yesoil engineered yeast cells: a yeast sensor for real extra virgin olive oil federico ii university
TRANSCRIPT
YesOilYesOil
ENGINEERED YEAST CELLSENGINEERED YEAST CELLS::A Yeast Sensor for real Extra Virgin A Yeast Sensor for real Extra Virgin
Olive OilOlive Oil
Federico II University
Giovanni,engineer
Lucia, mathematician
Maria Aurelia, biologist
Irene, biologist
Alda, biologist
Velia,biologist
Roberta, biologist
Giulia, biologist
We are from…
ITALYITALY
NAPLES
What’s a sensor?
A sensor is a type of transducer that converts a signal from one form to another.
In this case we want S.cerevisiae to convert a metabolic signal, that derives from oleic acid concentration, into light!
Olive Oil is classified as follows:
[oleic acid] < 2.8 mM EXTRA VIRGIN2.8 mM EXTRA VIRGIN
[oleic acid] < 7.1 mM VIRGIN7.1 mM VIRGIN
[oleic acid] > 7.1 mM NOT EDIBLE 7.1 mM NOT EDIBLE
Background•Oleic acid is the principal component of Olive Oil •It’s the indicator of Oil’s acidity
Oleic acid is yeast
alternative carbon
source in absence
of glucose
OLEIC ACID IS A COMMON POINT!
OLEIC ACID
OLIVE OIL’S
ACIDITY
YEAST METABOLISM
BIOLOGICALBIOLOGICAL MODELMODEL
BIOLOGICAL BIOLOGICAL RESPONSERESPONSE
MATHEMATICAL MATHEMATICAL MODELMODEL
d
dt Pho4p
SA αA [PHO4p]
Pho80d
dtSB αB [PHO80-PHO85]
Pho85p
[PHO80-PHO85]K3
d
dt
Pho8 gfp K3 [PHO4p]
[PHO8]
αC [PHO8]K1K3+K1K2
rfp
SIMULATIONSSIMULATIONS
PROJECTOVERVIEW
BIOLOGICAL CIRCUIT[O.A]<2.8 mM [O.A]<2.8 mM [O.A.]>7.1 mM [O.A.]>7.1 mM
RFP
WHAT HAPPENS?
2.8mM<[O.A]<7.1mM 2.8mM<[O.A]<7.1mM
Virgin OilVirgin Oil
INPUTS : Oleic acid concentrations
oleic acid concentration is less than less than
2.8 mM 2.8 mM
oleic acid concentration
is greater than greater than 7.1 mM 7.1 mM
Extra Virgin Olive OilExtra Virgin Olive OilNot edible Olive OilNot edible Olive Oil
oleic acid concentration is between between
2.8 and 7.1mM2.8 and 7.1mM
Virgin Olive oilVirgin Olive oil
OUTPUTS
[Oleic acid] < 2,8 mM [Oleic acid] > 7,1 mM
Virgin OilExtra Virgin Olive Oil Not edible Olive Oil
Biological ModelBiological Model
What microorganism?
Which promoters?
Which genes?
Choice of microorganism: Choice of microorganism: S.cerevisiaeS.cerevisiae
1. In yeast genome there are genes activated by Oleic Acid.
2. Yeast is not a dangerous microorganism for consumers that will use the oil
3. Yeast can be easily engineered
Choice of promoters: OREs sequencesWe cloned one ORE sequence and two OREs sequences from the FOX3 gene and we inserted them
upstream of a CYC1 promoter.
