Device

Part:BBa_K1998000

Designed by: Shauna Winchester   Group: iGEM16_Macquarie_Australia   (2016-10-12)
Revision as of 01:47, 19 October 2016 by SWinchester (Talk | contribs) (→‎Characterisation and Verification)


Mg-Chelatase Plasmid

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 4753
    Illegal NotI site found at 2666
    Illegal NotI site found at 4213
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 439
    Illegal BglII site found at 1095
    Illegal BglII site found at 1290
    Illegal BglII site found at 3371
    Illegal BglII site found at 3898
    Illegal BglII site found at 5755
    Illegal BglII site found at 5863
    Illegal BamHI site found at 487
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 1946
    Illegal NgoMIV site found at 2765
    Illegal NgoMIV site found at 3307
    Illegal NgoMIV site found at 7968
    Illegal AgeI site found at 6853
    Illegal AgeI site found at 6883
    Illegal AgeI site found at 7777
    Illegal AgeI site found at 7945
    Illegal AgeI site found at 9463
    Illegal AgeI site found at 9517
    Illegal AgeI site found at 9736
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 5553
    Illegal BsaI.rc site found at 5709
    Illegal BsaI.rc site found at 6330
    Illegal BsaI.rc site found at 9862
    Illegal SapI.rc site found at 7219
    Illegal SapI.rc site found at 9792


Overview

The fate of the PPIX is dependent upon which enzyme is present to convert PPIX to the next product. For instance, ferrochelatase converts PPIX to FePPIX – a precursor for heme. Our magnesium chelatase plasmid is an assembly of six biobricks previously registered by a past Macquarie iGEM team. They form the first part of the chlorophyll biosynthesis pathway. The six genes are in the order of ChlI1, ChlD, Gun4, ChlI2, CTH1, followed by ChlH. At the beginning of each gene, a ribosome binding site can be found. Before the ChlH gene, a Plac is located. One can also be found at the beginning of the plasmid. The genes encode for Magnesium chelatase subunit H (ChlH), Magnesium chelatase subunit I (Chli1/Chli2), Magnesium chelatase subunit D (ChlD), Genomes uncoupled 4 (GUN4) and Copper target 1 protein (Cth1). These genes are involved in converting protoporphyrin IX to divinyl protochlorophyllide in the presence of NADPH and O2.

Biology & Literature

Genes ChlI1 and ChlI2 form a Mg-cheltase complex (Magnesium cheltase subunit I). This complex catalyses the insertion of magnesium ion into protoporphyrin IX to yield Mg-protoporphyrin IX by forming an ATP dependent hexameric ring complex and a complex with the ChlD subunit. This complex then acts on protoporphyrin. The GUN4 gene encodes genomes uncoupled 4. This is a tetrapyrrole-binding protein which controls the production of Mg-protoporhyrin IX. The CTH1 gene encodes for a copper target protein. It forms when oxygen and copper are present catalysing Mg-protoporphyrin IX mono methyl, which converts divinyl protochlorophyllide when NADPH and O2 are present. The last gene is ChlH. This gene encodes for the magnesium shelters subunit H. This acts as a chloroplast precursor, catalysing the first step in the chlorophyl biosynthesis pathway by insertion of an Mg2+ ion into protoporphyrin IX to generate Mg-protoporphyrin IX.

The ChlH and GUN4 proteins bind protoporphyrin IX and form an activated substrate complex which behaves as a substrate for the motor complex to insert magnesium into the bound Protoporphyrin IX upon ATP hydrolysis. The assembly of this complex requires milliMolar concentrations of Mg2+ and ATP to assemble. While the substrate complex also requires microMolar concentrations of Protoporphyrin IX and ChlH for optimal activity.

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[] Adhikari, N.D., Froehlich, J.E., Strand, D.D., Buck, S.M., Kramer, D.M., Larkin, R.M. (2011) GUN4-Porphyrin Complexes Bind the ChlH/GUN5 Subunit of Mg-Chelatase and Promote Chlorophyll Biosynthesis in Arabidopsis. Plant Cell 23: 1449-1467.

Assembly and Design

Each individual biobrick was assembled in the following order using 3A assembly: pLac-ChlI1-ChlD-Gun4-ChlI2-CTH1-pLac-ChlH [BBa_R0010], [BBa_K1326008], [BBa_K1080011], [BBa_K1080005] and [BBa_K1640019]. Five of these genes code for different subunits of the enzyme Magnesium chelatase, with the CTH1 gene encoding a component of a later enzyme in the pathway, the oxidative cyclase.

