Team:TU Munich/Project/Xanthohumol

From 2012.igem.org

(Difference between revisions)
(Enzymes - Sequences, Translation and Assays)
Line 77: Line 77:
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==Enzymes - Sequences, Translation and Assays==
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==Enzymes Assays==
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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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===Enzyme 1: phenylalanine ammonia lyase (PAL)===
===Enzyme 1: phenylalanine ammonia lyase (PAL)===
-
 
-
we only use the sequence from start- to stopcodon ('''bold'''): 1-2151
 
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-
 
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'''Sequence'''
 
-
 
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>gi|18698155|emb|AX366866.1| Sequence 18 from Patent WO0208402
 
-
 
-
        1 '''atg'''gcaccct cgctcgactc gatctcgcac tcgttcgcaa acggcgtcgc atccgcaaag
 
-
      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
 
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    2401 caacgaaggc gagtggcagc ggctcactac cgcctcgag
 
-
 
-
 
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'''Translation'''
 
-
 
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>gi|18698155|emb|AX366866.1| 1-2151
 
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MAPSLDSISHSFANGVASAKQAVNGASTNLAVAGSHLPTTQVTQVDIVEKMLAAPTDSTLELDGYSLNLGDVVSAARKGRPVRVKDSDEIRSKIDKSVEFLRSQLSMSVYGVTTGFGGSADTRTEDAISLQKALLEHQLC
 
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GVLPSSFDSFRLGRGLENSLPLEVVRGAMTIRVNSLTRGHSAVRLVVLEALTNFLNHGITPIVPLRGTISASGDLSPLSYIAAAISGHPDSKVHVVHEGKEKILYAREAMALFNLEPVVLGPKEGLGLVNGTAVSASMAT
 
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LALHDAHMLSLLSQSLTAMTVEAMVGHAGSFHPFLHDVTRPHPTQIEVAGNIRKLLEGSRFAVHHEEEVKVKDDEGILRQDRYPLRTSPQWLGPLVSDLIHAHAVLTIEAGQSTTDNPLIDVENKTSHHGGNFQAAAVAN
 
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TMEKTRLGLAQIGKLNFTQLTEMLNAGMNRGLPSCLAAEDPSLSYHCKGLDIAAAAYTSELGHLANPVTTHVQPAEMANQAVNSLALISARRTTESNDVLSLLLATHLYCVLQAIDLRAIEFEFKKQFGPAIVSLIDQHF
 
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GSAMTGSNLRDELVEKVNKTLAKRLEQTNSYDLVPRWHDAFSFAAGTVVEVLSSTSLSLAAVNAWKVAAAESAISLTRQVRETFWSAASTSSPALSYLSPRTQILYAFVREELGVKARRGDVFLGKQEVTIGSNVSKIYE
 
-
AIKSGRINNVLLKMLA
 
-
 
-
 
-
 
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'''Compatibility (iGEM and ''S. cerevisiae'')'''
'''Compatibility (iGEM and ''S. cerevisiae'')'''
Line 167: Line 98:
===Enzyme 2: 4-coumarate - coenzym A ligase (4CL)===
===Enzyme 2: 4-coumarate - coenzym A ligase (4CL)===
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we only use the sequence from start- to stopcodon ('''bold'''): 6-1691
 
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>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
 
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      121 ctctccacga ctacatcttc caaaacatct ccgaattcgc cactaagcct tgcctaatca
 
-
      181 acggaccaac cggccacgtg tacacttact ccgacgtcca cgtcatctcc cgccaaatcg
 
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      241 ccgccaattt tcacaaactc ggcgttaacc aaaacgacgt cgtcatgctc ctcctcccaa
 
-
      301 actgtcccga attcgtcctc tctttcctcg ccgcctcctt ccgcggcgca accgccaccg
 
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      361 ccgcaaaccc tttcttcact ccggcggaga tagctaaaca agccaaagcc tccaacacca
 
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      421 aactcataat caccgaagct cgttacgtcg acaaaatcaa accacttcaa aacgacgacg
 
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      481 gagtagtcat cgtctgcatc gacgacaacg aatccgtgcc aatccctgaa ggctgcctcc
 
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      541 gcttcaccga gttgactcag tcgacaaccg aggcatcaga agtcatcgac tcggtggaga
 
-
      601 tttcaccgga cgacgtggtg gcactacctt actcctctgg cacgacggga ttaccaaaag
 
-
      661 gagtgatgct gactcacaag ggactagtca cgagcgttgc tcagcaagtc gacggcgaga
 
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      721 acccgaatct ttatttccac agcgatgacg tcatactctg tgttttgccc atgtttcata
 
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      781 tctacgcttt gaactcgatc atgttgtgtg gtcttagagt tggtgcggcg attctgataa
 
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      841 tgccgaagtt tgagatcaat ctgctattgg agctgatcca gaggtgtaaa gtgacggtgg
 
