Team:TU Munich/Project/Xanthohumol

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{{Team:TU_Munich/Header}}
{{Team:TU_Munich/Header}}
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=='''Background and principles'''==
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{{Team:TU_Munich/ExCol}}
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[[File:TUM12_4-coumaroyl_CoA.jpg|right|thumb|200px| '''4-coumaroyl-CoA''']]
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Plant secondary metabolites have proven or assumed beneficial properties and health promoting effects. Stilbenoids, flavonoids or lignins can result from 4-coumaroyl-coenzyme A, which is a nodal compound of phenylproponaoid metabolism in plants.
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===Biosynthesis:===
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= Xanthohumol =
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The biosynthetic pathway of 4-coumaroyl-coenzyme A starts with the conversion of L-Phenylalanine to cinnamate catalyzed by phenylalanin ammonia lyase (PAL). PAL also shows activity with converting tyrosine to p-coumarate, albeit to a lower efficiency. The cinnamate 4-hydroxylase (C4H) catalyzes the synthesis of p-hydroxycinnamate from cinnamate and 4-coumarate: CoA ligase (4CL) converts p-coumarate to its coenzyme-A ester, activating it for reaction with malonyl CoA [[Media:TUM_2009_Trantas_Metabolic_engineering_of_the_complete_pathway_leading_to_heterologous_biosynthesis_of_various_flavonoids_and_stilbenoids_in_Saccharomyces_cerevisiae.pdf‎| ''Emmanouil Trantas et al., 2009'']].
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<hr/>
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[[File:TUM12_PathwayTo4-coumarate.png|right|thumb|200px| '''metabolic pathway from phenylalanin to 4-coumarate''']]
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 +
[[File:Gruppe_Coumaryl_TUM12.jpg|350px|thumb||Responsible: Daniela Dichtler, Ingmar Polte, Maria Trumpfheller and Katrin Fischer]]
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The flavonoid biosynthetic pathway starts with the condensation of one molecule of 4-coumaroyl-CoA and three molecules of malonyl-CoA, yielding naringenin chalcone. This reaction is carried out by the enzyme chalcone synthase (CHS). Chalcone is isomerised to a flavanone by the enzyme chalcone flavanone isomerase (CHI). From these central intermediates, the pathway diverges into several side branches, each resulting in a different class of flavonoids, for example Xanthohumol.
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Flavonoids are valuable natural products with '''anti-inflammatory''', '''antiallergenic''' and '''antioxidant''' activities in humans. For the chemical synthesis of flavonoids, extreme reaction conditions and toxic chemicals are required. Hence, we chose the transfer of this metabolic pathway into ''Saccharomyces cerevisiae'' as an attractive alternative source of flavonoids.
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[[Media:TUM12_Biosynthesis_of_Xanthohumol_(2).jpg]] 
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After the successful implementation of the first steps of the phenylpropanoid pathway, the syntheses of different flavonoids are conceivable. Along with '''raspberry ketone''', the aroma compound of raspberries, plant substances providing beneficial effects to ones life could be synthesized, for example '''resveratrol''' or '''xanthohumol''', which we will focus on.  
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Our project will focus on the production of Xanthohumol, due to its characteristic as a cancer chemopreventive agent (see below).
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We successfully cloned all enzymes necessary for the pathway of xanthohumol in the new yeast expression vector [http://partsregistry.org/Part:BBa_K801004 pTUM104]. Every gene was sequenced and submitted as a BioBrick. So we established BioBricks in order to produce xanthohumol in yeast ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K801090 BBa_K801090], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K801091 BBa_K801091], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K801092 BBa_K801092], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K801093 BBa_K801093], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K801094 BBa_K801094], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K801095 BBa_K801095], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K801096 BBa_K801096], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K801097 BBa_K801097], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K801098 BBa_K801098],).
 +
Our next goals are to proof the expression of every single enzyme by Western Blot Analysis and to show the functionality with established enzyme assays.
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===Xanthohumol and its cancer related bioactivities:===
 
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[[File:TUM12_Xanthohumol.png|right|thumb|200px| '''Xanthohumol''']]
 
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====Inhibition of the metabolic activation of procarcinogens: ====
 
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2-amino-3-methylimidazo[4,5-f]quinolone, found in cooked meat, verified as a procarcinogen in an ames salmonella mutagenicity test. The inhibition is probably a result of an inhibition of the cytochrome P 450 enzymes Cyp1A1, Cyp1B1 and Cyp1A2 (phase 1 enzymes). But in order to achieve a clear inhibition, plasma concentrations of 1 µM would be necessary. In a study with male rats oral administration of xanthohumol (50 mg/kg) led to concentration maximums of 65 -180 nM after 4 h. Improved resorption of Xanthohumol could be a possible target for innovation (Yilmazer et al., 2001, Miranda et al., 2000, Henderson et al., 2000, Gerhauser et al., 2002).
 