All genes within this plasmid are sequences obtained from Chlamydomonas reinhardtii and codon optimised to be expressed in E. coli. Lac promoters are also present at the front of the ChlI1 and ChlH gene with an RBS sequence at the beginning of all genes.

Characterisation and Verification

The following information shows the characterisation process of this plasmid as well as it's verification.

1. The 150kDa ChlH protein is highly expressed and visible on SDS-PAGE and confirmed by proteomic analysis. This should sufficient to produce Mg-Protoporphyrin IX.

2. Mg-protoporphyrin is not produced in DH5-alpha E.coli containing this plasmid when induced with IPTG. BUT Mg-protoporphyrin IX is produced in a hemH mutant background of E.coli containing this plasmid when induced with IPTG. (link to CRISPR mutagenesis). This hemH strain accumulates protoporphyrin IX within the cell.

3. The Mg-protoporphyrin IX produced in this strain demonstrates that metabolic engineering of E. coli is required to generate sufficient protoporphyrin IX substrate for the assembled magnesium chelatase complex to successfully make Mg-protoporphyrin IX.

Protein information

ChlI1
Mass: 39.96kDa
Sequence:
MAATEVKAAEGRTEKELGQARPIFPFTAIVGQDEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALADLLPEMQVVANDPFNSDPTDPELMSEEVRNR VKAGEQLPVSSKKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLDDHLVDVLLDSAASGWNTVEREGISISHPARFIL VGSGNPEEGELRPQLLDRFGMHAQIGTVKDPRLRVQIVSQRSTFDENPAAFRKDYEAGQMALTQRIVDARKLLKQGEVNYDFRVKISQICSDLNVDGIRG DIVTNRAAKALAAFEGRTEVTPEDIYRVIPLCLRHRLRKDPLAEIDDGDRVREIFKQVFGME

ChlD
Mass: 63.84kDa
Sequence:
MRAMKVSEED SKGFDADVST RLARSYPLAA VVGQDNIKQA LLLGAVDTGL GGIAIAGRRG TAKSIMARGL HALLPPIEVV EGSICNADPE DPRSWEAGLA EKYAGGPVKT KMRSAPFVQI DGVNVVEREG ISISHPCRPL LIATYNPEEG PLREHLLDRI AIGLSADVPS TSDERVKAID AAIRFQDKPQ DTIDDTAELT DALRTSVILA REYLKDVTIA PEQVTYIVEE ARRGGVQGHR AELYAVKCAK ACAALEGRER VNKDDLRQAV QLVILPRATI LDQPPPEQEQ PPPPPPPPPP PPPQDQMEDE DQEEKEDEKE EEEKENEDQD EPEIPQEFMF ESEGVIMDPS ILMFAQQQQR AQGRSGRAKT LIFSDDRGRY IKPMLPKGDK VKRLAVDATL RAAAPYQKIR RQQAISEGKV QRKVYVDKPD MRSKKLARKA GALVIFVVDA SGSMALNRMS AAKGACMRLL AESYTSRDQV VMMVLITDGR ANVSLAKSNE DPEALKPDAP KPTADSLKDE VRDMAKKAAS AGINVLVIDT ENKFVSTGFA EEISKAAQGK YYYLPNASDA AIAAAASGAM AAAKGGY

Gun4
Mass: 24.36kDa
Sequence:
MAMRVTVAAG KLDSVSLFGG DTASLMGGSQ TVEKKKSGKE AVMEVQLSST AGIDYTVLRD HLANGEFREA EDETRALLIK LAGPEAVKRN WVYFTEVKNI SVTDFQTLDN LWKASSNNKF GYSVQKEIWV QNQKRWPKFF KQIDWTQGEN NNYRKWPMEF IYSMDAPRGH LPLTNALRGT QLFQAIMEHP AFEKSSTAKT LDQKAAEAAG RTQSLF

ChlI2
Mass: 39.56kDa
Sequence:
MPSTKAAKKP NFPFVKIQGQ EEMKLALLLN VVDPNIGGVL IMGDRGTAKS VAVRALVDML PDIDVVEGDA FNSSPTDPKF MGPDTLQRFR NGEKLPTVRM RTPLVELPLG ATEDRICGTI DIEKALTQGI KAYEPGLLAK ANRGILYVDE VNLLDDGLVD VVLDSSASGL NTVEREGVSI VHPARFIMIG SGNPQEGELR PQLLDRFGMS VNVATLQDTK QRTQLVLDRL AYEADPDAFV DSCKAEQTAL TDKLEAARQR LRSVKISEEL QILISDICSR LDVDGLRGDI VINRAAKALV AFEGRTEVTT NDVERVISGC LNHRLRKDPL DPIDNGTKVA ILFKRMTDPE IMKREEEAKK

