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Team:TU-Delft/part1
From 2012.igem.org
Content
IntroductionParts
Results
Conclusions
Recommendations
References
Introduction
Olfactory receptors
Animals sense their chemical environment through olfactory receptors (ORs). The olfactory receptors are a large group of proteins belonging to a subfamily of G protein-coupled receptors (GPCRs) that bind odorant ligands. If the receptor is activated by a ligand, the confirmation of the receptor is changed and there is an interaction with the α-subunit of the G-protein. This causes dissociation of the α-subunit from the Gβγ dimer and the signal is propagated [1]. Because of the sensitivity and selectivity of the of the olfactory system it can be of value in detection of environmental toxins [2] or pharmaceutical screening. In this iGEM project we aim to investigate if the ORs can be used as a diagnostics tool for tuberculosis.
Yeast G protein-coupled receptors
In this project we choose to work with the budding yeast Saccharomyces cerevisiae as a host organism because it utilizes already a GPCR pathway. Furthermore S. cerevisiae has been successfully used for functional expression of GPCR’s [3,4], a lot of genomic tools are available, and it has a fully characterized genome. In S. cerevisiae two GPCR cascades have been identified: a glucose sensing pathway and a mating pathway [5]. There are two sexes of yeast cells, MATa and MATα. Whenever pheromones (small peptides) of the opposite sex are bound to the specific G-protein coupled receptors (Ste2 p or Ste3p), the MAP kinase cascade is turned on, leading to induction of mating genes such as FUS1 and growth arrest mediated by the FAR1 promoter. This mating response can be seen in the form of a morphological change, called shmoo formation. In figure 1 an overview of the pheromone and glucose signaling pathways in S. cerevisiae is shown.
Overview of pheromone and glucose signaling in S. cerevisiae. Figure adapted from Versele et al.
Introduction of a new olfactory receptor
Previously it was found that that the yeast pheromone signaling pathway can be coupled to a mammalian olfactory receptor. Minic et al. succeeded in functional expressing the rat 17 OR and its trafficking to the plasma membrane in S. cerevisiae. Between the three GPCRs that are known in S. cerevisiae, Ste2, Ste3 and Gpr1, the sequence similarity is limited. Except for pheromone receptors in Schizosaccharomyces pombe and Kluyveromyces lactis, Ste2 and Ste3 are largely unrelated in sequence to other GPCRs [5]. Nevertheless, the yeast pheromone receptors can be functionally replaced by several mammalian GPCRs so that the pheromone pathway can be activated by the corresponding ligands [4]. For localization of the receptor into the membrane and a higher affinity with the alpha-subunit we made a chimeric design of the receptor, after the research of Radhika et al. [7]. For a detailed design, and how to do this yourself, look at the DIY receptor design page
Niacin olfactory receptor
The receptors GPR109A and GPR109B are known to bind the compound nicotinic acid [8]. It was previously described that GPR109B acts a low affinity receptor for nicotinic acid and GPR109A acts as a high affinity receptor for nicotinic acid and other compounds with related pharmacology [molecular identification of high and low affinity receptors]. The chemical compound methyl nicotinate is closely related to nicotinic acid. Because one of the compounds in the breath of tuberculosis patients is methyl nicotinate [9,10], the high affinity receptor for niacin is a good candidate for testing the ‘olfactory yeast’ as a diagnostics tool.
Isoamylacetate olfactory receptor
The first iGEM team of MIT 2006 made a biobrick called the ‘banana odor generator’. With this part E. coli cells can generate the isoamyl acetate molecule. We aim to let yeast detect this isoamyl acetate signal with a olfactory receptor. The idea is that in future work the yeast should couple this back to the bacteria to have gaseous yeast/bacteria communication on plates.
The human receptor OR1G1 and mouse receptor Olfr154 are known to react on isoamyl acetate [11] and therefor these two receptors were used in this iGEM project.
Parts
A design of the receptor construct was made with the olfactory receptors placed between the N-terminal and the C-terminal part of the rat I7 receptor. As a promoter the strong constitutive GPD promoter is used and as a terminator the CYC1 terminator. The receptor can be replaced by using the restriction sites BamHI and NdeI. A FLAG tag is added upstream of the receptor sequence to look at the localization of the receptor in the membrane.