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====Induction of carcinogen-detoxifying enzymes (phase 2 enzymes): ====
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==Background and Principles==
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P450-activated carcinogens get conjugated to endogenous ligands (gluthathione, glucoronic acid, acetate and sulfate) by phase 2 enzymes to facilitate excretion. Therefore the induction of phase 2 enzymes should enhance the protection against carcinogenesis. Xanthohumol cat concentrations of 2.1-10.1 µM could induce quinone reductase (detoxification of quinones by ceonversion to hydroquinones which can be conjugated) in hepatoma Hepa 1c1c7 cells. It was shown that xanthohumol could selectively induce quinone reductase without causing a transcriptional activation of Cyp1A1. (Miranda et al., 2000, Gerhauser et al., 2002)
+
----
 +
[[File:TUM12_4-coumaroyl_CoA.jpg|right|thumb|300px| '''Fig. 1: Structure of 4-coumaroyl-CoA.''']]
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====Inhibition of tumor growth at an early stage:====
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Plant secondary metabolites have proven or assumed beneficial properties and health promoting effects. Stilbenoids, flavonoids or lignins can result from 4-coumaroyl-coenzyme A (see Fig. 1), which is a nodal compound of the phenylproponaoid metabolism in plants. 
-
Xantohumol showed an inhibition of the proliferation of breast cancer (MCF-7) and ovarian cancer (A-2780) in vitro at IC50 values of 13 and 0.52 µM (Miranda et al., 1999). Furthermore xanthohumol can inhibit the endogenous prostaglandin synthesis through inhibition of cyclooxygenase (COX-1 and COX-2) with IC50 values of 17 and 42 µM. An increased prostaglandin production has been associated with the uncontrolled proliferation of tumor cells (Gerhauser et al., 2002).
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<div style="clear:both">
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Pharmacokinetic studies for xanthohumol based on beverages with an xanthohumol content of 50 mg/l in humans are part of actual research activities. According to a scientist at the TA-XAN AG the first results will be published in June at a conference in Florenz.  
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===Biosynthesis===
 +
</div>
 +
<div>
 +
[[File:TUM12_Biosynthesis_of_Xanthohumol.png|right|thumb|300px| '''Fig. 2: Biosynthesis of xanthohumol.''']]
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====Antioxidant activities: ====
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The biosynthetic pathway of 4-coumaroyl-coenzyme A starts with the conversion of L-Phenylalanine to cinnamate, being catalyzed by phenylalanin ammonia lyase (PAL) ['''A''']. PAL also shows activity in converting tyrosine to p-coumarate, but with a lower efficiency ['''B''']. The cinnamate 4-hydroxylase (C4H) catalyzes the synthesis of p-hydroxycinnamate from cinnamate and 4-coumarate ['''C''']: CoA ligase (4CL) converts p-coumarate to its coenzyme-A ester, activating it for reaction with malonyl CoA ['''D''']  [[http://www.ncbi.nlm.nih.gov/pubmed/19631278 Trantas ''et al.'', 2009]].
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Xanthohumol at 5 µM decreased conjugated diene formation as a measure for lipid peroxidation by more than 70 % after 5 h of incubation in an in vitro assay (protection of LDL from Cu2+ induced oxidation). Furthermore Xanthohumol was shown to scavenge hydroxyl-, peroxyl- and superoxide anion radicals (Miranda et al., 2000).
+
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=='''Idea'''==
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The flavonoid biosynthetic pathway starts with the condensation of one molecule of 4-coumaroyl-CoA and three molecules of malonyl-CoA, yielding naringenin chalcone. This reaction is carried out by the enzyme chalcone synthase (CHS) ['''E''']. Chalcone is isomerised to a flavanone by the enzyme chalcone flavanone isomerase (CHI). From these central intermediates, the pathway diverges into several side branches, each resulting in a different class of flavonoids, such as xanthohumol.
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The idea is to perform a heterologous gene expression of all enzymes required for Xanthohumol biosynthesis in ''Saccharomyces cerevisiae''. First, each enzyme should be expressed individually and the activities should be tested individually to ensure the functionality. Each gene should be inserted in a yeast expression vector under the control of a GAL10 promotor.  
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The final goal is the expression of all required genes in a single modified yeast to produce Xanthohumol out of the substrate L-Tyrosin.
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Our project will focus on the '''production of xanthohumol''' (see Fig. 3), due to its characteristic as a cancer chemopreventive agent (see below).
 +
The idea is to perform a heterologous gene expression of all enzymes required for xanthohumol biosynthesis in ''Saccharomyces cerevisiae''. First, each enzyme should be expressed individually, with the activities being also tested individually to ensure the functionality. Each gene should be inserted in a yeast expression vector under the control of a GAL1 promotor.
 +
The final goal is the expression of all required genes in a single modified yeast-stem to produce xanthohumol out of the substrate L-Tyrosin.
 +
</div>
 +
There are 5 enzymes necessary for the '''biosynthesis of xanthohumol''' (see Fig. 2) ([http://biocyc.org/META/NEW-IMAGE?type=NIL&object=PWY-5135 MetaCyc]):
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=='''General remarks'''==
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Enzyme ['''A''']: PAL = phenylalanine ammonia lyase:    L-phenylalanin --> trans-cinnamate
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[[File:TUM12_Jiang_detailofpaper.png|right|thumb|300px| '''Detail of Jiang et al., 2004''']]
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====Proof of principle====
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Jiang et al succeed in the biosynthesis of several flavonoids in ''Saccharomyces cerevisiae'' by the assembly of a plasmid which contains three required enzymes (pKS2µHyg-PAL-4CL-CHS).
+
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The activity of each enzyme was demonstrated and  the presence of naringenin, which forms the product of the three enzymes(PAL, 4CL, CHS; see also picture on the right) was shown.
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[[Media:TUM12_2004_Metabolic Engineering of the phenylpropanoid pathway in Saccharomyces.pdf‎| ''Hanxiao Jiang et al., 2004'']]
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 +
Enzyme ['''D''']: 4CL = 4-coumarate - coenzym A ligase:  4-coumarate --> 4-coumaroyl-CoA
 +
Enzyme ['''E''']: CHS = naringenin - chalcone synthase:  4-coumaroyl-CoA --> naringeninchalcone
 +
Enzyme ['''F''']: APT = aromatic prenyltransferase:      naringeninchalcone --> desmethylxanthohumol
 +
Enzyme ['''G''']: OMT1 = chalcone O-methyltransferase:    desmethylxanthohumol --> xanthohumol
 +
Jiang et al succeeded in the biosynthesis of several flavonoids in ''Saccharomyces cerevisiae'' by the assembly of a plasmid containing three required enzymes (pKS2µHyg-PAL-4CL-CHS) and thereby showed the '''proof of principle'''. The activity of each enzyme was demonstrated and the presence of naringenin, which forms the product of the three enzymes( PAL, 4CL, CHS), was shown.
 +
[[http://www.ncbi.nlm.nih.gov/pubmed/14704995 Jiang and Morgan, 2004]]
 +
===The Molecular and Physiological Effects of Xanthohumol===
 +
<div>
 +
[[File:TUM12_Xanthohumol.png|right|thumb|200px| '''Fig. 3: Structure of xanthohumol.''']]
 +
====Inhibition of Metabolic Activation of Procarcinogens: ====
 +
2-amino-3-methylimidazo[4,5-f]quinolone, found in cooked meat, verified as a procarcinogen in an ames salmonella mutagenicity test. The inhibition is probably a result of an inhibition of the cytochrome P 450 enzymes Cyp1A1, Cyp1B1 and Cyp1A2 (phase 1 enzymes). But in order to achieve a clear inhibition, plasma concentrations of 1 µM would be necessary. In a study with male rats oral administration of xanthohumol (50 mg/kg) led to concentration maximums of 65 -180 nM after 4 h. Improved resorption of xanthohumol could be a possible target for innovation [[http://www.ncbi.nlm.nih.gov/pubmed/11240137 Yilmazer ''et al.'' 2001a], [http://www.ncbi.nlm.nih.gov/pubmed/10995285 Miranda ''et al.'' 2000b], [http://www.ncbi.nlm.nih.gov/pubmed/10752639 Henderson ''et al.'', 2000], [http://www.ncbi.nlm.nih.gov/pubmed/12481418 Gerhauser ''et al.'', 2002]].
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=='''Necessary enzymes for the biosynthesis of xanthohumol'''==
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====Induction of Carcinogen-Detoxifying Enzymes (Phase 2 Enzymes): ====
-
[[File:TUM12_Biosynthesis_of_Xanthohumol(2).jpg|right|thumb|200px| '''Biosynthesis of Xanthohumol''']]
+
P450-activated carcinogens get conjugated to endogenous ligands (gluthathione, glucoronic acid, acetate and sulfate) by phase 2 enzymes to facilitate excretion. Therefore the induction of phase 2 enzymes should enhance the protection against carcinogenesis. Xanthohumol cat concentrations of 2.1-10.1 µM could induce quinone reductase (detoxification of quinones by conversion to hydroquinones which can be conjugated) in hepatoma Hepa 1c1c7 cells. It was shown that xanthohumol could selectively induce quinone reductase without causing a transcriptional activation of Cyp1A1 [[http://www.ncbi.nlm.nih.gov/pubmed/11038156 Miranda ''et al.'', 2000c], [http://www.ncbi.nlm.nih.gov/pubmed/12481418 Gerhauser ''et al.'', 2002]].
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ENZYME 1:  PAL = phenylalanine ammonia lyase:    L-phenylalanin --> trans-cinnamate
+
-
ENZYME 2: 4CL = 4-coumarate - coenzym A ligase: 4-coumarate --> 4-coumaroyl-CoA
+
====Inhibition of Tumor Growth at an Early Stage:====
 +
Xanthohumol showed an inhibition of the proliferation of breast cancer (MCF-7) and ovarian cancer (A-2780) in vitro at IC50 values of 13 and 0.52 µM [[http://www.ncbi.nlm.nih.gov/pubmed/10418944 Miranda ''et al.'', 1999]]. Furthermore xanthohumol can inhibit the endogenous prostaglandin synthesis through inhibition of cyclooxygenase (COX-1 and COX-2) with IC50 values of 17 and 42 µM. An increased prostaglandin production has been associated with the uncontrolled proliferation of tumor cells [[http://www.ncbi.nlm.nih.gov/pubmed/12481418 Gerhauser ''et al.'', 2002]].
 +
Pharmacokinetic studies for xanthohumol based on beverages with an xanthohumol content of 50 mg/l in humans are part of actual research activities.
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ENZYME 3: CHS = naringenin - chalcone synthase:  4-coumaroyl-CoA --> naringeninchalcone
+
====Antioxidant Activities: ====
 +
Xanthohumol at 5 µM decreased conjugated diene formation as a measure for lipid peroxidation by more than 70 % after 5 h of incubation in an in vitro assay (protection of LDL from Cu2+ induced oxidation). Furthermore xanthohumol was shown to scavenge hydroxyl-, peroxyl- and superoxide anion radicals [[http://www.ncbi.nlm.nih.gov/pubmed/11038156 Miranda ''et al.'', 2000c]].
 +
</div>
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ENZYME 4: APT = aromatic prenyltransferase:      naringeninchalcone --> desmethylxanthohumol
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==Results==
 +
----
 +
===BioBricks===
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ENZYME 5: OMT1 = chalcone O-methyltransferase:    desmethylxanthohumol --> xanthohumol
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The following BioBricks were constructed to achieve the production of xanthohumol.
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Source: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=PWY-5135
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==== Overview====
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[[File:TUM12 experiment overwiew xanto2.png|thumb|center|800px|'''Fig. 4: Metabolic pathway of xanthohumol and designed BioBricks.''']]
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<div class="mfull bezel">
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==== [http://partsregistry.org/Part:BBa_K801090 BBa_K801090] and [http://partsregistry.org/Part:BBa_K801091 BBa_K801091] RFC10 compatible BioBricks encoding the enzyme PAL ====
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Both RFC10 compatible BioBricks encode the enzyme phenylalanine ammonia lyase (PAL). BBa_K801090 contains the yeast consensus sequence (improved ribosome binding), BBa_K801091 does not.  PAL is catalyzing the first reaction step of the xanthohumol biosynthesis pathway resulting in 4-coumarate.
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'''Further Information:'''
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* [http://www.ncbi.nlm.nih.gov/nuccore/AX366866 NCBI]
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* UniProt entry: P11544
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* E.C. Number: 4.3.1.25
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* Origin of the enzyme: ''Rhodosporidium toruloides''
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</div>
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<div class="mfull bezel">
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==== [http://partsregistry.org/Part:BBa_K801092 BBa_K801092] and [http://partsregistry.org/Part:BBa_K801093 BBa_K801093] RFC25 compatible BioBricks encode the enzyme 4CL====
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Both RFC25 compatible BioBricks encode the enzyme 4-coumarate-coenzyme A ligase (4CL). BBa_K801092 contains the yeast consensus sequence, BBa_K801093 does not. 
 +
'''Further Information:'''
 +
* [http://www.ncbi.nlm.nih.gov/nucleotide/609339/ NCBI]
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* UniProt entry: Q42524
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* E.C. Number: 6.2.1.12
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* Origin of the enzyme: ''Arabidopsis thaliana''
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</div>
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<div class="mfull bezel">
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==== [http://partsregistry.org/Part:BBa_K801094 BBa_K801094] and [http://partsregistry.org/Part:BBa_K801095 BBa_K801095]  RFC25 compatible BioBricks encoding the enzyme CHS====
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Both RFC25 compatible BioBricks encode the enzyme naringenin-chalcone synthase (CHS). BBa_K801094 contains the yeast consensus sequence, BBa_K801095 does not. 
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=='''Enzymes - Sequences, Translation and Assays'''==
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'''Further Information:'''
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* [http://www.ncbi.nlm.nih.gov/nucleotide/11096318/ NCBI]
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* UniProt entry: Q9FUB7
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* E.C. Number: 2.3.1.74
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* Origin of the enzyme: ''Hypericum androsaemum''
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</div>
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<div class="mfull bezel">
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Sequences of PAL, 4Cl and CHS come from Paper [[Media:TUM12_2004_Metabolic Engineering of the phenylpropanoid pathway in Saccharomyces.pdf‎| ''Hanxiao Jiang et al., 2004'']]
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==== [http://partsregistry.org/Part:BBa_K801096 BBa_K801096] RFC25 compatible BioBrick encoding the enzyme APT ====
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This RFC25 compatible BioBrick encodes the enzyme aromatic prenyltransferase (APT).
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'''Further Information:'''
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* [http://www.ncbi.nlm.nih.gov/nuccore/AB543053 NCBI]
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* UniProt entry: E5RP65
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* E.C. Number: EC 2.5.1
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* Origin of the enzyme: ''Humulus lupulus''
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</div>
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<div class="mfull bezel">
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===='''Enzyme 1: phenylalanine ammonia lyase (PAL)'''====
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==== [http://partsregistry.org/Part:BBa_K801097 BBa_K801097] and [http://partsregistry.org/Part:BBa_K801098 BBa_K801098] RFC25 compatible BioBricks encoding the enzyme OMT1 ====
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we only use the sequence from start- to stopcodon ('''bold'''): 1-2151
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Both RFC25 compatible BioBricks encode the enzyme O-methyltransferase 1 (OMT1). BBa_K801097 contains the yeast consensus sequence, BBa_K801095 does not. 
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'''Further Information:'''
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* [http://www.ncbi.nlm.nih.gov/nucleotide/167613934/ NCBI]
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* UniProt entry: B0ZB55
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* E.C. Number: EC 2.1.1
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* Origin of the enzyme: ''Humulus lupulus''
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</div>
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<div style="clear:both">
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'''Sequence'''
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===Characterization===
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</div>
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----
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We have successfully cloned all 5 enzymes which are necessary for the biosynthesis of xanthohumol in [http://partsregistry.org/Part:BBa_K801004 pTUM104] as well as in pSB1C3. Except for APT each enzyme was designed in two versions:  one with a proposed yeast consensus sequence and one without.  In yeast this sequence should result in improved ribosome binding (TACACA) and was added 5’ of the start codon ATG. All BioBricks were sequenced. Sequences can be found in the registry of standard biological parts:
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[http://partsregistry.org/Part:BBa_K801090 BBa_K801090],
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[http://partsregistry.org/Part:BBa_K801091 BBa_K801091],
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[http://partsregistry.org/Part:BBa_K801092 BBa_K801092],
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[http://partsregistry.org/Part:BBa_K801093 BBa_K801093],
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[http://partsregistry.org/Part:BBa_K801094 BBa_K801094],
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[http://partsregistry.org/Part:BBa_K801095 BBa_K801095],
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[http://partsregistry.org/Part:BBa_K801096 BBa_K801096],
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[http://partsregistry.org/Part:BBa_K801097 BBa_K801097],
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[http://partsregistry.org/Part:BBa_K801098 BBa_K801098].
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>gi|18698155|emb|AX366866.1| Sequence 18 from Patent WO0208402
 
