IGEM:MIT/2006/System brainstorming/Smell-o-Rama: Difference between revisions
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==Summary (pros/cons)== | ==Summary (pros/cons)== | ||
==References== | ==References== | ||
==Bacterial scents== | |||
{| border="1" | |||
|- | |||
|'''Precursor''' | |||
|'''Enzyme''' | |||
|'''Compound''' | |||
|'''Scent''' | |||
|'''References''' | |||
|- | |||
|benzoic acid & ''S''-adenosyl-L-methionine (SAM) | |||
|S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase (BAMT) | |||
|[[Wikipedia:Methyl benzoate|methyl benzoate]] | |||
|pleasant smell | |||
|<cite>Pott-PlantPhysiol-2004</cite> | |||
|- | |||
|''trans''-cinnamic acid & ''S''-adenosyl-L-methionine (SAM) | |||
|? | |||
|[[Wikipedia:Methyl cinnamate|methyl cinnamate]] | |||
|cinnamon? | |||
| | |||
|- | |||
|jasmonic acid & ''S''-adenosyl-L-methionine (SAM) | |||
|S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase (JMT) | |||
|[[Wikipedia:Methyl jasmonate|methyl jasmonate]] | |||
|jasmine | |||
| | |||
|- | |||
|salicylic acid (SA) & ''S''-adenosyl-L-methionine (SAM) | |||
|S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase (SAMT) | |||
|[[Wikipedia:Methyl salicylate|methyl salicylate]] | |||
|wintergreen | |||
|<cite>Ross-ArchBiochemBiophys-1999, Negre-ArchBiochemBiophys-2002, Zubieta-PlantCell-2003</cite> | |||
|} | |||
===Expert advice=== | |||
From Natalia Dudareva, Purdue University: | |||
*thinks that you can smell wintergreen from E. coli cultures expressing SAMT with salicylic acid in the media | |||
From [http://www.biology.lsa.umich.edu/research/labs/pichersky/ Eran Pichersky], University of Michigan: | |||
*E. coli cultures expressing SAMT with salicylic acid in the media will have a detectable wintergreen smell | |||
*eliminate indole pathway (responsible for bad E. coli smell) to strengthen the scent. | |||
*have shown production of several scent compounds in E. coli | |||
===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=== | |||
<biblio> | |||
#Negre-ArchBiochemBiophys-2002 pmid=12361714 | |||
#Ross-ArchBiochemBiophys-1999 pmid=10375393 | |||
#Pott-PlantPhysiol-2004 pmid=15310828 | |||
#Zubieta-PlantCell-2003 pmid=12897246 | |||
</biblio> | |||
===Terpenes and terpenoids=== | |||
*Terpenes are hydrocarbons: combinations of several isoprenes. (Sometimes encompasses terpenoids.) | |||
*Terpernoids are modified terpenes with methyl groups added/removed or oxygens added | |||
*From Wikipedia: "Terpenoids contribute to the scent of eucalyptus, the flavors of cinnamon, cloves and ginger and the color of yellow flowers. Well-known terpenoids include citral, menthol, camphor and the cannabinoids found in the Cannabis plant." | |||
E. coli has the Δ<sup>3</sup>-isopentenyl-pyrophosphate pathway, and the enzymes to produce geranyl-PP. This pathway is less effective than the mevalonate pathway, but this has been cloned into an E. coli strain by Keastling's group. Many scented compounds can be made from isopentenyl-PP and geranyl-PP with one or two enzymes, including lemon, orange, pine, etc. See [http://www.ecocyc.org Ecocyc] for the pathways (type IPP as a compound and look at the synthetic and reactant pathways that link to it). | |||
Terpenes are also the precursor to rubber and many of the resins and gums. | |||
===Indole elimination=== | |||
Indole is the precursor to and degradation product of tryptophan. We could knock out the relevant two enzymes and supply tryptophan exogenously. Also, we could supply tryptophan exogenously and see if that is sufficient to inhibit indole formation via feedback inhibition in a "normal" strain. [from TK] | |||
[http://biocyc.org/ECOLI/NEW-IMAGE?type=COMPOUND&object=INDOLE Indole] can act as an extracellular signal so indole can probably get in and out of the cell. | |||
====Relevant reactions==== | |||
In Pathway Reactions as a Reactant: | |||