-
      901 ctccgatggt tccgccgatt gtgttggcca ttgcgaagtc ttcggagacg gagaagtatg
 
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      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
 
Line 232: Line 116:
=== Enzyme 3: naringenin - chalcone synthase(CHS)===
=== Enzyme 3: naringenin - chalcone synthase(CHS)===
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-
 
-
we only use the sequence from start- to stopcodon ('''bold'''): 76-1248
 
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-
>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'')'''
'''Compatibility (iGEM and ''S. cerevisiae'')'''
Line 288: Line 134:
=== Enzyme 4: aromatic prenyltransferase (APT) ===
=== 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'')'''
'''Compatibility (iGEM and ''S. cerevisiae'')'''
Line 342: Line 153:
=== Enzyme 5: chalcone O-methyltransferase(OMT1) ===
=== 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
 
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IFNNAMASIVPIYMGAVLSSYKDGLGCIKGTVVDVGGGTGGSISELMKYYPNIKGINFDLPHVIATAPALDGVTHISGDIFESIPSADAVLMKGVLHCFSDEKCVKVLRNCRKAITDKKNGKIIILEIVLDPTSNQIFDETRMVYDLLIPXFSGGKERTE
 
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LEWKRLLNEAGFTSIKITKIPIIPAIIEAFLV
 
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'''Compatibility (iGEM and ''S. cerevisiae'')'''
'''Compatibility (iGEM and ''S. cerevisiae'')'''
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Revision as of 14:15, 15 August 2012


Contents

Xanthohumol

Background and principles

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, which is a nodal compound of phenylproponaoid metabolism in plants.

Biosynthesis:

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 Emmanouil Trantas et al., 2009.

metabolic pathway from phenylalanin to 4-coumarate


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. Media:TUM12_Biosynthesis_of_Xanthohumol_(2).jpg

Our project will focus on the production of Xanthohumol, due to its characteristic as a cancer chemopreventive agent (see below).


Xanthohumol and its cancer related bioactivities:

Xanthohumol

Inhibition of the 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., 2001, Miranda et al., 2000, 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 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)

Inhibition of tumor growth at an early stage:

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). 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.

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., 2000).

Idea

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.

The final goal is the expression of all required genes in a single modified yeast to produce Xanthohumol out of the substrate L-Tyrosin.

General remarks

Detail of Jiang et al., 2004

Proof of principle

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). 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. Hanxiao Jiang et al., 2004





Necessary enzymes for the biosynthesis of xanthohumol

Biosynthesis of Xanthohumol

ENZYME 1: PAL = phenylalanine ammonia lyase: L-phenylalanin --> trans-cinnamate

ENZYME 2: 4CL = 4-coumarate - coenzym A ligase: 4-coumarate --> 4-coumaroyl-CoA

ENZYME 3: CHS = naringenin - chalcone synthase: 4-coumaroyl-CoA --> naringeninchalcone

ENZYME 4: APT = aromatic prenyltransferase: naringeninchalcone --> desmethylxanthohumol

ENZYME 5: OMT1 = chalcone O-methyltransferase: desmethylxanthohumol --> xanthohumol

Source: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=PWY-5135






Enzymes Assays

Enzyme 1: phenylalanine ammonia lyase (PAL)

Compatibility (iGEM and S. cerevisiae)

Name Length RFC10 RFC25 Codon Usage NCBI
Phenylalanine ammonia lyase 2439bp bzw. 2151bp ok 6xNgoMIV (1438,1684,1852,1995,2329) 0 AS<10% [1]


Purification and Assay

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)

Compatibility (iGEM and S. cerevisiae)

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% [2]

Purification and Assay

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)

Compatibility (iGEM and S. cerevisiae)

Name Length RFC10 RFC25 Codon Usage NCBI
Hypericum androsaemum chalcone synthase 1402 bp 1xSpeI (469) ok after RFC10 2 AS<10%

[3]


Purification and Assay

Name used restriction sites purification assay
Hypericum androsaemum chalcone synthase XbaI, AgeI Strep tag II subtrate:

Enzyme 4: aromatic prenyltransferase (APT)

Compatibility (iGEM and S. cerevisiae)

Name Length RFC10 RFC25 Codon Usage NCBI
Humulus lupulus aromatic prenyltransferase 1236 bp ok ok optimized by GeneArt

[4]


Purification and Assay

Name used restriction sites purification assay
Humulus lupulus aromatic prenyltransferase XbaI, AgeI Strep tag II substrate:

Enzyme 5: chalcone O-methyltransferase(OMT1)

Compatibility (iGEM and S. cerevisiae)

Name Length RFC10 RFC25 Codon Usage NCBI
Humulus lupulus O-methyltransferase 1 1058 ok ok 2 AS<10%

[5]


Purification and Assay

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