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        1 '''atg'''gcaccct cgctcgactc gatctcgcac tcgttcgcaa acggcgtcgc atccgcaaag
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Our next goal is to prove enzyme expression via SDS-PAGE and Western Blot analysis. Afterwards activities will be tested in in-vitro assays to ensure the functionality of the 5 enzymes.
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      61 caggctgtca atggcgcctc gaccaacctc gcagtcgcag gctcgcacct gcccacaacc
+
-
      121 caggtcacgc aggtcgacat cgtcgagaag atgctcgccg cgccgaccga ctcgacgctc
+
-
      181 gaactcgacg gctactcgct caacctcgga gacgtcgtct cggccgcgag gaagggcagg
+
-
      241 cctgtccgcg tcaaggacag cgacgagatc cgctcaaaga ttgacaaatc ggtcgagttc
+
-
      301 ttgcgctcgc aactctccat gagcgtctac ggcgtcacga ctggatttgg cggatccgca
+
-
      361 gacacccgca ccgaggacgc catctcgctc cagaaggctc tcctcgagca ccagctctgc
+
-
      421 ggtgttctcc cttcgtcgtt cgactcgttc cgcctcggcc gcggtctcga gaactcgctt
+
-
      481 cccctcgagg ttgttcgcgg cgccatgaca atccgcgtca acagcttgac ccgcggccac
+
-
      541 tcggctgtcc gcctcgtcgt cctcgaggcg ctcaccaact tcctcaacca cggcatcacc
+
-
      601 cccatcgtcc ccctccgcgg caccatctct gcgtcgggcg acctctctcc tctctcctac
+
-
      661 attgcagcgg ccatcagcgg tcacccggac agcaaggtgc acgtcgtcca cgagggcaag
+
-
      721 gagaagatcc tgtacgcccg cgaggcgatg gcgctcttca acctcgagcc cgtcgtcctc
+
-
      781 ggcccgaagg aaggtctcgg tctcgtcaac ggcaccgccg tctcagcatc gatggccacc
+
-
      841 ctcgctctgc acgacgcaca catgctctcg ctcctctcgc agtcgctcac ggccatgacg
+
-
      901 gtcgaagcga tggtcggcca cgccggctcg ttccacccct tccttcacga cgtcacgcgc
+
-
      961 cctcacccga cgcagatcga agtcgcggga aacatccgca agctcctcga gggaagccgc
+
-
    1021 tttgctgtcc accatgagga ggaggtcaag gtcaaggacg acgagggcat tctccgccag
+
-
    1081 gaccgctacc ccttgcgcac gtctcctcag tggctcggcc cgctcgtcag cgacctcatt
+
-
    1141 cacgcccacg ccgtcctcac catcgaggcc ggccagtcga cgaccgacaa ccctctcatc
+
-
    1201 gacgtcgaga acaagacttc gcaccacggc ggcaatttcc aggctgccgc tgtggccaac
+
-
    1261 accatggaga agactcgcct cgggctcgcc cagatcggca agctcaactt cacgcagctc
+
-
    1321 accgagatgc tcaacgccgg catgaaccgc ggcctcccct cctgcctcgc ggccgaagac
+
-
    1381 ccctcgctct cctaccactg caagggcctc gacatcgccg ctgcggcgta cacctcggag
+
-
    1441 ttgggacacc tcgccaaccc tgtgacgacg catgtccagc cggctgagat ggcgaaccag
+
-
    1501 gcggtcaact cgcttgcgct catctcggct cgtcgcacga ccgagtccaa cgacgtcctt
+
-
    1561 tctctcctcc tcgccaccca cctctactgc gttctccaag ccatcgactt gcgcgcgatc
+
-
    1621 gagttcgagt tcaagaagca gttcggccca gccatcgtct cgctcatcga ccagcacttt
+
-
    1681 ggctccgcca tgaccggctc gaacctgcgc gacgagctcg tcgagaaggt gaacaagacg
+
-
    1741 ctcgccaagc gcctcgagca gaccaactcg tacgacctcg tcccgcgctg gcacgacgcc
+
-
    1801 ttctccttcg ccgccggcac cgtcgtcgag gtcctctcgt cgacgtcgct ctcgctcgcc
+
-
    1861 gccgtcaacg cctggaaggt cgccgccgcc gagtcggcca tctcgctcac ccgccaagtc
+
-
    1921 cgcgagacct tctggtccgc cgcgtcgacc tcgtcgcccg cgctctcgta cctctcgccg
+
-
    1981 cgcactcaga tcctctacgc cttcgtccgc gaggagcttg gcgtcaaggc ccgccgcgga
+
-
    2041 gacgtcttcc tcggcaagca agaggtgacg atcggctcga acgtctccaa gatctacgag
+
-
    2101 gccatcaagt cgggcaggat caacaacgtc ctcctcaaga tgctcgct'''ta g'''acactcttc
+
-
    2161 ccactctcgc atcccttcca taccctatcc cgcctgcact cttaggactc gcttcttgtc
+
-
    2221 ggactcggat ctcgcatcgc ttctttcgtt cttggctgcc tctctagacc gtgtccgtat
+
-
    2281 tacctcgaga ttgtgaatac aagcagtacc catccacgca tccgataaat cagggagaga
+
-
    2341 atctacgctt gcgggagctt cttgcgcata aactgtcgag tgcgggcgtt agtgcgaagt
+
-
    2401 caacgaaggc gagtggcagc ggctcactac cgcctcgag
+
-
 