[http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=TRPSYN-PWY tryptophan biosynthesis] : | |||
indole + L-serine = L-tryptophan + H2O | |||
In Pathway Reactions as a Product: | |||
[http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=TRPSYN-PWY tryptophan biosynthesis] : | |||
indole-3-glycerol-phosphate = indole + D-glyceraldehyde-3-phosphate | |||
[http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=TRYPDEG-PWY tryptophan degradation II (via pyruvate)] : | |||
L-tryptophan + H2O = indole + pyruvate + ammonia | |||
====Relevant enzymes==== | |||
trpB (biosynthesis) and tnaA (degradation) | |||
====References==== | |||
<biblio> | |||
#Freundlich-JBacteriol-1960 pmid=13701820 | |||
#Phillips-ArchBiochemBiophys-1992 pmid=1632641 | |||
</biblio> |
Revision as of 11:39, 5 June 2006
Description
Requirements
Design
Construction
Testing
Feasibility & Timeline
Parallelizability
Intermediate goals
Significance
Safety & ethics
Summary (pros/cons)
References
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:
- thinks that you can smell wintergreen from E. coli cultures expressing SAMT with salicylic acid in the media
From Eran Pichersky, University of Michigan:
- E. coli cultures expressing SAMT with salicylic acid in the media will have a detectable wintergreen smell
- eliminate indole pathway (responsible for bad E. coli smell) to strengthen the scent.
- have shown production of several scent compounds in E. coli
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
- 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 |
- 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 |
- 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 |
- 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 |
Terpenes and terpenoids
- Terpenes are hydrocarbons: combinations of several isoprenes. (Sometimes encompasses terpenoids.)
- Terpernoids are modified terpenes with methyl groups added/removed or oxygens added
- From Wikipedia: "Terpenoids contribute to the scent of eucalyptus, the flavors of cinnamon, cloves and ginger and the color of yellow flowers. Well-known terpenoids include citral, menthol, camphor and the cannabinoids found in the Cannabis plant."
E. coli has the Δ3-isopentenyl-pyrophosphate pathway, and the enzymes to produce geranyl-PP. This pathway is less effective than the mevalonate pathway, but this has been cloned into an E. coli strain by Keastling's group. Many scented compounds can be made from isopentenyl-PP and geranyl-PP with one or two enzymes, including lemon, orange, pine, etc. See Ecocyc for the pathways (type IPP as a compound and look at the synthetic and reactant pathways that link to it).
Terpenes are also the precursor to rubber and many of the resins and gums.
Indole elimination
Indole is the precursor to and degradation product of tryptophan. We could knock out the relevant two enzymes and supply tryptophan exogenously. Also, we could supply tryptophan exogenously and see if that is sufficient to inhibit indole formation via feedback inhibition in a "normal" strain. [from TK]
Indole can act as an extracellular signal so indole can probably get in and out of the cell.
Relevant reactions
In Pathway Reactions as a Reactant:
tryptophan biosynthesis : indole + L-serine = L-tryptophan + H2O
In Pathway Reactions as a Product:
tryptophan biosynthesis : indole-3-glycerol-phosphate = indole + D-glyceraldehyde-3-phosphate
tryptophan degradation II (via pyruvate) : L-tryptophan + H2O = indole + pyruvate + ammonia
Relevant enzymes
trpB (biosynthesis) and tnaA (degradation)
References
- FREUNDLICH M and LICHSTEIN HC. Inhibitory effect of glucose on tryptophanase. J Bacteriol. 1960 Nov;80(5):633-8. DOI:10.1128/jb.80.5.633-638.1960 |
- Phillips RS and Dua RK. Indole protects tryptophan indole-lyase, but not tryptophan synthase, from inactivation by trifluoroalanine. Arch Biochem Biophys. 1992 Aug 1;296(2):489-96. DOI:10.1016/0003-9861(92)90602-s |