IGEM:MIT/2006/System brainstorming: Difference between revisions

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===Expert advice===
===Expert advice===
From Natalia Dudareva Purdue University:
From Natalia Dudareva, Purdue University:
I don't remember exactly, but my memory tells me that I was able to smell the compound in E. coli, although the smell was not very strong.
I don't remember exactly, but my memory tells me that I was able to smell the compound in E. coli, although the smell was not very strong.
I have also BAMT from snapdragon and BSMT from petunia, but SAMT can make both compounds, methylsalycilate and methylbenzoate, depending on provided substrate, so you don't really need different enzymes.
I have also BAMT from snapdragon and BSMT from petunia, but SAMT can make both compounds, methylsalycilate and methylbenzoate, depending on provided substrate, so you don't really need different enzymes.

Revision as of 16:34, 26 April 2006

Post your project ideas here.

See the brainstorming of last year's team.

Rough Ideas

  1. Lava Lamp (RS)
  2. Minty Fresh (RS)
  3. Diagnostic Bacteria (BC)
  4. Analog Clock (AC)
  5. Square Bacteria (JK)
  6. Maze (JK)
  7. Algae (JK)
  8. Mitochondrial Liberation & Synthetic organelle(BC)
  9. genome transfer (DE)
  10. meso laundry list (DE)
  11. rhodopsin (AC)
  12. scrapped
  13. wood eater (SS)
  14. wood-o-genesis(SS)

Bacterial scents

Precursor Enzyme Compound Scent References
benzoic acid & S-adenosyl-L-methionine (SAM) S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase (BAMT) methyl benzoate pleasant smell [1]
trans-cinnamic acid & S-adenosyl-L-methionine (SAM) ? methyl cinnamate cinnamon?
jasmonic acid & S-adenosyl-L-methionine (SAM) S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase (JMT) methyl jasmonate jasmine
salicylic acid (SA) & S-adenosyl-L-methionine (SAM) S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase (SAMT) methyl salicylate wintergreen [2, 3, 4]

Expert advice

From Natalia Dudareva, Purdue University: I don't remember exactly, but my memory tells me that I was able to smell the compound in E. coli, although the smell was not very strong. I have also BAMT from snapdragon and BSMT from petunia, but SAMT can make both compounds, methylsalycilate and methylbenzoate, depending on provided substrate, so you don't really need different enzymes. Yes, I can provide you a construct expressing the SAMT.

SAMT

C. breweri

  • DNA and protein sequence known
  • Expressed in E. coli
  • Methyl salicylate has been extracted from spent medium of E. coli cells when medium was supplemented with salicylic acid
  • Genbank AF133053
  • also can use benzoic acid as a substrate but with lower efficiency
  • crystal structure available

A. majus (Snapdragon)

  • DNA and protein sequence known
  • Expressed in E. coli
  • Methyl salicylate has been extracted from spent medium of E. coli cells when medium was supplemented with salicylic acid
  • also can use benzoic acid as a substrate but with lower efficiency
  • Methyl benzoate has been extracted from spent medium of E. coli cells when medium was supplemented with benzoic acid

S. floribunda

  • Genbank AJ308570

A belladonna

  • Genbank AB049752

JMT

  • A. thaliana AY008434

BAMT

  • Snapdragon AF198492

References

  1. Pott MB, Hippauf F, Saschenbrecker S, Chen F, Ross J, Kiefer I, Slusarenko A, Noel JP, Pichersky E, Effmert U, and Piechulla B. Biochemical and structural characterization of benzenoid carboxyl methyltransferases involved in floral scent production in Stephanotis floribunda and Nicotiana suaveolens. Plant Physiol. 2004 Aug;135(4):1946-55. DOI:10.1104/pp.104.041806 | PubMed ID:15310828 | HubMed [Pott-PlantPhysiol-2004]
  2. Ross JR, Nam KH, D'Auria JC, and Pichersky E. S-Adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme involved in floral scent production and plant defense, represents a new class of plant methyltransferases. Arch Biochem Biophys. 1999 Jul 1;367(1):9-16. DOI:10.1006/abbi.1999.1255 | PubMed ID:10375393 | HubMed [Ross-ArchBiochemBiophys-1999]
  3. Negre F, Kolosova N, Knoll J, Kish CM, and Dudareva N. Novel S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme responsible for biosynthesis of methyl salicylate and methyl benzoate, is not involved in floral scent production in snapdragon flowers. Arch Biochem Biophys. 2002 Oct 15;406(2):261-70. DOI:10.1016/s0003-9861(02)00458-7 | PubMed ID:12361714 | HubMed [Negre-ArchBiochemBiophys-2002]
  4. Zubieta C, Ross JR, Koscheski P, Yang Y, Pichersky E, and Noel JP. Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. Plant Cell. 2003 Aug;15(8):1704-16. DOI:10.1105/tpc.014548 | PubMed ID:12897246 | HubMed [Zubieta-PlantCell-2003]

All Medline abstracts: PubMed | HubMed

Diagnostic bacteria

I'd like to be able to add a small number of diagnostic bacteria into a larger culture to detect the presence of cells containing engineered devices in the culture. Presumably there would be BB DNA floating around from lysed bacteria (does it get cut up?). The diagnostic bacteria would need to responsd to BB DNA by glowing green or smelling minty fresh:) The response might be mediated by uptake of DNA into the diagnostic bacteria and then use the mixed connective site as a riboregulator or maybe have a membrane protein that binds specific DNA sequences and triggers a two component system. Very sketchy proposal right now. Unless we could find easy ways of doing this it would be a protein engineering project.

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