+
==References==
-
'''Translation'''
+
----
-
 
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/12481418 Gerhauser et al., 2002]] Gerhauser, C., Alt, A., Heiss, E., Gamal-Eldeen, A., Klimo, K., Knauft, J., Neu- mann, I., Scherf, H.-R., Frank, N., Bartsch, H., and Becker, H. (2002). Cancer chemopreventive activity of xanthohumol, a natural product derived from hop. ''Mol Cancer Ther'', 1(11):959–69.
-
>gi|18698155|emb|AX366866.1| 1-2151
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/10752639 Henderson et al., 2000]] Henderson, M. C., Miranda, C. L., Stevens, J. F., Deinzer, M. L., and Buhler, D. R. (2000). In vitro inhibition of human p450 enzymes by prenylated flavonoids from hops, ''humulus lupulus''. ''Xenobiotica'', 30(3):235–51.
-
 
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/14704995 Jiang and Morgan, 2004]] Jiang, H. and Morgan, J. A. (2004). Optimization of an in vivo plant p450 monooxygenase system in ''Saccharomyces cerevisiae''. ''Biotechnol Bioeng'', 85(2):130–7.
-
MAPSLDSISHSFANGVASAKQAVNGASTNLAVAGSHLPTTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLC
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/10737704 Miranda et al., 2000a]] Miranda, C. L., Aponso, G. L., Stevens, J. F., Deinzer, M. L., and Buhler, D. R. (2000a). Prenylated chalcones and flavanones as inducers of quinone reductase in mouse hepa 1c1c7 cells. ''Cancer Lett'', 149(1-2):21–9.
-
GVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMAT
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/10418944 Miranda et al., 1999]] Miranda, C. L., Stevens, J. F., Helmrich, A., Henderson, M. C., Rodriguez, R. J., Yang, Y. H., Deinzer, M. L., Barnes, D. W., and Buhler, D. R. (1999). Antiproliferative and cytotoxic effects of prenylated flavonoids from hops (''Humulus lupulus'') in human cancer cell lines. ''Food Chem Toxicol'', 37(4):271–85.
-
LALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVAN
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/10995285 Miranda et al., 2000b]] Miranda, C. L., Stevens, J. F., Ivanov, V., McCall, M., Frei, B., Deinzer, M. L., and Buhler, D. R. (2000b). Antioxidant and prooxidant actions of prenylated and nonprenylated chalcones and flavanones in vitro. ''J Agric Food Chem'', 48(9):3876–84.
-
TMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHF
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/11038156 Miranda et al., 2000c]] Miranda, C. L., Yang, Y. H., Henderson, M. C., Stevens, J. F., Santana-Rios, G., Deinzer, M. L., and Buhler, D. R. (2000c). Prenylflavonoids from hops inhibit the metabolic activation of the carcinogenic heterocyclic amine 2-amino-3-methylimidazo[4, 5-f]quinoline, mediated by cdna-expressed human cyp1a2. ''Drug Metab Dispos'', 28(11):1297–302.
-
GSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYE
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/19631278 Trantas et al., 2009]] Trantas, E., Panopoulos, N., and Ververidis, F. (2009). Metabolic engineering of the complete pathway leading to heterologous biosynthesis of various flavonoids and stilbenoids in ''Saccharomyces cerevisiae''. ''Metab Eng'', 11(6):355–66.
-
AIKSGRINNVLLKMLA
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/11240137 Yilmazer et al., 2001a]] Yilmazer, M., Stevens, J. F., and Buhler, D. R. (2001a). In vitro glucuronidation of xanthohumol, a flavonoid in hop and beer, by rat and human liver microsomes. ''FEBS Lett'', 491(3):252–6.
-
 
+
*[[http://www.ncbi.nlm.nih.gov/pubmed/11181488 Yilmazer et al., 2001b]] Yilmazer, M., Stevens, J. F., Deinzer, M. L., and Buhler, D. R. (2001b). In vitro biotransformation of xanthohumol, a flavonoid from hops (''Humulus lupulus''), by rat liver microsomes. ''Drug Metab Dispos'', 29(3):223–31.
-
 
+
-
 
+
-
 
+
-
 
+
-
'''Compatibility (iGEM and ''S. cerevisiae'')'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || Length || RFC10 || RFC25 || Codon Usage || NCBI
+
-
|-
+
-
| Phenylalanine ammonia lyase || 2439bp bzw. 2151bp || ok || 6xNgoMIV (1438,1684,1852,1995,2329) || 0 AS<10% || [http://www.ncbi.nlm.nih.gov/nuccore/AX366866]
+
-
|}
+
-
 
+
-
 
+
-
'''Purification and Assay'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || used restriction sites || purification || assay
+
-
|-
+
-
| Phenylalanine ammonia lyase || XbaI, AgeI || Strep tag II || substrate: L-tyrosin, product: 4-coumarate
+
-
|}
+
-
 
+
-
 
+
-
===='''Enzyme 2: 4-coumarate - coenzym A ligase (4CL)'''====
+
-
 
+
-
we only use the sequence from start- to stopcodon ('''bold'''): 6-1691
+
-
 
+
-
 
+
-
>gi|609339|gb|U18675.1|ATU18675 Arabidopsis thaliana 4-coumarate--coenzyme A ligase (At4CL1) mRNA, complete cds
+
-
+
-
        1 ttaca<span style="color:#0000CD">'''atg'''gc gccacaagaa caagcagttt ctcaggtgat ggagaaacag agcaacaaca
+
-
      61 acaacagtga cgtcattttc cgatcaaagt taccggatat ttacatcccg aaccacctat
+
-
      121 ctctccacga ctacatcttc caaaacatct ccgaattcgc cactaagcct tgcctaatca
+
-
      181 acggaccaac cggccacgtg tacacttact ccgacgtcca cgtcatctcc cgccaaatcg
+
-
      241 ccgccaattt tcacaaactc ggcgttaacc aaaacgacgt cgtcatgctc ctcctcccaa
+
-
      301 actgtcccga attcgtcctc tctttcctcg ccgcctcctt ccgcggcgca accgccaccg
+
-
      361 ccgcaaaccc tttcttcact ccggcggaga tagctaaaca agccaaagcc tccaacacca
+
-
      421 aactcataat caccgaagct cgttacgtcg acaaaatcaa accacttcaa aacgacgacg
+
-
      481 gagtagtcat cgtctgcatc gacgacaacg aatccgtgcc aatccctgaa ggctgcctcc
+
-
      541 gcttcaccga gttgactcag tcgacaaccg aggcatcaga agtcatcgac tcggtggaga
+
-
      601 tttcaccgga cgacgtggtg gcactacctt actcctctgg cacgacggga ttaccaaaag
+
-
      661 gagtgatgct gactcacaag ggactagtca cgagcgttgc tcagcaagtc gacggcgaga
+
-
      721 acccgaatct ttatttccac agcgatgacg tcatactctg tgttttgccc atgtttcata
+
-
      781 tctacgcttt gaactcgatc atgttgtgtg gtcttagagt tggtgcggcg attctgataa
+
-
      841 tgccgaagtt tgagatcaat ctgctattgg agctgatcca gaggtgtaaa gtgacggtgg
+
-
      901 ctccgatggt tccgccgatt gtgttggcca ttgcgaagtc ttcggagacg gagaagtatg
+
-
      961 atttgagctc gataagagtg gtgaaatctg gtgctgctcc tcttggtaaa gaacttgaag
+
-
    1021 atgccgttaa tgccaagttt cctaatgcca aactcggtca gggatacgga atgacggaag
+
-
    1081 caggtccagt gctagcaatg tcgttaggtt ttgcaaagga accttttccg gttaagtcag
+
-
    1141 gagcttgtgg tactgttgta agaaatgctg agatgaaaat agttgatcca gacaccggag
+
-
    1201 attctctttc gaggaatcaa cccggtgaga tttgtattcg tggtcaccag atcatgaaag
+
-
    1261 gttacctcaa caatccggca gctacagcag agaccattga taaagacggt tggcttcata
+
-
    1321 ctggagatat tggattgatc gatgacgatg acgagctttt catcgttgat cgattgaaag
+
-
    1381 aacttatcaa gtataaaggt tttcaggtag ctccggctga gctagaggct ttgctcatcg
+
-
    1441 gtcatcctga cattactgat gttgctgttg tcgcaatgaa agaagaagca gctggtgaag
+
-
    1501 ttcctgttgc atttgtggtg aaatcgaagg attcggagtt atcagaagat gatgtgaagc
+
-
    1561 aattcgtgtc gaaacaggtt gtgttttaca agagaatcaa caaagtgttc ttcactgaat
+
-
    1621 ccattcctaa agctccatca gggaagatat tgaggaaaga tctgagggca aaactagcaa
+
-
    1681 atggattg'''tg a'''</span>tggatgatt tcaaccaaaa agcaaagatg atttcaatgt gtatatacat
+
-
    1741 acaactgttt gacccaacca aggaaacaaa ctcatacgaa ccattgtctt ttgttgttgt
+
-
    1801 tgttgttgtt gttgttgctg ttcttgcttg attcatgtaa tgagcctttg tgatgaaggt
+
-
    1861 ggtttcttt
+
-
 
