Difference between revisions of "Part:BBa K801060"
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===Usage and Biology===
 
===Usage and Biology===
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===Characterization===
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==== Gel Picture of finished constructs ====
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[[file:TUM12_limonenegel.png|thumb|300px|right|Fig. 3: Gel electrophoresis of [https://parts.igem.org/Part:BBa_K801060 K801060] and [https://parts.igem.org/Part:BBa_K801061 K801061] after analytical restrigtion digest with EcoR1 and Pst1.]]
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We wanted to analyze (+)-Limonene synthase 1 expression in yeast depending on existence of a consensus sequence. For further experiments ligation and cloning of (+)-Limonene synthase 1 in a new yeast expression vector pTUM100 for protein expression in yeast and in pSB1C3 for submissions for iGEM competition were made. To check success of ligation, double-stranded DNA fragments were separated by length via agarose gel-electrophoresis using ethidium bromide as a nucleic acid stain.
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(+)-Limonene synthase 1 coding region without yeast consensus sequence [[https://parts.igem.org/Part:BBa_K801061 BBa_K801061]] in pSB1C3 is shown next to (+)-Limonene synthase 1 with Strep-tag and yeast consensus sequence [[https://parts.igem.org/Part:BBa_K801060 BBa_K801060]] after restriction digest with EcoR-1 and Pst-1 restriction enzymes. As expected, the 1665 bp fragment of [[https://parts.igem.org/Part:BBa_K801061 BBa_K801061]] and the 1708 bp fragment of [[https://parts.igem.org/Part:BBa_K801060 BBa_K801060]] could be detected additionally to the pSB1C3 vector (2070 bp).
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==== Investigation of the yeast consensus sequence ====
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[[file:TUM12_consensus.png|thumb|450px|right|Fig. 4: Comparison of limonene synthase biobricks ([https://parts.igem.org/Part:BBa_K801065 BBa_K801065] and [https://parts.igem.org/Part:BBa_K801060 BBa_K801060]) with and without yeast consensus sequence.]]
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[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC340751/ Hamilton et al., 1987]] reported of a consensus sequence upstream of the AUG start codon in yeast.
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Although not as strong as the mammalian Kozak translation initiation sequence, the yeast consensus sequence is thought to have a 2–3-fold effect on the efficiency of translation initiation [[http://tools.invitrogen.com/content/sfs/manuals/pyes2_man.pdf pYES2 manual]].
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We designed duplicates of limonene synthase encoding biobricks; one having the yeast consensus sequence, the other one not having the consensus sequence.
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We have not been able to show significant differences in expression between the two biobricks [[https://parts.igem.org/Part:BBa_K801065 BBa_K801065] and [https://parts.igem.org/Part:BBa_K801060 BBa_K801060]] via coomassie staining and western blot. The difficulties of showing the difference via SDS-page may result from variations in the amount of protein applied.
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Our in vivo analysis indicates that the consensus sequence does lead to a 2-3-fold enhanced expression in yeast, though (see Fig. 6B). This is consistent with findings of others [[http://tools.invitrogen.com/content/sfs/manuals/pyes2_man.pdf pYES2 manual]].
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====Purification of recombinant limonene synthase====
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[[File:TUM12_SApurification.png|thumb|200px|left|Streptavidin Affinity (SA) chromatography]]
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[[File:TUM12_gelfiltration.png|thumb|450px|right|Analytical gelfiltration of limonene synthase]]
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'''Streptavidin affinity chromatography'''<br>
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The yeast cell extract that was obtained by cell lyse using glass beads of 0,5mm was centrifuged at 11000 RPM in a SLA-3000 rotor for 60 minutes and subsequently dialysed against 5 liters of 1x Streptavidin Affinity buffer (SA-buffer)over night. The cell extract was then filtrated using a syringe filter with a pore size of 0.45μm and susequently applied on a SA-column. After the sample was applied the column was washed using 1xSA buffer until a base line was reached and then the bound protein was eluted using 5mM Biotin in 1x SA buffer. The chromatogramm of the purification is shown on the left side.<br><br>
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'''Gelfiltration of the SA purified protein'''
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The protein sample that was eluted from the SA-column was concentrated using a centrifugation concentrator with a molecular size limit of 30 kDA and filtrated afterwards. From this solution 250μl were applied on a analytical gel filtration colum Superdex 200 10/30 with BSA as running buffer at a flow rate of 0.5 ml/min. In the chromatogramm (shown in the figure on the right in section B)there is a aggregation peak that may be caused by the preceding concentration at the exclusion limit and a major peak at an elution volume of 13.580 ml. The calibration line that was obtained from the calibration proteins b-amylase, alcohol dehydrogenase, BSA, Obalbumine, carboanhydrase, cytochrome C and Aprotinin filtrated with the same experimental setup resulted in a regression line with the formula y = -39206 x + 3.3463. When calculating from the elution volume of the limonene synthase a apparent molecular mass of 70.1 kDa could be determinded. This fits quite well the theoretical molecular mass that was calculated using [http://web.expasy.org/cgi-bin/protparam/protparam ExPASy ProtParam] to be 65977.1 Da. The four killo daltons difference could also be caused by posttranslational modifications which should be tested using mass spectromety.
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==== In vitro detection of limonene====
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[[file:TUM12_limonene_invivo.png|450px|thumb|right|Fig. 5: Spectrum of in vitro detection of limonene (enzyme assay with [https://parts.igem.org/wiki/index.php?title=Part:BBa_K801060 BBa_K801060]) and reference spectrum.]]
