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Team:Imperial College London/Extras/Brainstorming/Bioremediation test
From 2011.igem.org
Brainstorming
This page contains a summary of the ideas we developed throughout our brainstorming sessions at the beginning of the project. These ideas can be classified into 4 main categories as shown below. Click on the tabs to find out more about the ideas in each category.
Ideas
Converting Fallen Leaves into Useful Products
Fuel from Food Waste
Feather-Eating Bacteria
Food Fermentation
Estrogenic Endocrine Disruptors in Waste Water
Anammox Bacteria to Treat Eutrophication
Polycyclic Aromatic Hydrocarbon (PAH)
Converting Fallen Leaves into Useful Products
-Aquatic hyphomycetes has been recognized as critical for controlling the process of leaf litter breakdown. The activity of this fungus is affected by C:N ratio, lignin content, pH of water, temperature, and abundance of nutrients (i.e. O2). They produce B-glucosidase, Cellobiohyhrolase (cbhI family), B-xylosidase (xlnR) and phenoloxidase (Pox2) to promote leaf degradation.
-As leaves decay, they produce heat. Leaves will decompose into an excellent organic soil amendment that can be used as a soil conditioner. -The decomposition process is slow (i.e. leaves require 5 months to 2 years to decompose), could combine with Nick’s gene expression amplification? -However, rapid decomposition would consume a large amount of O2 and create anaerobic conditions. Could we engineer all these into facultative anaerobes?
References: [1] FEMSMicrobiolLett 264(2006)246–254, DOI:10.1111/j.1574-6968.2006.00462.x [2] E.N. Tamayo et al. / Fungal Genetics and Biology 45 (2008) 984–993, doi:10.1016/j.fgb.2008.03.002 [3] APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June 2008, p. 3481–3489, doi:10.1128/AEM.02893-07 [4] Mutagenesis Advance Access published June 15, 2006, doi:10.1093/mutage/gel025 [5]http://herbarium.usu.edu/fungi/funfacts/decay.htm [6] http://onlinelibrary.wiley.com/doi/10.1002/iroh.201111355/pdf (Text by Yuanwei)
Fuel from Food Waste
-Microbes in food waste like heterotrophs, cyanobacteria, microalgae and purple bacteria produce biohydrogen. Hydrogen has more potential energy than petrol. Hence, food waste can be turned into valuable energy. Fermentative bacteria use carbohydrates like sugar to produce hydrogen and acids. Purple bacteria, use light to produce energy (photosynthesis) and make hydrogen to help them break down molecules such as acids.http://www.sciencedaily.com/releases/2008/07/080716204805.htm
-Hydrogen is produced by feeding waste products from a chocolate factory to Escherichia coli bacteria. E coli ferments the sugars in the chocolate waste, which generated organic acids so toxic to the bacteria that they began converting formic acid to hydrogen.http://environment.about.com/od/renewableenergy/a/chocolatefuel.htm
-Cellulose waste can be converted to energy by using enzyme cellulase. The gene that codes for cellulase has been isolated and grown in large quantities by E. coli. A number of photosynthetic bacteria, nonphotosynthetic bacteria, cyanobacteria, and green, red, and brown algae produced the enzyme hydrogenase, which is necessary to make hydrogen. http://www.accessexcellence.org/RC/AB/BA/Future_Fuel.php (Text by Yuanwei)
Feather-Eating Bacteria
Bacillus licheniformis strain PWD-1 breaks down feathers into a feather-lysate compound. Feather-lysate provides a low-cost, highly digestible protein source for livestock feed. Bacillus has also been shown to secrete a keratinase enzyme that hydrolyzes proteins such as collagen, elastin, and keratin. Potential application in breakdown of livestock carcasses. The gene encoding the enzyme keratinase of Bacillus licheniformis is kerA.http://www.accessexcellence.org/RC/AB/BA/The_Smell_of_Wealth.php, "http://aem.asm.org/cgi/content/abstract/61/4/1469 (Text by Yuanwei)
Food Fermentation
- Thermoanaerobacterium thermosaccharolyticum can be used to convert food waste into hydrogen (1) However, I could not find information on the genes responsible for this and they may not have been identified yet.
- Lactic acid bacteria can be used in food fermentation as "starter cultures". They produce several compounds and help extend the shelf life of the product (2).
- Lactic acid bacteria can produce a compound that fights Staph aureus, increasing food safety (3)
References: (1) O-Thong, S., Prasertsan, P., Karakashev, D., & Angelidaki, I. (2008). Thermophilic fermentative hydrogen production by the newly isolated thermoanaerobacterium thermosaccharolyticum PSU-2. International Journal of Hydrogen Energy, 33(4), 1204-1214. and Shin, H. S., & Youn, J. H. (2005). Conversion of food waste into hydrogen by thermophilic acidogenesis. Biodegradation, 16(1), 33-44.
(2) Leroy, F., & De Vuyst, L. (2004). Lactic acid bacteria as functional starter cultures for the food fermentation industry. Trends in Food Science & Technology, 15(2), 67-78. (3) Cavadini, C., Hertel, C., & Hammes, W. P. (1998). Application of lysostaphin-producing lactobacilli to control staphylococcal food poisoning in meat products. Journal of Food Protection 174;, 61(4), 419-424. (Text by Rebekka)
Estrogenic Endocrine Disruptors in Waste Water
- Estrogenic compounds are released by multiple sources (1)
- In addition, many compounds in drinking water can act as mimics of estrogen in human and animal bodies (2)
- This is problematic because endocrine disruptors interfere with the hormone balances of humans and animals, in particular fish (9)
- Biosensors for this already exist (3), (4)
- This could perhaps be coupled to a degradation mechanism, involving e.g. laccases, which degrade one type of xenoestrogen (5)
- However, laccase degradation of bisphenol A leads to the production of corrosive compounds (6). It may therefore by preferable to use horseradish peroxidase, which appears to be able to degrade a range of estrogens and estrogen-like compounds (7)
- Horseradish peroxidase works most efficiently at around neutral pH (8), which is close to that of most waste water (buffering may be an issue?).