+
-
 
+
-
'''Translation'''
+
-
6-1691
+
-
 
+
-
MAPQEQAVSQVMEKQSNNNNSDVIFRSKLPDIYIPNHLSLHDYIFQNISEFATKPCLINGPTGHVYTYSDVHVISRQIAANFHKLGVNQNDVVMLLLPNCPEFVLSFLAASFRGATATAANPFFTPAEIAKQAKASNTKLIITEARYVDKIKPLQNDDGV
+
-
VIVCIDDNESVPIPEGCLRFTELTQSTTEASEVIDSVEISPDDVVALPYSSGTTGLPKGVMLTHKGLVTSVAQQVDGENPNLYFHSDDVILCVLPMFHIYALNSIMLCGLRVGAAILIMPKFEINLLLELIQRCKVTVAPMVPPIVLAIAKSSETEKYDL
+
-
SSIRVVKSGAAPLGKELEDAVNAKFPNAKLGQGYGMTEAGPVLAMSLGFAKEPFPVKSGACGTVVRNAEMKIVDPDTGDSLSRNQPGEICIRGHQIMKGYLNNPAATAETIDKDGWLHTGDIGLIDDDDELFIVDRLKELIKYKGFQVAPAELEALLIGH
+
-
PDITDVAVVAMKEEAAGEVPVAFVVKSKDSELSEDDVKQFVSKQVVFYKRINKVFFTESIPKAPSGKILRKDLRAKLANGL
+
-
 
+
-
 
+
-
'''Compatibility (iGEM and ''S. cerevisiae'')'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || Length || RFC10 || RFC25 || Codon Usage || NCBI
+
-
|-
+
-
| Arabidopsis thaliana 4-coumarate--coenzyme A ligase || 1869 bp bzw. 1685 bp || 2xEcoRI (149-154, 309-314), 1x Spe1 (679-684) || ok after RFC10 || 0 AS<10% || [http://www.ncbi.nlm.nih.gov/nucleotide/609339/]
+
-
|}
+
-
 
+
-
'''Purification and Assay'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || used restriction sites || purification || assay 
+
-
|-
+
-
| Arabidopsis thaliana 4-coumarate--coenzyme A ligase || XbaI, PstI || crude protein extraction || substrate: 4-coumarate, product: 4-coumaryl-CoA
+
-
|}
+
-
 
+
-
 
+
-
====''' Enzyme 3: naringenin - chalcone synthase(CHS)'''====
+
-
 
+
-
 
+
-
we only use the sequence from start- to stopcodon ('''bold'''): 76-1248
+
-
 
+
-
>gi|11096318|gb|AF315345.1| Hypericum androsaemum chalcone synthase mRNA, complete cds
+
-
+
-
        1 aaactctgtc accacattat tgtaccttgt aacagcaagg tgcttaactg gttgatttaa
+
-
      61 acataaacaa ggaag'''atg'''gt gaccgtggaa gaagtcagga aggcgcagcg ggccgagggt
+
-
      121 ccggccaccg tgatggccat cggaacggcc gtcccgccga actgcgttga ccaagcgacg
+
-
      181 taccccgact attatttccg tatcaccaac agcgagcaca aggccgagct caaggagaag
+
-
      241 ttccaacgca tgtgtgataa gtctcaaatc aagaaacgtt acatgtacct gaacgaggag
+
-
      301 gtcctcaaag agaaccccaa tatgtgtgct tacatggcac cttctctgga tgctaggcaa
+
-
      361 gacattgtgg tggtggaagt gcccaaacta ggtaaagagg cagcagttaa ggccatcaag
+
-
      421 gaatggggcc agcctaagtc caagatcacc cacttggtct tttgcaccac tagtggagtg
+
-
      481 gacatgcccg gggccgacta ccagctcacc aagctattgg gcctccgccc gtcggtgaag
+
-
      541 cgcctcatga tgtaccagca gggctgcttt gccggtggca cggtcctccg tctcgccaag
+
-
      601 gatctcgccg agaacaacaa gggtgcacgc gtccttgtcg tctgctcgga gatcacggcc
+
-
      661 gttaccttcc gtgggcccac cgacactcac ctcgacagcc ttgtgggcca ggcattgttc
+
-
      721 ggtgacggcg ctgccgccat catcatcggc tcggacccga tccccgaagt cgagaagccc
+
-
      781 ttgttcgagc tggtctccgc agcccagacc attctaccgg acagtgaggg tgcgatagac
+
-
      841 ggacatctcc gcgaggttgg gcttacattc cacttgctca aggatgttcc cgggttgatc
+
-
      901 tctaagaacg ttgagaagag cctcactgag gccttcaaac cgttgggcat ttcagattgg
+
-
      961 aactccctgt tttggatcgc ccacccaggc ggcccagcaa tcttggacca ggtagaggcc
+
-
    1021 aagttgagcc tcaagcccga gaagctacgg gccacaaggc acgtactttc cgagtacgga
+
-
    1081 aacatgtcta gtgcctgtgt gcttttcatc ttagacgaga tgaggaggaa gtccaaggaa
+
-
    1141 gacgggctta agaccacagg ggaaggaatc gagtggggag tgctttttgg atttgggcct
+
-
    1201 gggcttaccg ttgagaccgt tgtccttcac agtgtcgcca ttaac'''tag'''gt caaggtcgtt
+
-
    1261 gctttgcgtt ttttactttg ttgttgcctg taatattttc actacttggc gtcttttttt
+
-
    1321 cactttctaa cttctaatgt tttacctctg ggtcaaacat atgtggtgca gtgaaaaact
+
-
    1381 gaaaaaaaaa aaaaaaaaaa aa
+
-
 
+
-
'''Translation'''
+
-
76-1248
+
-
 
+
-
MVTVEEVRKAQRAEGPATVMAIGTAVPPNCVDQATYPDYYFRITNSEHKAELKEKFQRMCDKSQIKKRYMYLNEEVLKENPNMCAYMAPSLDARQDIVVVEVPKLGKEAAVKAIKEWGQPKSKITHLVFCTTSGVDMPGADYQLTKLLGLRPSVKRLMMY
+
-
QQGCFAGGTVLRLAKDLAENNKGARVLVVCSEITAVTFRGPTDTHLDSLVGQALFGDGAAAIIIGSDPIPEVEKPLFELVSAAQTILPDSEGAIDGHLREVGLTFHLLKDVPGLISKNVEKSLTEAFKPLGISDWNSLFWIAHPGGPAILDQVEAKLSLK
+
-
PEKLRATRHVLSEYGNMSSACVLFILDEMRRKSKEDGLKTTGEGIEWGVLFGFGPGLTVETVVLHSVAIN
+
-
 
