Team:TU Delft/project/hydrocarbon tolerance

From 2010.igem.org

(Difference between revisions)
(Proposed Method)
(Solvent Tolerance)
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|[http://partsregistry.org/Part:BBa_K398001 alkB2]
 
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|Alkane 1-monooxygenase (Gordonia sp. TF6)
 
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|[http://partsregistry.org/Part:BBa_B0015 B0015]
|[http://partsregistry.org/Part:BBa_B0015 B0015]
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|p15A replication origin
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|[http://partsregistry.org/Part:BBa_J61100 J61100]
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|[http://partsregistry.org/Part:BBa_J61107 J61107]
|RBS Anderson family
|RBS Anderson family
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|Promoter
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|[http://partsregistry.org/Part:BBa_P1005 P1005]
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|[http://partsregistry.org/Part:BBa_P1004 P1004]
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|TetR
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|CmR
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|[http://partsregistry.org/Part:BBa_K398002 rubA3]
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|[http://partsregistry.org/Part:BBa_K398400 PhPFD-alpha]
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|Rubredoxin A3 (Gordonia sp. TF6)
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|Prefoldin alpha-subunit (Pyrococcus horikoshii OT3)
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|[http://partsregistry.org/Part:BBa_K398003 rubA4]
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|[http://partsregistry.org/Part:BBa_K398401 PhPFD-beta]
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|Rubredoxin A4 (Gordonia sp. TF6)
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|Prefoldin beta-subunit (Gordonia sp. TF6)
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|[http://partsregistry.org/Part:BBa_K398004 rubR]
|[http://partsregistry.org/Part:BBa_K398004 rubR]
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|Rubredoxin reductase (Gordonia sp. TF6)
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|Rubredoxin reductase (Pyrococcus horikoshii OT3)
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[https://static.igem.org/mediawiki/2010/0/04/406C.gb Genebank annotated file available here!]
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[https://static.igem.org/mediawiki/2010/0/04/406C.gb Genbank annotated file available here!]
===Step 2: Characterization===
===Step 2: Characterization===

Revision as of 10:01, 13 August 2010

Contents

Solvent Tolerance

It is known that hydrocarbons and other solvents have toxic effects on cells. Due to this fact, it is necessary to confer Escherichia coli K12 hydrocarbon/solvent tolerance, so that it can grow on biphasic systems with toxic concentrations of these compounds.

Aim

To functionally express the protein prefoldin from Pyrococcus horikoshii OT3 in Escherichia coli K12.

Proposed Method

Based on: Okochi M., Kanie K., Kurimoto M., Yohda M. and Honda H.. Over expression of prefoldin from the hyperthermophilic arechaeum Pyrococus horikoshii OT3 endowed Escherichia coli with organic solvent tolerance. Appl. Microbiol. Biotechnol. 79:443-449 (2008)


For this part of our project, we will insert and functionally express the alpha and beta sub-units of Pyrococcus horikoshii OT3 prefoldin; this protein confers solvent/hydrocarbon tolerance to E. coli K12 cells, according to the cited literature. Prefoldin is a jellyfish-shaped hexameric chaperone that captures a protein-folding intermediate and transfers it to the group II chaperonin for correct folding, this is the molecular mechanism behind solvent/hydrocarbon resistance prefoldin-associated.

Prefoldin alpha and prefoldin beta will be ligated to the appropriate RBS and promoter. The selection criterion for RBS and promoter will depend on the results obtained during the RBS characterization protocol. Tentatively, the most used promoter will be BBa_J23109, which gives a medium to low transcription level and the most used RBS will be BBa_B0032 which gives a medium translation level.


Step 1: Formation of Prefoldin BioBrick

Aim: Creation of a BioBrick for the expression of both the alpha and beta subunits of prefoldin. A medium-transcription level promoter as well as a medium-translation level ribosomal binding site is utilized.

Before any design, we checked on literature about reports related to solvent/hydrocarbon tolerance. The paper published by Okochi and co-workers caught our attention up, according to their paper E. coli expressing prefoldin from Pyrococcus horikoshii OT3 grows quite well in the presence of high concentrations (10%v/v) of cyclohexane. Cyclohexane causes membrane leaking and other toxic effects, which makes it a good candidate for testing solvent/hydrocarbon tolerance.

The original prefoldin alpha and prefoldin beta DNA sequences differ in composition from the E. coli sequences and also contained some undesired restriction sites, that's why we decided to enhance our sequence for a successful expression on E. coli, for that purpose we used jcat website. Once we had the enhanced sequence, we added the standard biobrick prefix and suffix and couple of weeks later our dear Mr. Gene sent us back the sequences in a pANY plasmid.

Check the Mr. Gene sequences by clicking on the links: Prefoldin alpha and Prefoldin beta

In silico constructions were made, and you can check below our final construct; the image displayed was generated using Serial Cloner 2.1 .

406C.jpg
Feature Function
B0015 Transcriptional (double) terminator
B0042 Transcriptional terminator
B0053 Transcriptional terminator
B0054 Transcriptional terminator
B0055 Transcriptional terminator
B0062 Transcriptional terminator
G00000 Standard prefix
G00001 Standard suffix
G00100 VF2 primer binding site
G00102 VR primer binding site
I50032 p15A replication origin
J61107 RBS Anderson family
J23100 Promoter
P1004 CmR
PhPFD-alpha Prefoldin alpha-subunit (Pyrococcus horikoshii OT3)
PhPFD-beta Prefoldin beta-subunit (Gordonia sp. TF6)
rubR Rubredoxin reductase (Pyrococcus horikoshii OT3)

Genbank annotated file available here!

Step 2: Characterization

Strains:

  • Prefoldin: E.coli K12/407C
  • Negative control: E.coli K12
  • Positive control: Pseudomonas putida OCT

Characterization of E. coli K12/407C will involve its culturing on M9-modified liquid medium containing varying levels of cyclohexane (0%, 4%, 8%, 12% v/v). The positive control will be a colony of the P. putida OCT strain and the negative control will be an E.coli K12 colony, both grown under the same conditions. OD600 will be determined at various intervals between inoculation and 72 hours thereafter. Using these measurements the growth-related properties of each strain can be determined and analyzed accordingly.