IGEM:Stanford/2009/Plastic Degradation: Difference between revisions
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==What We Know== | ==What We Know== | ||
Tsai et al. isolated a strain of yeast capable of degrading both phenol (meta-fission) and formaldehyde, but acknowledged that “a microbe with a biodegrading power toward phenol and formaldehyde concurrently has been scarcely reported.” | Previous research has focused on characterizing '''organisms that are shown to degrade phenol or formaldehyde''': | ||
*Tsai et al. isolated a strain of '''yeast capable of degrading both phenol (meta-fission) and formaldehyde''', but acknowledged that “a microbe with a '''biodegrading power toward phenol and formaldehyde concurrently has been scarcely reported'''.” | |||
*Gusse et al. isolated '''white-rot fungus capable of degrading phenolic resins''' but efficiency uncertain. | |||
*Hidalgo et al. showed the ability of '''Rhodococcus erythropolis UPV-1 to grow on phenol and remove formaldehyde'''. | |||
However, '''most research has described organisms that can degrade one or the other'''. Introducing both pathways into a genetically tractable and well-studied organism like E. coli would not only combine pathways in a useful way from an environmental standpoint but it would also leave ourselves and others more room to alter these pathways to make them more efficient. | |||
However, most research has described organisms that can degrade one or the other. Introducing both pathways into a genetically tractable and well-studied organism like E. coli would not only combine pathways in a useful way from an environmental standpoint but it would also leave ourselves and others more room to alter these pathways to make them more efficient. | |||
==What We Don't Know (but need to know)== | ==What We Don't Know (but need to know)== | ||
| Line 20: | Line 18: | ||
Potential subprojects: | Potential subprojects: | ||
#'''Phenol Degradation''' | |||
Goal: Engineer E. coli to metabolize phenol as a carbon source, linking it to cellular respiration | #*'''Goal''': Engineer E. coli to '''metabolize phenol as a carbon source, linking it to cellular respiration''' | ||
#*To achieve this, we would need to '''transduce genes (already in the database in PubMed)''' from some type of fungus or bacteria (such as Pseudomonas aeruginosa AT2, Burkholderia cepacia PW3, or Aspergillus fumigatus ATCC 28282) into E. coli via a plasmid vector. Our choice of genes will depend on whether we decide to introduce enzymes responsible for meta- or ortho- phenol metabolism. The former will result in byproducts that are used in glycolysis; the latter will yield intermediates of the TCA cycle. | |||
To achieve this, we would need to transduce genes (already in the database in PubMed) from some type of fungus or bacteria (such as Pseudomonas aeruginosa AT2, Burkholderia cepacia PW3, or Aspergillus fumigatus ATCC 28282) into E. coli via a plasmid vector. Our choice of genes will depend on whether we decide to introduce enzymes responsible for meta- or ortho- phenol metabolism. The former will result in byproducts that are used in glycolysis; the latter will yield intermediates of the TCA cycle. | #*''[[User:Isis Trenchard|Isis Trenchard]] 17:24, 30 March 2009 (EDT)'': | ||
#**How do you get the enzyme from PubMed? | |||
#**What kind of vector will you use? What are the selection markers? | |||
Goal: Engineer E. coli to metabolize formaldehyde as respiration precursor, bypassing the detoxification pathway | #**How do you transform genes? What is the protocol? | ||
#'''Formaldehyde Degradation''' | |||
This would require introducing genes for two enzymes (3-Hexulose-6-Phosphate Synthase and phospho-3-hexuloisomerase) into the E. coli genome through a plasmid vector to introduce the pathway necessary for formaldehyde assimilation. Also, we would have to control the formaldehyde oxidation pathway in E. coli, which detoxifies formaldehyde but does not assimilate it into biomass as a carbon source, either by knocking out or downregulating expression of the genes involved in this pathway. | #*'''Goal''': Engineer E. coli to '''metabolize formaldehyde as respiration precursor''', bypassing the detoxification pathway | ||
#*This would require '''introducing genes for two enzymes''' (3-Hexulose-6-Phosphate Synthase and phospho-3-hexuloisomerase) into the E. coli genome through a plasmid vector to introduce the pathway necessary for formaldehyde assimilation. Also, we''' would have to control the formaldehyde oxidation''' pathway in E. coli, which detoxifies formaldehyde but does not assimilate it into biomass as a carbon source, either''' by knocking out or downregulating expression of the genes involved in this pathway'''. | |||
#*''[[User:Isis Trenchard|Isis Trenchard]] 17:24, 30 March 2009 (EDT)'': How do you knock out or downregulate expression? | |||
==Important/Interesting Papers== | ==Important/Interesting Papers== | ||
<biblio>Tsai pmid=16377894</biblio> | |||
<biblio>Gusse pmid=16856735</biblio> | |||
<biblio>Hidalgo pmid=11876421</biblio> | |||
==Questions/Discussion== | ==Questions/Discussion== | ||
Is it possible to make phenol and formaldehyde the sole carbon source for E. coli? | *Is it possible to make phenol and formaldehyde the sole carbon source for E. coli? | ||
Would there be any way to compartmentalize phenol or formaldehyde degradation, using previous iGEM work on creating a synthesome? | *Would there be any way to compartmentalize phenol or formaldehyde degradation, using previous iGEM work on creating a synthesome? | ||
Would there be any crosstalk between the pathways for formaldehyde and phenol degradation that would harm the cells? | *Would there be any crosstalk between the pathways for formaldehyde and phenol degradation that would harm the cells? | ||
Latest revision as of 14:24, 30 March 2009
Project Summary
Can we convert environmentally hazardous phenols and formaldehyde (the primary components of a class of widely used resins) into a carbon source for E. coli?