+
-
 
+
-
'''Compatibility (iGEM and ''S. cerevisiae'')'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || Length || RFC10 || RFC25 || Codon Usage || NCBI
+
-
|-
+
-
| Hypericum androsaemum chalcone synthase || 1402 bp || 1xSpeI (469) || ok after RFC10 || 2 AS<10% ||
+
-
[http://www.ncbi.nlm.nih.gov/nucleotide/11096318/]
+
-
|}
+
-
 
+
-
 
+
-
'''Purification and Assay'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || used restriction sites || purification || assay 
+
-
|-
+
-
| Hypericum androsaemum chalcone synthase || XbaI, AgeI || Strep tag II || subtrate:
+
-
|}
+
-
 
+
-
====''' Enzyme 4: aromatic prenyltransferase (APT)'''====
+
-
 
+
-
we decided to have the gene synthesized
+
-
 
+
-
>gi|11096318|gb|(AB543053.1)| optimized sequence with restriction sites (XbaI and AgeI) (gene synthesis)
+
-
+
-
    1 tctagatggctttgtcatccgtttcttcattttctttgggtaccaacccattcatctcca
+
-
    61 tcccacataacaacaacaacttgaaggtttcttcctactgctgcaaatctaagtccagag
+
-
  121 ttatcaactccactaactctaaacattgctccccaaacaacaacaacaacacttctaaca
+
-
  181 agaccacccatttgttgggtttatacggtcaatcaagatgcttgttgaagccattgtctt
+
-
  241 tcatctcttgcaacgatcaaagaggtaactctattagagcttccgcccaaattgaagata
+
-
  301 gaccaccagaatctggtaacttgtctgctttgactaacgttaaggatttcgtttctgttt
+
-
  361 gctgggaatacgttagaccatatactgctaagggtgttatcatttgctcctcttgtttgt
+
-
  421 tcggtagagaattattggaaaacccaaacttgttctccagaccattgattttcagagcct
+
-
  481 tgttgggtatgttggctattttgggttcttgtttttacaccgccggtatcaatcaaatct
+
-
  541 tcgatatggatatcgacagaatcaacaagccagatttgccattggtttccggtagaattt
+
-
  601 ctgttgaatctgcttggttgttgactttgtccccagctattattggtttcatcttgatct
+
-
  661 tgaagttgaactccggtcctttgttgacctcattatactgtttggcaatcttgtccggta
+
-
  721 ctatctattctgttccaccttttagatggaagaagaatccaattaccgccttcttgtgca
+
-
  781 ttttgatgattcatgctggtttgaacttctccgtttactatgcttcaagagctgctttgg
+
-
  841 gtttggcttttgcttggtcaccatctttttctttcattaccgctttcatcaccttcatga
+
-
  901 ctttgactttggcttcctctaaggatttgtccgatattaacggtgatagaaagttcggtg
+
-
  961 ttgaaactttcgctacaaaattgggtgctaagaacatcaccttgttaggtactggtttgt
+
-
  1021 tattattgaactacgttgctgctatttccaccgctattatttggcctaaagctttcaagt
+
-
  1081 ccaacatcatgttgttgtcccatgctatcttggccttttcattgatctttcaagctagag
+
-
  1141 aattggacagaactaactacactccagaagcttgtaagtccttctacgaatttatctgga
+
-
  1201 ttttgttctccgccgaatacgttgtttacttgttcatcaccggt
+
-
 
+
-
 
+
-
'''Translation'''
+
-
1-1236
+
-
MELSSVSSFSLGTNPFISIPHNNNNLKVSSYCCKSKSRVINSTNSKHCSPNNNNNTSNKTTHLLGLYGQSRCLLKPLSFISCNDQRGNSIRASAQIEDRPPESGNLSALTNVKDFVSVCWEYVRPYTAKGVIICSSCLFGRELLENPNLFSRPLIFRALL
+
-
GMLAILGSCFYTAGINQIFDMDIDRINKPDLPLVSGRISVESAWLLTLSPAIIGFILILKLNSGPLLTSLYCLAILSGTIYSVPPFRWKKNPITAFLCILMIHAGLNFSVYYASRAALGLAFAWSPSFSFITAFITFMTLTLASSKDLSDINGDRKFGVE
+
-
TFATKLGAKNITLLGTGLLLLNYVAAISTAIIWPKAFKSNIMLLSHAILAFSLIFQARELDRTNYTPEACKSFYEFIWILFSAEYVVYLFI
+
-
 
+
-
 
+
-
 
+
-
'''Compatibility (iGEM and ''S. cerevisiae'')'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || Length || RFC10 || RFC25 || Codon Usage || NCBI
+
-
|-
+
-
| Humulus lupulus aromatic prenyltransferase || 1236 bp || ok  || ok  || optimized by GeneArt ||
+
-
[http://www.ncbi.nlm.nih.gov/nuccore/AB543053]
+
-
|}
+
-
 
+
-
 
+
-
'''Purification and Assay'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || used restriction sites || purification || assay 
+
-
|-
+
-
| Humulus lupulus aromatic prenyltransferase || XbaI, AgeI || Strep tag II || substrate:
+
-
|}
+
-
 
+
-
====''' Enzyme 5: chalcone O-methyltransferase(OMT1)'''====
+
-
 
+
-
 
+
-
we only use the sequence from start- to stopcodon (50-1108'''bold'''):  
+
-
 
+
-
Humulus lupulus O-methyltransferase 1 (OMT1) mRNA, complete cds, Genbank EU309725.1
+
-
+
-
              1 ggacacaatt caatctattt tacccaaaaa ataactaaga aagaccaat'''a tg'''gaatctct
+
-
      61 aagaggccaa gaacagatat ggcaactcat gttcagcttt gtcgactcca tggccttgaa
+
-
      121 atgcgccatc gagcttcgca ttgctgacat cattcactct catggcaaac ctataactct
+
-
      181 ctcccaaata gcttctggca ttcgatcaaa ctccaactcc tccatatctc cgaatattcc
+
-
      241 ttacctctct cgcatcatga gatttcttgt tcgaaagaat atcttcactg aacatcaaga
+
-
      301 agataatgat gaggtgatct cattgtacgg gctaagtgat agctcgagat ggctgttgcg
+
-
      361 ggattttaag tcaagcctgg ctcccatggt gctcatgcag actcatccat tgtcgatggc
+
-
      421 ggtgtggcat ttccttgagg attatgtgag aaacagcagc aacactttcg aaaaggctca
+
-
      481 cggttgtaac atttgggagt tttcctcagc caatccagat ttcaacaaga tcttcaacaa
+
-
      541 tgccatggcg agtattgtgc caatatacat gggggctgtg ctttcaagtt ataaggatgg
+
-
      601 tcttggttgt attaaaggaa cagtggtgga cgttgggggt ggtacgggcg gctccatatc
+
-
      661 agagcttatg aaatattatc caaacatcaa agggattaac tttgacctgc cacatgtgat
+
-
      721 tgccacagca ccggcattgg atggtgttac ccatattagt ggtgacatat tcgagtcaat
+
-
      781 tcctagtgct gatgcggttt taatgaaggg tgtactacat tgcttcagcg atgaaaaatg
+
-
      841 tgtaaaagta ttgagaaatt gtcgaaaagc aataacagac aaaaagaatg ggaagattat
+
-
      901 cattttggag attgtgttgg acccaaccag caatcaaata tttgacgaga ctcgaatggt
+
-
      961 gtacgattta ttgattccay tctttagtgg tggaaaagag agaactgagc ttgaatggaa
+
-
    1021 aaggctatta aacgaggctg gttttacttc tatcaaaatc accaaaattc caattatacc
+
-
    1081 tgctattatt gaggcctttc tagtg'''tga'''ca acrtcgatct atctatatat atataaacta
+
-
    1141 ggttatgttg ctttcaacaa taagttccct atgtactgtt acggttatgt atggtttgct
+
-
    1201 gtgattaata taatatgttg gc
+
-
 
+
-
 
+
-
'''Translation'''
+
-
50-1108
+
-
MESLRGQEQIWQLMFSFVDSMALKCAIELRIADIIHSHGKPITLSQIASGIRSNSNSSISPNIPYLSRIMRFLVRKNIFTEHQEDNDEVISLYGLSDSSRWLLRDFKSSLAPMVLMQTHPLSMAVWHFLEDYVRNSSNTFEKAHGCNIWEFSSANPDFNK
+
-
IFNNAMASIVPIYMGAVLSSYKDGLGCIKGTVVDVGGGTGGSISELMKYYPNIKGINFDLPHVIATAPALDGVTHISGDIFESIPSADAVLMKGVLHCFSDEKCVKVLRNCRKAITDKKNGKIIILEIVLDPTSNQIFDETRMVYDLLIPXFSGGKERTE
+
-
LEWKRLLNEAGFTSIKITKIPIIPAIIEAFLV
+
-
 