The plasmid construct for the receptor expression was obtained by restriction of the synthesized receptor construct and ligation in the pRSII415 expression vector. The following biobricks are created:
BBa_K775000
BBa_K775001
BBa_K775002
BBa_K775003
Results
Transformations
After transformation of the plasmids in the yeast strain a PCR reaction was performed in order to verify if the plasmid was correctly transformed. Since the PCR reactions were performed with single colonies we expected to obtain one PCR product with the length of the receptor part. However, for all the receptors we saw multiple PCR products on the gel; products with the length of the receptor, and products indicating that only the plasmid backbone was present (without the receptor). This indicates that during growth of the yeast a part of the plasmid was emitted.
1% Agarose Gel run on 80 V, showing S. cerevisiae extracted plasmid DNA of our olfactory receptor construct. Lane 2 shows DNA smartladder. Lane 1 shows a typical bands for the S. cerevisae plasmid extract. The bright band at the height of 2000 nt is the expected PCR band. The secondary bands observed have DNA sizes of approximately 1200 and 400-500 nt.
Expression and localization of the ORs
Setup
NR1, BR1 and BR2 transformed cells and WT cells were stained with conjugated anti-FLAG antibodies according to the immunofluorescence staining protocol and viewed under a widefield fluorescence microscope (NR1) and a confocal microscope (BR1 and BR2) with the goal of imaging the expression of our GPCR chimeras and image their localization in the cell. The image was analyzed with ImageJ to compare the fluorescence of the cell and cell membrane to the overall fluorescence of the whole picture.Outcome
It can be seen that there is expression of the receptor: +NR1 cells are fluorescent (figure 4 below) and the reference strain is very weakly fluorescent (figure 4 top). In some of the +NR1 cells there is clear halo structure visible, which indicates localization of the receptor on the membrane. Below such a typical halo is shown (figure 4). For +BR1 and +BR2 cells receptor expression can be shown also by the fluorescent signal (figure 5, other experiment). The location of the signal indicates expression unequally distributed over the cells, indicating that localization in the membrane is not fully functioning. Contrast of these pictures are not optimal. The reference strain (figure 5, top) showed very little fluorescence. Further, a small percentage of the cells (~5 %) was found to be fluorescent, indicating that constitutive mRNA expression by the GPD promoter did not lead to constitutive protein expression in all cells.
Figure 4: FLAG immunolocalization of +NR1 yeast cells expressing a receptor with DYKDDDDK tag.
Figure 5: FLAG immunolocalization of +BR1 and +BR2 yeast cells expressing a receptor with DYKDDDDK tag.
Ligand activation
Setup
If the downstream pathway of the olfactory system is activated one of the responses is that the cell goes in growth arrest. If the cells go in growth arrest they will stop growing in the G1 phase and hence the DNA content of the cells should be 1N. By staining the DNA of the cells with a fluorescent dye we watched with flow cytometry at the DNA content and thereby at the cell cycle phase.
The niacin receptors and the two isoamylacetate receptors were induced with the ligand. After staining (see protocols) the DNA content was measured. A fluorescence microscopy imaging experiment was also performed.
Outcome GPR109A
Flow cytometer results of I7-Gpr109A transformed cells induced with ligands. Cells were DNA stained and measured after 4.40 hours.
The picture shows DNA content distribution of two strains, wildtype cells and cells transformed with I7-Gpr109A, 4.40 hours after induction. The I7-Gpr109A without induction shows one peak. WT cells with nicotinic acid show similar cell clouds and peak intensity. The alpha pheromone induced cells however shows a small cloud shifting towards the left. The methyl nicotinate induced cells shows a peak similar to the non-induced cells. The Niacin induced I7-GPR109A transformed cells however, show two clear clouds after 4.40 induction. This indicates that DNA replication has halted, leaving the cells in their haploid state.
Outcome I7-OR1G1
Figure 7: OR1G1 transformed cells with isoamylacetate as inducing agent at an estimated concentration of 200mM.
