uni-tuebingen.de/plantphys/AFGN/atgenex.htm Arabidopsis study on gene expression under a variety of conditions] - Of particular interest is the gene expression during oxidative and heat stress.
| |
| - |
| |
| - | [http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]
| |
| - |
| |
| - | ====External Links====
| |
| - | [http://www.mybioinfo.info/ Search engine for genes and their associated promoters in animals]
| |
| - |
| |
| - | [http://arabidopsis.med.ohio-state.edu/ A similar resource for Arabidopsis]
| |
| - |
| |
| - |
| |
| - | ===Discussion===
| |
| - | I've found a book on abiotic stress response that had a chapter based on the Arabidopsis study mentioned above. The responses to oxidative stress had more to do with [http://wikipedia.org/Paraquat Paraquat], an herbicide that interferes with electron transfer. The response to heat stress may be more important, and given what we know about when photorespiration occurs, that's probably a more reasonable pursuit. I'd be somewhat surprised if genes specific to ''high'' oxygen concentrations exist. [http://www.ncbi.nlm.nih.gov/gene/827496 Arabidopsis thaliana heat-shock factor 1] seems like a good candidate. --[[User:Jmason|Jmason]]
| |
| - |
| |
| - | Also, the activity of heat-shock transcription factors seems to be conserved among all eukaryotes. --[[User:Jmason|Jmason]]
| |
| - |
| |
| - | Searching 'oxygen' in the [http://www.partsregistry.org parts registry] gives a number of parts related to oxygen sensitive detection, binding, and regulation. It is a good idea to look at these to determine if there is something here that would accomodate our ideas. --[[User:Skearney|Skearney]]
| |
| - | <html><br></html>
| |
| - | <partinfo>BBa_K258005</partinfo>
| |
| - |
| |
| - | Here are some files on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS.pdf Algal photorespiration], [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%282%29.pdf algal biofuels], and another on [https://2010.igem.org/Image:LGY_PHOTOSYNTHESIS%283%29.pdf biofuels.] --[[User:Lgyoung|Lgyoung]]
| |
| - |
| |
| - | Brainstorming Page:
| |
| | {{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}} | | {{Team:Purdue/link|Oxygen Sequestration Brainstorming & Thoughts}} |
Low oxygen level, or hypoxic, environments are issues in both plant and mammalian systems. From water-logged soils to overpopulated regions of tumors, hypoxic regions provide a niche for novel technologies to be put into place to exploit this condition.
Plants in areas with improper levels of oxygen will have to switch from aerobic respiration to lactic and then alcohol fermentation in order to sustain their metabolic processes. Unfortunately this switch to alcohol fermentation will lead to the accumulation of byproducts that are detrimental to a plant’s life. So a synthetic biological circuit centering on the Adh promoter has been developed to indicate when these low oxygen levels (less than 5% oxygen) are present.
Hypoxia is also very prevalent in densely populated regions of tumors. It is believed that these areas may initiate hypoxia-driven angiogenesis, a process which aides greatly in tumor proliferation. Accordingly, an additional circuit has been created that will highlight the areas where hypoxic regions (less than 1% oxygen) have arisen during tumor development. The development and characterization of these novel circuits will help to lay down foundation for potential remedies to these consequences of hypoxia in both mammalian and plant systems.
"