1ORE:1ORE:One oleate response element (ORE) One oleate response element (ORE)
1ORE
2ORE
2ORE:2ORE:Two sequences of oleate response Two sequences of oleate response
element (OREs) element (OREs)
1. " Fungi and animals may share a common ancestor to nuclear receptors " Morag MacLean, Richard J. Fagan, and Didier Picard Chris Phelps, Valentina
Gburcik, Elena Suslova, Peter Dudek, Fedor Forafonov, Nathalie Bot,Morag MacLean, Richard J. Fagan, and Didier Picard.PNAS 2006;103;7077-7081
Choice of genes :
PHO-patway
PHO4pPHO4p
PHO8 PROMOTERPHO8 PROMOTER
PHO8p-GFPPHO8p-GFP
PHO80p-RFPPHO80p-RFP
PHO85pPHO85p
PHO4pPHO4p
OOLEIC ACID
2ORE PROMOTER FIREFLY LUCIFERASE
Promoter efficiencyWe cloned the luciferase gene downstream of 2ORE
We tested the perfomance of We tested the perfomance of 2ORE-Cyc1 2ORE-Cyc1 via via luc-assayluc-assay
0
200000
400000
600000
800000
1000000
1200000
1400000
Lu
min
escen
ce/m
icro
g
0NT 5mMNT 0 0,2 0,4 0,6 0,8 1 2 3 4 5
oleic acid mM
Luciferase Assay
Extravirg
in Oliv
e Oil
Extravirg
in Oliv
e Oil
Virgin O
live oil
Virgin O
live oil
Mathematical Model• We modeled our biochemical network as a
system of non linear ODEs
assuming that
Component concentrations are continous functions of time;
trascription factor timescales are much larger than protein-protein interactions;
input changes are very rapid;the system is closed.
d
dt
PHO85p
PHO8gfp [ Pho4 free ]
K1 + [Pho4 free]αC
[PHO8]
Pho80
d
dt
d
dt
Pho4p
rfp
SA αA[PHO4p]
SB αB[PHO80-PHO85]
Mathematical ModelInputs
Michaelis-Menten Term
Degradations
d
dt
Pho4P
K2 [PHO80-PHO85] [PHO4pfree] K3 [PHO4P]
STEADY STATE ASSUMPTION (since protein-protein interaction is much faster than transcriptional interaction)
[ Pho4 free ]K3 [PHO4p]
K2 [PHO80-PHO85]
Pho4p
PHO8 PHO8 CDS
PHO85p
Pho80
ddt
Pho4pSA αA [PHO4p]
Pho80
ddt
rfp
SB αB [PHO80-PHO85]Pho85p
[PHO80-PHO85]K3
d
dt
Pho8 gfp K3 [PHO4p]
[PHO8]
αC [PHO8]
K1K3+K1K2
Full Mathematical Model
Including Oleic acid into the model
Than we begun analysis;
we wanted to have our inputs
as functions of Oleic acid concentration.
So we used data from luciferase assay as input data to perform simulations.
SA SB
0
200000
400000
600000
800000
1000000
1200000
1400000
Lu
min
esce
nce
/mic
rog
0NT 5mMNT 0 0,2 0,4 0,6 0,8 1 2 3 4 5
oleic acid mM
Luciferase Assay
Simulations: good parameters choiceSimulations: good parameters choice
Simulations: bad parameters choiceSimulations: bad parameters choice
We performed simulations for different values of parameters.
K1=0.5
uncorrected behaviour !!!
the repression of PHO8 is too weak when
[Oleic acid] >7.1 mM.
Our sist
em is R
obust !!!
..also with other values...
Conclusions• We tested and implemented one
promoter (2ORE) able to identify Extravergine Olive Oil
• We cloned it upstream of the resistence natMX4 in a yeast vector (pAG25)
• We integrated “GFP-KanMX6” cassette in yeast strain W303
• Response to low conc. of oleic acid
• The cassette 2ORE-natMX4 is now ready to be integrated
• This is going to be our output for extravergin olive oil
Future work
• Integration of the second
promoter “1ORE”
• Deletion of the endogenous Pho80 promoter from yeast strain W303 via insertion of the hphMX4 resistance
• Cloning of RFP downstream of 1 ORE- pho80 CDS
Our BioBrick parts• In the Igem Registry 2007 there were nine Yeast
parts available but none of them working...Now with our work the total number of yeast parts
is fourteen and our five parts are all “ready to use!!”
Registration number Part's Name
BBa_1735007 Pho80CDS
BBa_1735008 1ore-Cyc1 promoter
BBa_1735009 2ore-Cyc1 promoter
BBa_1735010 Fox3 promoter
BBa_1735011 1ore-pho80 cds
Thanks to...
Instructors:Maria Pia CosmaDiego di BernardoMario di Bernardo