- This peroxidase is especially useful as its reaction products non-enzymatically aggregate and can be separated from waste water by traditional processes. Horseradish peroxidase also degrades phenol (7), which may give it another useful application in clearing industrial waste from waste water.
- Maybe modify chemotaxis to make bacteria swim towards target? Might be able to use the module from Imperial iGEM '08 (Text by Rebekka)
References: (1) http://www.sciencedirect.com/science/article/pii/S0160412002000752
(2) http://pubs.acs.org/doi/full/10.1021/es801845a
(3) http://www.sciencedirect.com/science/article/pii/S0022283605004080
(4) http://www.sciencedirect.com/science/article/pii/S0048969709012303
(5) http://mic.sgmjournals.org/content/151/1/45.full
(6) http://www.sciencedirect.com/science/article/pii/S096085240500338X
(7) http://www.sciencedirect.com/science/article/pii/S0045653507004183
(8) http://www.sciencedirect.com/science/article/pii/S0043135406003228
(9) http://www.sciencedirect.com/science/article/pii/S0048969709005579
Anammox Bacteria to Treat Eutrophication
- eutrophication = biomass accumulation in waterbodies
- causes unbalanced spieces
- anammox bacteria = anaerobic ammonium oxidation
NH4+ + NO2- = N2 + H2O
turning ammonium and nitrite into di-nitrogen gas
- Anammoxosome
special membrane bound compartment consists of ladderane lipids
• Consist of 2 or more cyclobutane rings
• Highly strained structure
• Can be isolated from ammonia oxidising bacteria living in sea
• Process of synthesis not clear
• Anaerobic ammonium oxidising bacteria have cell membranes consisting of concatenated cyclobutane moieties (ladderane lipids). This structure is a result of the process of converting ammonia to nitrogen gas in the absence of oxygen.
• One possible pathway: Gene clusters of K. stuttgartiensis -> anaerobic synthesis of PUFA -> ladderane lipids.
• Possible application as building blocks in optoelectronic
Anammoxosome contains the enzymes of the redox reactions, prevents the poison intermediates (hydrazine and hydroxylamine ) from killing the bacteria.
Reaction process:-
- Reduction of nitrite by nitrite reductase
- Production of hydrazine by hydrazine hydrolase
- Oxidation of hydrazine into nitrogen gas by oxidizing enzyme
- Production of ATP (proton motive force)
Enzyme sulfite reductase (ferredoxin):- ammonium + oxidized ferredoxin + H2O = nitrite + reduced ferredoxin + H+ ferredoxin acts as an electron transfer of this reaction may this reaction bi-pass the production of hydrazine ?
Polycyclic Aromatic Hydrocarbon (PAH)
Problem: PAHs are a class of organic compounds that are toxic and carcinogenic. PAHs are released into the environment through processes like the combustion of fossil fuels, plastic, coke production and vehicle exhaust. PAHs can be found in air (cigarette smoke) and accumulate in soil. It can also be found in water due to industrial effluents and oil spills. The poor water solubility of PAH causes it to be deposited in sediments and aquatic organisms, affecting fish farms, etc.
Solution: Factories release PAHs into water or ponds which affect survival of fishes in fish farm. Bacillus subtilis can break up the PAHs and eliminate this pollutant. In addition, the Bacillus also contains gene which codes for the production of vitamin which is beneficial to the growth of the fish. To exploit this benefit, we need to find a way for Zooplankton (found in aquatic environment) to incorporate the Bacillus and its vitamin-producing gene. The fish feeding on the zooplankton will then receive a good source of vitamin for its growth. To do this, we can engineer Bacillus bacteria to act as a vector which can deliver vitamin to the cytoplasms of zooplankton which is a phagocytic eukaryote. Essentially, this project allows us to not only clear up the pollutant PAH, but it also provides a source of nutrients for the fish. In addition, the waste product of the fish can also be used by the Bacillus to provide nutrients for the fish.
PAH or poly aromatic hydrocarbon has been one of the major water pollutant in many tropical countries due to incorrect water waste regulation in the plastics and fuel industry. Its carcinogenicity is considered highly toxic to both human and the river creatures and hence causes major health and agricultural problem. PAH primarily accumulates inside the soil and contaminates the plankton on the riverbed. The toxicity is transmitted as the fish eat the plankton and is eaten by human respectively. Our idea is to convert this highly dangerous substance into a useful product where PHA ,polyhydroxyalkaonate, since it uses the same precursor that could be broken down by PAH, acetyl CoA and succinyl CoA. PHA is also biodegradable, thereby safe for environment, has higher elasticity, strength and and thermal stability than polyethelene and polypropylene, the non-biodegradable plastics using in everyday-life.
The solution is by engineering the bacteria that can convert the PAH to acetylCoA using the mechanism below. The bacteria can sense the breakdown of catechol which will acts as a transcription activator for the expression of AHL, allows the aggregation of the bacteria to promote PAH breakdown into acetyl CoA and sucinyl CoA. Another module that is incorporated into the bacteria are the genes responsible for PHA production as well as the gas vesicle protein and RFP. Therefore after collecting the plastics (density = 1.48 g/ml > water density) The bacteria can float up and will be easily detected. Eventually the plastic producing bacteria could be collected for plastics extraction and the region contaminated by PAH could be identified where more bacteria could be applied for more breakdown.