+
-
'''Compatibility (iGEM and ''S. cerevisiae'')'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || Length || RFC10 || RFC25 || Codon Usage || NCBI
+
-
|-
+
-
| Humulus lupulus O-methyltransferase 1  || 1058  || ok || ok || 2 AS<10% ||
+
-
[http://www.ncbi.nlm.nih.gov/nucleotide/167613934/]
+
-
|}
+
-
 
+
-
 
+
-
'''Purification and Assay'''
+
-
{| class="wikitable" cellpadding="10" border=1px
+
-
| Name || used restriction sites || purification || assay 
+
-
|-
+
-
| Humulus lupulus O-methyltransferase 1  || XbaI, AgeI || Strep tag II || subtrate:
+
-
|}
+
-
 
+
-
=='''References'''==
+
-
 
+
-
*C Gerhauser, A Alt, E Heiss, A Gamal-Eldeen, K Klimo, J Knauft, I Neumann, H.R Scherf, N Frank, H Bartsch, H Becker Cancer chemopreventive activity of xanthohumol, a natural product derived from hop Mol. Cancer Ther., 1 (2002), pp. 959–969
+
-
 
+
-
*M.C Henderson, C.L Miranda, J.F Stevens, M.L Deinzer, D.R Buhler In vitro inhibition of human P450 enzymes by prenylated flavonoids from hops, Humulus lupulus Xenobiotica, 30 (2000), pp. 235–251
+
-
 
+
-
*C.L Miranda, G.L Aponso, J.F Stevens, M.L Deinzer, D.R Buhler Prenylated chalcones and flavanones as inducers of quinone reductase in mouse Hepa 1c1c7 cells Cancer Lett., 149 (2000), pp. 21–29
+
-
 
+
-
*C.L Miranda, J.F Stevens, A Helmrich, M.C Henderson, R.J Rodriguez, Y.H Yang, M.L Deinzer, D.W Barnes, D.R Buhler Antiproliferative and cytotoxic effects of prenylated flavonoids from hops (Humulus lupulus) in human cancer cell lines Food Chem. Toxicol., 37 (1999), pp. 271–285
+
-
 
+
-
*C.L Miranda, J.F Stevens, V Ivanov, M McCall, B Frei, M.L Deinzer, D.R Buhler Antioxidant and prooxidant actions of prenylated and nonprenylated chalcones and flavanones in vitro J. Agric. Food Chem., 48 (2000), pp. 3876–3884
+
-
 
+
-
*C.L Miranda, Y.H Yang, M.C Henderson, J.F Stevens, G Santana-Rios, M.L Deinzer, D.R Buhler, Prenylflavonoids from hops inhibit the metabolic activation of the carcinogenic heterocyclic amine 2-amino-3-methylimidazo[4,5-f]quinoline, mediated by cDNA-expressed human CYP1A2 Drug Metab. Dispos., 28 (2000), pp. 1297–1302
+
-
 
+
-
*M Yilmazer, J.F Stevens, M.L Deinzer, D.R Buhler In vitro biotransformation of xanthohumol, a flavonoid from hops (Humulus lupulus), by rat liver microsomes Drug Metab. Dispos., 29 (2001), pp. 223–231
+
-
 
+
-
*M Yilmazer, J.F Stevens, D.R Buhler In vitro glucuronidation of xanthohumol, a flavonoid in hop and beer, by rat and human liver microsomes FEBS Lett., 491 (2001), pp. 252–256
+

Latest revision as of 19:27, 26 October 2012


Contents

Xanthohumol


Responsible: Daniela Dichtler, Ingmar Polte, Maria Trumpfheller and Katrin Fischer

Flavonoids are valuable natural products with anti-inflammatory, antiallergenic and antioxidant activities in humans. For the chemical synthesis of flavonoids, extreme reaction conditions and toxic chemicals are required. Hence, we chose the transfer of this metabolic pathway into Saccharomyces cerevisiae as an attractive alternative source of flavonoids. After the successful implementation of the first steps of the phenylpropanoid pathway, the syntheses of different flavonoids are conceivable. Along with raspberry ketone, the aroma compound of raspberries, plant substances providing beneficial effects to ones life could be synthesized, for example resveratrol or xanthohumol, which we will focus on.

We successfully cloned all enzymes necessary for the pathway of xanthohumol in the new yeast expression vector pTUM104. Every gene was sequenced and submitted as a BioBrick. So we established BioBricks in order to produce xanthohumol in yeast (BBa_K801090, BBa_K801091, BBa_K801092, BBa_K801093, BBa_K801094, BBa_K801095, BBa_K801096, BBa_K801097, BBa_K801098,).

Our next goals are to proof the expression of every single enzyme by Western Blot Analysis and to show the functionality with established enzyme assays.


Background and Principles


Fig. 1: Structure of 4-coumaroyl-CoA.

Plant secondary metabolites have proven or assumed beneficial properties and health promoting effects. Stilbenoids, flavonoids or lignins can result from 4-coumaroyl-coenzyme A (see Fig. 1), which is a nodal compound of the phenylproponaoid metabolism in plants.

Biosynthesis

Fig. 2: Biosynthesis of xanthohumol.

The biosynthetic pathway of 4-coumaroyl-coenzyme A starts with the conversion of L-Phenylalanine to cinnamate, being catalyzed by phenylalanin ammonia lyase (PAL) [A]. PAL also shows activity in converting tyrosine to p-coumarate, but with a lower efficiency [B]. The cinnamate 4-hydroxylase (C4H) catalyzes the synthesis of p-hydroxycinnamate from cinnamate and 4-coumarate [C]: CoA ligase (4CL) converts p-coumarate to its coenzyme-A ester, activating it for reaction with malonyl CoA [D] [Trantas et al., 2009].

The flavonoid biosynthetic pathway starts with the condensation of one molecule of 4-coumaroyl-CoA and three molecules of malonyl-CoA, yielding naringenin chalcone. This reaction is carried out by the enzyme chalcone synthase (CHS) [E]. Chalcone is isomerised to a flavanone by the enzyme chalcone flavanone isomerase (CHI). From these central intermediates, the pathway diverges into several side branches, each resulting in a different class of flavonoids, such as xanthohumol.

Our project will focus on the production of xanthohumol (see Fig. 3), due to its characteristic as a cancer chemopreventive agent (see below). The idea is to perform a heterologous gene expression of all enzymes required for xanthohumol biosynthesis in Saccharomyces cerevisiae. First, each enzyme should be expressed individually, with the activities being also tested individually to ensure the functionality. Each gene should be inserted in a yeast expression vector under the control of a GAL1 promotor. The final goal is the expression of all required genes in a single modified yeast-stem to produce xanthohumol out of the substrate L-Tyrosin.

There are 5 enzymes necessary for the biosynthesis of xanthohumol (see Fig. 2) (MetaCyc):

Enzyme [A]: PAL = phenylalanine ammonia lyase: L-phenylalanin --> trans-cinnamate

Enzyme [D]: 4CL = 4-coumarate - coenzym A ligase: 4-coumarate --> 4-coumaroyl-CoA

Enzyme [E]: CHS = naringenin - chalcone synthase: 4-coumaroyl-CoA --> naringeninchalcone

Enzyme [F]: APT = aromatic prenyltransferase: naringeninchalcone --> desmethylxanthohumol

Enzyme [G]: OMT1 = chalcone O-methyltransferase: desmethylxanthohumol --> xanthohumol

Jiang et al succeeded in the biosynthesis of several flavonoids in Saccharomyces cerevisiae by the assembly of a plasmid containing three required enzymes (pKS2µHyg-PAL-4CL-CHS) and thereby showed the proof of principle. The activity of each enzyme was demonstrated and the presence of naringenin, which forms the product of the three enzymes( PAL, 4CL, CHS), was shown. [Jiang and Morgan, 2004]

The Molecular and Physiological Effects of Xanthohumol

Fig. 3: Structure of xanthohumol.

Inhibition of Metabolic Activation of Procarcinogens:

2-amino-3-methylimidazo[4,5-f]quinolone, found in cooked meat, verified as a procarcinogen in an ames salmonella mutagenicity test. The inhibition is probably a result of an inhibition of the cytochrome P 450 enzymes Cyp1A1, Cyp1B1 and Cyp1A2 (phase 1 enzymes). But in order to achieve a clear inhibition, plasma concentrations of 1 µM would be necessary. In a study with male rats oral administration of xanthohumol (50 mg/kg) led to concentration maximums of 65 -180 nM after 4 h. Improved resorption of xanthohumol could be a possible target for innovation [Yilmazer et al. 2001a, Miranda et al. 2000b, Henderson et al., 2000, Gerhauser et al., 2002].