Original Presentation: Tough Plastic: Degrading Phenol Resins
What We Know
Previous research has focused on characterizing organisms that are shown to degrade phenol or formaldehyde:
- Tsai et al. isolated a strain of yeast capable of degrading both phenol (meta-fission) and formaldehyde, but acknowledged that “a microbe with a biodegrading power toward phenol and formaldehyde concurrently has been scarcely reported.”
- Gusse et al. isolated white-rot fungus capable of degrading phenolic resins but efficiency uncertain.
- Hidalgo et al. showed the ability of Rhodococcus erythropolis UPV-1 to grow on phenol and remove formaldehyde.
However, most research has described organisms that can degrade one or the other. Introducing both pathways into a genetically tractable and well-studied organism like E. coli would not only combine pathways in a useful way from an environmental standpoint but it would also leave ourselves and others more room to alter these pathways to make them more efficient.
What We Don't Know (but need to know)
Experiment Ideas
Potential subprojects:
- Phenol Degradation
- Goal: Engineer E. coli to metabolize phenol as a carbon source, linking it to cellular respiration
- To achieve this, we would need to transduce genes (already in the database in PubMed) from some type of fungus or bacteria (such as Pseudomonas aeruginosa AT2, Burkholderia cepacia PW3, or Aspergillus fumigatus ATCC 28282) into E. coli via a plasmid vector. Our choice of genes will depend on whether we decide to introduce enzymes responsible for meta- or ortho- phenol metabolism. The former will result in byproducts that are used in glycolysis; the latter will yield intermediates of the TCA cycle.
- Isis Trenchard 17:24, 30 March 2009 (EDT):
- How do you get the enzyme from PubMed?
- What kind of vector will you use? What are the selection markers?
- How do you transform genes? What is the protocol?
- Formaldehyde Degradation
- Goal: Engineer E. coli to metabolize formaldehyde as respiration precursor, bypassing the detoxification pathway
- This would require introducing genes for two enzymes (3-Hexulose-6-Phosphate Synthase and phospho-3-hexuloisomerase) into the E. coli genome through a plasmid vector to introduce the pathway necessary for formaldehyde assimilation. Also, we would have to control the formaldehyde oxidation pathway in E. coli, which detoxifies formaldehyde but does not assimilate it into biomass as a carbon source, either by knocking out or downregulating expression of the genes involved in this pathway.
- Isis Trenchard 17:24, 30 March 2009 (EDT): How do you knock out or downregulate expression?
Important/Interesting Papers
Error fetching PMID 16377894:
- Error fetching PMID 16377894:
- Gusse AC, Miller PD, and Volk TJ. White-rot fungi demonstrate first biodegradation of phenolic resin. Environ Sci Technol. 2006 Jul 1;40(13):4196-9. DOI:10.1021/es060408h |
- Hidalgo A, Lopategi A, Prieto M, Serra JL, and Llama MJ. Formaldehyde removal in synthetic and industrial wastewater by Rhodococcus erythropolis UPV-1. Appl Microbiol Biotechnol. 2002 Feb;58(2):260-3. DOI:10.1007/s00253-001-0876-5 |
Questions/Discussion
- Is it possible to make phenol and formaldehyde the sole carbon source for E. coli?
- Would there be any way to compartmentalize phenol or formaldehyde degradation, using previous iGEM work on creating a synthesome?
- Would there be any crosstalk between the pathways for formaldehyde and phenol degradation that would harm the cells?