CTH1
Mass: 43.88kDa
Sequence:
MVAATAAPQE VEGFKVMRDG IKVASDETLL TPRFYTTDFD EMERLFSLEL NKNMDMEEFE AMLNEFKLDY NQRHFVRNET FKEAAEKIQG PTRKIFIEFL ERSCTAEFSG FLLYKELGRR LKATNPVVAE IFTLMSRDEA RHAGFLNKAM SDFNLALDLG FLTKNRKYTF FKPKFIFYAT YLSEKIGYWR YISIYRHLQR NPDNQLYPLF EYFENWCQDE NRHGDFFTAV LKARPEMVND WAAKLWSRFF CLSVYITMYL NDHQRDAFYS SLGLNTTQFN QHVIIETNKS TERIFPAVPD VENPEFFRRM DLLVKYNAQL VNIGSMNLPS PIKAIMKAPI LERMVAEVFQ VFIMTPKESG SYDLDANKTA LVY

ChlH
Mass:144.14
Sequence:
MCNVATGPRP PMTTFTGGNK GPAKQQVSLD LRDDGAGMFT STSPEMRRVV PDDVKGRVKV KVVYVVLEAQ YQSAISAAVK NINAKNSKVC FEVVGYLLEE LRDQKNLDML KEDVASANIF IGSLIFIEEL AEKIVEAVSP LREKLDACLI FPSMPAVMKL NKLGTFSMAQ LGQSKSVFSE FIKSARKNND NFEEGLLKLV RTLPKVLKYL PSDKAQDAKN FVNSLQYWLG GNSDNLENLL LNTVSNYVPA LKGVDFSVAE PTAYPDVGIW HPLASGMYED LKEYLNWYDT RKDMVFAKDA PVIGLVLQRS HLVTGDEGHY SGVVAELESR GAKVIPVFAG GLDFSAPVKK FFYDPLGSGR TFVDTVVSLT GFALVGGPAR QDAPKAIEAL KNLNVPYLVS LPLVFQTTEE WLDSELGVHP VQVALQVALP ELDGAMEPIV FAGRDSNTGK SHSLPDRIAS LCARAVNWAN LRKKRNAEKK LAVTVFSFPP DKGNVGTAAY LNVFGSIYRV LKNLQREGYD VGALPPSEED LIQSVLTQKE AKFNSTDLHI AYKMKVDEYQ KLCPYAEALE ENWGKPPGTL NTNGQELLVY GRQYGNVFIG VQPTFGYEGD PMRLLFSKSA SPHHGFAAYY TFLEKIFKAD AVLHFGTHGS LEFMPGKQVG MSGVCYPDSL IGTIPNLYYY AANNPSEATI AKRRSYANTI SYLTPPAENA GLYKGLKELK ELISSYQGMR ESGRAEQICA TIIETAKLCN LDRDVTLPDA DAKDLTMDMR DSVVGQVYRK LMEIESRLLP CGLHVVGCPP TAEEAVATLV NIAELDRPDN NPPIKGMPGI LARAIGRDIE SIYSGNNKGV LADVDQLQRI TEASRTCVRE FVKDRTGLNG RIGTNWITNL LKFTGFYVDP WVRGLQNGEF ASANREELIT LFNYLEFCLT QVVKDNELGA LVEALNGQYV EPGPGGDPIR NPNVLPTGKN IHALDPQSIP TQAALKSARL VVDRLLDRER DNNGGKYPET IALVLWGTDN IKTYGESLAQ VMMMVGVKPV ADALGRVNKL EVIPLEELGR PRVDVVVNCS GVFRDLFVNQ AVENSSWSDE SQLQEMYLKR KSYAFNSDRP GAGGEMQRDV FETAMKTVDV TFQNLDSSEI SLTDVSHYFD SDPTKLVASL RNDGRTPNAY IADTTTANAQ VRTLGETVRL DARTKLLNPK WYEGMLASGY EGVREIQKRM TNTMGWSATS GMVDNWVYDE ANSTFIEDAA MAERLMNTNP NSFRKLVATF LEANGRGYWD AKPEQLERLR QLYMDVEDKI EGVE

References

[edit]
Categories
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Parameters
None