Induction of Carcinogen-Detoxifying Enzymes (Phase 2 Enzymes):

P450-activated carcinogens get conjugated to endogenous ligands (gluthathione, glucoronic acid, acetate and sulfate) by phase 2 enzymes to facilitate excretion. Therefore the induction of phase 2 enzymes should enhance the protection against carcinogenesis. Xanthohumol cat concentrations of 2.1-10.1 µM could induce quinone reductase (detoxification of quinones by conversion to hydroquinones which can be conjugated) in hepatoma Hepa 1c1c7 cells. It was shown that xanthohumol could selectively induce quinone reductase without causing a transcriptional activation of Cyp1A1 [Miranda et al., 2000c, Gerhauser et al., 2002].

Inhibition of Tumor Growth at an Early Stage:

Xanthohumol showed an inhibition of the proliferation of breast cancer (MCF-7) and ovarian cancer (A-2780) in vitro at IC50 values of 13 and 0.52 µM [Miranda et al., 1999]. Furthermore xanthohumol can inhibit the endogenous prostaglandin synthesis through inhibition of cyclooxygenase (COX-1 and COX-2) with IC50 values of 17 and 42 µM. An increased prostaglandin production has been associated with the uncontrolled proliferation of tumor cells [Gerhauser et al., 2002]. Pharmacokinetic studies for xanthohumol based on beverages with an xanthohumol content of 50 mg/l in humans are part of actual research activities.

Antioxidant Activities:

Xanthohumol at 5 µM decreased conjugated diene formation as a measure for lipid peroxidation by more than 70 % after 5 h of incubation in an in vitro assay (protection of LDL from Cu2+ induced oxidation). Furthermore xanthohumol was shown to scavenge hydroxyl-, peroxyl- and superoxide anion radicals [Miranda et al., 2000c].

Results


BioBricks

The following BioBricks were constructed to achieve the production of xanthohumol.

Overview

Fig. 4: Metabolic pathway of xanthohumol and designed BioBricks.


BBa_K801090 and BBa_K801091 RFC10 compatible BioBricks encoding the enzyme PAL

Both RFC10 compatible BioBricks encode the enzyme phenylalanine ammonia lyase (PAL). BBa_K801090 contains the yeast consensus sequence (improved ribosome binding), BBa_K801091 does not. PAL is catalyzing the first reaction step of the xanthohumol biosynthesis pathway resulting in 4-coumarate.

Further Information:

  • NCBI
  • UniProt entry: P11544
  • E.C. Number: 4.3.1.25
  • Origin of the enzyme: Rhodosporidium toruloides

BBa_K801092 and BBa_K801093 RFC25 compatible BioBricks encode the enzyme 4CL

Both RFC25 compatible BioBricks encode the enzyme 4-coumarate-coenzyme A ligase (4CL). BBa_K801092 contains the yeast consensus sequence, BBa_K801093 does not.

Further Information:

  • NCBI
  • UniProt entry: Q42524
  • E.C. Number: 6.2.1.12
  • Origin of the enzyme: Arabidopsis thaliana

BBa_K801094 and BBa_K801095 RFC25 compatible BioBricks encoding the enzyme CHS

Both RFC25 compatible BioBricks encode the enzyme naringenin-chalcone synthase (CHS). BBa_K801094 contains the yeast consensus sequence, BBa_K801095 does not.

Further Information:

  • NCBI
  • UniProt entry: Q9FUB7
  • E.C. Number: 2.3.1.74
  • Origin of the enzyme: Hypericum androsaemum

BBa_K801096 RFC25 compatible BioBrick encoding the enzyme APT

This RFC25 compatible BioBrick encodes the enzyme aromatic prenyltransferase (APT).

Further Information:

  • NCBI
  • UniProt entry: E5RP65
  • E.C. Number: EC 2.5.1
  • Origin of the enzyme: Humulus lupulus

BBa_K801097 and BBa_K801098 RFC25 compatible BioBricks encoding the enzyme OMT1

Both RFC25 compatible BioBricks encode the enzyme O-methyltransferase 1 (OMT1). BBa_K801097 contains the yeast consensus sequence, BBa_K801095 does not.

Further Information:

  • NCBI
  • UniProt entry: B0ZB55
  • E.C. Number: EC 2.1.1
  • Origin of the enzyme: Humulus lupulus

Characterization


We have successfully cloned all 5 enzymes which are necessary for the biosynthesis of xanthohumol in pTUM104 as well as in pSB1C3. Except for APT each enzyme was designed in two versions: one with a proposed yeast consensus sequence and one without. In yeast this sequence should result in improved ribosome binding (TACACA) and was added 5’ of the start codon ATG. All BioBricks were sequenced. Sequences can be found in the registry of standard biological parts: BBa_K801090, BBa_K801091, BBa_K801092, BBa_K801093, BBa_K801094, BBa_K801095, BBa_K801096, BBa_K801097, BBa_K801098.


Our next goal is to prove enzyme expression via SDS-PAGE and Western Blot analysis. Afterwards activities will be tested in in-vitro assays to ensure the functionality of the 5 enzymes.

References


  • [Gerhauser et al., 2002] Gerhauser, C., Alt, A., Heiss, E., Gamal-Eldeen, A., Klimo, K., Knauft, J., Neu- mann, I., Scherf, H.-R., Frank, N., Bartsch, H., and Becker, H. (2002). Cancer chemopreventive activity of xanthohumol, a natural product derived from hop. Mol Cancer Ther, 1(11):959–69.
  • [Henderson et al., 2000] Henderson, M. C., Miranda, C. L., Stevens, J. F., Deinzer, M. L., and Buhler, D. R. (2000). In vitro inhibition of human p450 enzymes by prenylated flavonoids from hops, humulus lupulus. Xenobiotica, 30(3):235–51.
  • [Jiang and Morgan, 2004] Jiang, H. and Morgan, J. A. (2004). Optimization of an in vivo plant p450 monooxygenase system in Saccharomyces cerevisiae. Biotechnol Bioeng, 85(2):130–7.
  • [Miranda et al., 2000a] Miranda, C. L., Aponso, G. L., Stevens, J. F., Deinzer, M. L., and Buhler, D. R. (2000a). Prenylated chalcones and flavanones as inducers of quinone reductase in mouse hepa 1c1c7 cells. Cancer Lett, 149(1-2):21–9.
  • [Miranda et al., 1999] Miranda, C. L., Stevens, J. F., Helmrich, A., Henderson, M. C., Rodriguez, R. J., Yang, Y. H., Deinzer, M. L., Barnes, D. W., and Buhler, D. R. (1999). Antiproliferative and cytotoxic effects of prenylated flavonoids from hops (Humulus lupulus) in human cancer cell lines. Food Chem Toxicol, 37(4):271–85.
  • [Miranda et al., 2000b] Miranda, C. L., Stevens, J. F., Ivanov, V., McCall, M., Frei, B., Deinzer, M. L., and Buhler, D. R. (2000b). Antioxidant and prooxidant actions of prenylated and nonprenylated chalcones and flavanones in vitro. J Agric Food Chem, 48(9):3876–84.
  • [Miranda et al., 2000c] Miranda, C. L., Yang, Y. H., Henderson, M. C., Stevens, J. F., Santana-Rios, G., Deinzer, M. L., and Buhler, D. R. (2000c). Prenylflavonoids from hops inhibit the metabolic activation of the carcinogenic heterocyclic amine 2-amino-3-methylimidazo[4, 5-f]quinoline, mediated by cdna-expressed human cyp1a2. Drug Metab Dispos, 28(11):1297–302.
  • [Trantas et al., 2009] Trantas, E., Panopoulos, N., and Ververidis, F. (2009). Metabolic engineering of the complete pathway leading to heterologous biosynthesis of various flavonoids and stilbenoids in Saccharomyces cerevisiae. Metab Eng, 11(6):355–66.
  • [Yilmazer et al., 2001a] Yilmazer, M., Stevens, J. F., and Buhler, D. R. (2001a). In vitro glucuronidation of xanthohumol, a flavonoid in hop and beer, by rat and human liver microsomes. FEBS Lett, 491(3):252–6.
  • [Yilmazer et al., 2001b] Yilmazer, M., Stevens, J. F., Deinzer, M. L., and Buhler, D. R. (2001b). In vitro biotransformation of xanthohumol, a flavonoid from hops (Humulus lupulus), by rat liver microsomes. Drug Metab Dispos, 29(3):223–31.