Conclusions
The active site of an olfactory receptor, GPR109A placed between the N-terminal and the C-terminal part of the rat I7 receptor was successfully expressed in yeast. For all the yeast strains that were used in the experiments the transformations of receptor parts ( I7-Olfr154, I7-OR1G1, I7-GPR109A, I7-odr10 ) were confirmed with PCR. In one of the transformants ( I7-GPR109A ) a halo structure is confirmed, by means of FLAG-tag localization. This points to localization of the receptor on the membrane. This stain was further researched in a subsequent DNA staining cell cytometry experiment that indicated growth arrest with niacin at T=4.40 and a similar trend with the positive control with alpha-pheromone was observed. With the alternative ligand Methyl Nicotinate no such trend was observed, although such a trend for the alternative ligand could be present. An explanation for this could be that methyl nicotinate is not the primary ligand and therefore does not strongly bind to the receptor.For I7-OR1G1 a DNA staining experiment was performed with the goal of observing growth arrest. In these experiments growth arrest was not observed. Parallel imaging with fluorescence microscope however showed a change of cellular morphology by isoamylacetate. It was also observed that isoamylacetate dissolves poorly in water. This could explain why no growth arrest is observed with the I7-OR1G1 transformants.
Recommendations
During growth of yeast cells transformed with the expression vector we observed two things: not all the cells maintain the right plasmid and the cells grew slower than wild type cells. A reason for this could be that the expression of the receptor is disadvantageously for the cells. Therefor we recommend for future work to use an inducible promoter instead of a strong constitutive promoter. In that case one can make the yeast cells expressing the receptor just before testing the strain.
References
[1] Haiqing Zhao, Lidija Ivic, Joji M. Otaki, Mitsuhiro Hashimoto, Katsuhiro Mikoshiba, Stuart Firestein*Functional Expression of a Mammalian Odorant Receptor, Science 279, 237 (1998)
[2] Venkat Radhika, Tassula Proikas-Cezanne, Muralidharan Jayaraman, Djamila Onesime, Ji Hee Ha &Danny N Dhanasekaran, Chemical sensing of DNT by engineered olfactory yeast strain Nature Chemical Biology 3 (2007)
[3] Jasmina Minic, Marie-annick Persuy, Elodie Godel, Josiane Aioun, Ian Connerton, Roland Salesse, Functional expression of olfactory receptors in yeast and development of a bioassay for odorant screening, FEBS Journal (2005)
[4] Brown et al, Functional coupling of mammalian receptors to the yeast mating pathway using novel yeast/mammalian G protein a-subunit chimeras, Yeast (2000)
[5] Matthias Versele, Katleen Lemaire, and Johan M. Thevelein, Sex and sugar in yeast: two distinct GPCR systems, EMBO Rep. 2001
[6] Dietmar Krautwurst, King-Wai Yau, and Randall R. Reed, Identification of Ligands for Olfactory Receptors by Functional Expression of a Receptor Library, Cell (1998)
[7] Venkat Radhika, Tassula Proikas-Cezanne, Muralidharan Jayaraman, Djamila Onesime, Ji Hee Ha & Danny N Dhanasekaran, Chemical sensing of DNT by engineered olfactory yeast strain, Nature Chemical biology (2007)
[8] Alan Wise, Steven M. Foord, Neil J. Fraser, Ashley A. Barnes,e Nabil Elshourbagy, Michelle Eilert,g Diane M. Ignarg Paul R. Murdock, Klaudia Steplewski,h Andrew Green,Andrew J. Brown, Simon J. Dowell, Philip G. Szekeres, David G. Hassall, Fiona H. Marshall,a, j Shelagh Wilson, and Nicholas B. Pike
Molecular Identification of High and Low Affinity Receptors for Nicotinic Acid, The journal of biological chemistry (2003)
[9] Georgies F. Mgode Bart J. Weetjens Thorben Nawrath, Christophe Cox, Maureen Jubitana, Robert S. Machang’, Stephan Cohen-Bacrie,e Marielle Bedotto, Michel Drancourt,e Stefan Schulz and Stefan H. E. Kaufmann, Diagnosis of Tuberculosis by Trained African Giant Pouched Rats and Confounding Impact of Pathogens and Microflora of the Respiratory Tract, Journal of clinical microbiology (2011)
[10] Mona Syhre, Stephen T. Chambers, The scent of Mycobacterium tuberculosis, Elsevier (2008)
[11 Valery Matarazzo, Olivier Clot-Faybesse, Brice Marcet, Gaelle Guiraudie-Capraz, Boriana Atanasova, Gerard Devauchelle, Martine Cerutti, Patrick Etievant and Catherine Ronin,Functional Characterization of Two Human Olfactory Receptors Expressed in the Baculovirus Sf9 Insect Cell System, Chem. Senses (2005).