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To test the functionality of purified limonene synthase in vitro, we used an optimized protocol of an enzyme assay with extraction of [[http://www.ncbi.nlm.nih.gov/pubmed/17662687 Landmann et al, 2007]]. The limonene synthase was purified via Strep-tag. The enzyme assay was carried out in 25 mM Tris-HCl buffer with 5% Glycerol, 1mM DTT and cofactors (10 mM MgCl2, 1 mg/ml BSA). 50 µM substrate (geranyl pyrophosphate) and 10 ng purified recombinant limonene synthase were added to the reaction batch. Negative controls were reaction batches without enzyme. The reaction was incubated for 15 min at room temperature. Afterwards limonene was extracted with pentane, dried with sodiumsulfate and reduced under a stream of nitrogen. Three replicates of both sample and negative control were done.
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The pentane extracts were analyzed with gas chromatography-mass spectrometry ("5890 Series II GC" coupled to a "Finnigan Mat 55 S MS") to identify the enzymatically synthesized products.
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All enzyme reactions (three replicates) led to the production of limonene while the negative controls did not show limonene. Therefore, we showed that our purified limonene synthase is functional and leads to the production of limonene.
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==== In vivo detection of limonene====
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[[file:TUM12_limoneneinvivo.png|450px|thumb|right|Fig. 6: Detection of limonene in headspace above cell culture supernatant. [A] Spectrum of limonene obtained when analyzing cell culture that was transformed with pTUM104 containing construct of [https://parts.igem.org/wiki/index.php?title=Part:BBa_K801060 BBa_K801060]. [B] Overview about different measurements.]]
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Because limonene is a VOC (volatile organic compound) [[http://www.ncbi.nlm.nih.gov/pubmed/15763095 Pierucci et al., 2005]], we expected an arbitrarily amount of limonene in the gaseous phase above the cell culture supernatant as in the cell culture. Therefore, we measured limonene via headspace (SPME needle) GC-MS.
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We showed limonene to be produced by the yeasts that were transformed with pTUM104 carrying limonene synthase coding regions (see [https://parts.igem.org/wiki/index.php?title=Part:BBa_K801061 BBa_K801061] and [https://parts.igem.org/wiki/index.php?title=Part:BBa_K801060 BBa_K801060]).
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We detected more limonene in the sample that contained a limonene synthase with consensus sequence. Hence, we showed that the yeast consensus sequence might increase the expression of limonene synthase and therefore lead to enhanced limonene production.
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Furthermore, we could not detect a significant difference between samples that had additional GPP (educt) versus the ones that did not. This might be due to the inability of GPP to diffuse into the cells (hydrophilic character). Since we were able to detect limonene in both samples, it implies that the GPP present in the cells is sufficient for limonene production. This is consistent with the findings of [http://www.ncbi.nlm.nih.gov/pubmed/18155949| [Herrero et al., 2008]] that showed that S. cerevisiae cells (from laboratory and wine strains) contain enough free GPP to be catalytically transformed by monoterpene synthases into monoterpenes.
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==== Detection of limonene in beer====
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[[File:TUM12_SPME.jpg|200px|thumb|left|Fig. 7: Preparation of sample for GC-MS with SPME.]]
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[[File:TUM12_LSbeer.jpg|200px|thumb|right||Fig. 8: iGEM's first and finest SynBio Beer with limonene.]]
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A first attempt to use our genetically engineered yeasts to brew a SynBio Beer were conducted using a transient transfection with a constitutive promoter. The drawback is that in the gyle the selection pressure is not preserved and the loss of the plasmid is possible.<br>
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Three liters of gyle were inoculated with 100ml of a stationary yeast culture grown in YPD that was transiently transfected with a plasmid harboring a constitutive expression cassette for the limonene synthase.
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We analyzed this first beer for limonene content via headspace (SPME needle) GC-MS. Unfortunately we could not yet proof a significant difference between the beer containing limonene and the negative control beer. This might be due to a loss of the plasmid which encodes limonene synthase. We will try to integrate the limonene synthase expression cassette into the genome of yeast and afterwards we will repeat the experiment.
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==== Toxicity Assay ====
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To establish whether limonene has an effect on yeast cells , we inoculated three different yeast strains  with different concentrations of limonene. Limonene was added to the medium and the used yeast strains were the laboratory strain INVSc1, a strain which is used for brewing beer and a strain which can be purchased in a supermarket.
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Limonene at high concentrations affects the growth of yeast cells. We could show an inhibition of growth  at 1 mM and even a lethal effect at 100 mM. At lower concentrations (1 µM, 10 µM, 100 µM) no inhibition could be observed. The growth rates of yeast cells which were incubated with low concentrations of limonene do not show a difference compared to the negative control (incubation of analogous yeast strains with YPD without limonene).
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The in vivo GCMS detection of limonene [B] displayed a concentration of 50 µM. Hence the amount of limonene we will produce with the modified yeast will not reach a toxic concentration at all. 
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[[File:TUM12_Toxicity_Limonene.png|800px|thumb|center|Fig. 9: Limonene toxicity assay evaluation.]]
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Revision as of 00:04, 27 September 2012

(+)-Limonene synthase 1 with Strep-tag and yeast consensus sequence.

This part contains the (+)-Limonene Synthase 1 of Citrus limon. It is preceeded by the yeast consensus sequence for improved expression and carries a C-Terminal Strep-Tag for purification or detection by westernblot. It is an improved version of BBa_I742111. Also see the experience pages of BBa_I742111 and BBa_K118025.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1683
    Illegal SapI.rc site found at 107