Coding

Part:BBa_K1998013

Designed by: Shauna Winchester   Group: iGEM16_Macquarie_Australia   (2016-10-13)
Revision as of 00:28, 19 October 2016 by SWinchester (Talk | contribs) (→‎References)


MgPPIX to Chlorophyll a plasmid


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 912
    Illegal BglII site found at 2365
    Illegal BglII site found at 5647
    Illegal BglII site found at 6136
    Illegal BamHI site found at 316
    Illegal BamHI site found at 3128
    Illegal BamHI site found at 5416
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 1904
    Illegal AgeI site found at 1955
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 478
    Illegal BsaI.rc site found at 4018


Overview

This composite part makes up one of our operons in the chlorophyll biosynthesis pathway. It is composed of YCF54, ChlM, POR, DVR1, ChlP and ChlG. These genes are Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase (YCF54) and Magnesium-protoporphyrin O-methyltransferase (ChlM), Light-dependent protochlorophyllidereductase (POR), 3,8-divinyl, Geranylgeranyl reductase(ChlP), protochlorophyllidea 8-vinyl reductase (DVR1) and Chlorophyll synthetase (ChlG).
These genes are part of the chlorophyll biosynthetic pathway and are involved in converting Mg-protoporphyrin IX to chlorophyll

ChlorophyllBiosynthesisDiagram

Biology & Literature

The first gene, YCF54, works with the CTH1 gene and Plastocyanin within the oxidative cyclase pathway. It's interaction with other genes results in the catalysis of the biosynthesis pathway from Mg-protoporphyrin IX to Protochlorophyllide [1]. Deletion studies have detected the importance of YCF54 in maintaining levels of Mg-protoporphyrin IX methyl ester indicating that the YCF54 gene is critical to both the assembly and function of the cyclase complex [1].

The second gene in this part is ChlM. ChlM encodes for a magnesium protoporhyrin IX methytransferase. ChlM's role in the pathway is to methylate Mg-protoporphyrin IX which then aids the catalysis of Mg-cheltase [2]. This then facilitates the formation of the final protochlorophyllide. Involved in the second step of the pathway, the ChlM gene is involved in the transfer of a methyl group onto one of the rings of magnesium protoporphyrin which forms the magnesium prootoporhyrin IX monomethylester [3, 4].

The POR gene is a light dependent protochlorophyllidereductase. It's role is to convert protochlorophyllide to chlorophyllide using NADPH and light as the reductant. Formation of the POR protein in plants is important as without it the chloroplasts do not function [5, 6]. The protochlorophyllide reduces to chlorophyllide by being excited through light functioning as a catalysis. The excitation of the POR molecule and therefore the transformation of it to chlorophyllide cause the conversion of the membranes from an inactive state into active chloroplast [7]. Through this transformation into active chloroplasts, energy is produced and now able to be used by the plant.

DVR1 encodes for an enzyme, 3,8-divinyl protochlorophyllide 8-vinyl reductase, which reduces divinly protochlorophyllide a to a monovinyl protochlorophyllide a [8]. By reducing the protochlorophyllide, POR can convert it to chlorophyllide.

The ChlP gene encodes for an enzyme, geranylgeranyl reductase. This enzyme adds the geranylgeranyl pyrophosphate chain to the chlorophyllide molecule. Through hydrogenation of geranylgeranyl diphosphate (GGPP), it reduces the GGPP's double bonds [9]. This allows the synthesis of chlorophylls another components of the pathway.

The final gene in this part is ChlG which encodes the enzyme chlorophyll synthetase. This enzyme catalyses the esterification of chlorophyllide with GGPP, allowing for the production of chlorophyll.

Protein information

YCF54
Mass: 17.08kDa
Sequence: MAPAAASADKATAAEYYALVCNAEWFFMDPQNESVAEQLREKVRFFKEQNKERDFFIVPNPKWLDAKFPEQAKQVKRPCVALVSTDKMWITFMKLRLDRVLKIDLKSM PASEVLAAGEALPDFKPDGKWTAPYARYTPGWWNVFLPNH

ChlM
Mass: 30.45kDa Sequence: MASEIAQTADVGSLTFAVGGVGAVVGLGALLVATDHQKRRSEQMKSFDGDEKEAVKDYFNTAGFERWRKIYGETDEVNKVQLDIRTGHAQTVDKVLRWVDEEGSVQGIT VADCGCGTGSLAIQLALRGAAVSASDISAAMASEAEQRYQQAVAAGQGKAPKVAPKFEALDLESVKGKYDTVTCLDVMIHYPQDKVDAMITHLAGLSDRRLIISFAPKTL SYSILKRIGELFPGPSKATRAYLHREEDVEAALKRAGFKVTKREMTATSFYFSRLLEAIRE

POR
Mass: 41.87kDa
Sequence:
MVVCAATATAPSPSLADKFKPNAIARVPATQQKQTAIITGASSGLGLNAAKALAATGEWHVVMACRDFLKAEQAAKKVGMPAGSYSILHLDLSSLESVRQFVQNFKASGR RLDALVCNAAVYLPTAKEPRFTADGFELSVGTNHLGHFLLTNLLLDDLKNAPNKQPRCIIVGSITGNTNTLAGNVPPKANLGDLSGLAAGVPAANPMMDGQEFNGAKAYK DSKVACMMTV RQMHQRFHDATGITFASLYPGCIAETGLFREHVPLFKTLFPPFQKYITKGYVSEEEAGRRLAAVISDPKLNKSGAYWSWSSTTGSFDNK

DVR1
Mass: 37kDa
Sequence:
MAMAASRQAVRVAAAVDADYRKREPKDVRVLVVGPTGYIGKFVVKELVSRGYNVVAFARENAGIKGKMGREDIVKEFHGAEVRFGSVLDPASLRDVAFKDPVDVVVSCLA SRTGGKKDSWLIDYTATKNSLDVARASGAKHFVLLSAICVQKPLLEFQKAKLQFESDLQAAGDITYSIVRPTAFFKSIAGQIDIVKKGNPYVMFGDGNLAACKPISEADLASF IADCVTEQNKVNKVLPIGGPSKAFTAKQQADLLFNITGLPPKYFPVPVALMDGMIGLFDSLAKLFPQLEDSAEFARIGKYYATESMLVYDEARGVYRKTKRLVTARTRWKTS SLVQ

ChlP
Mass: 47kDa
Sequence:
MVIGGGPSGACAAETLAKGGVETFLLERKLDNCKPCGGAIPLCMVEEFDLPMEIIDRRVTKMKMISPSNREVDVGKTLSETEWIGMCRREVFDDYLRNRAQKLGANIVNGL FMRSEQQSAEGPFTIHYNSYEDGSKMGKPATLEVDMIIGADGANSRIAKEIDAGEYDYAIAFQERIRIPDDKMKYYENLAEMYVGDDVSPDFYGWVFPKYDHVAVGTGTVVN KTAIKQYQQATRDRSKVKTEGGKIIRVEAHPIPEHPRPRRCKGRVALVGDAAGYVTKCSGEGIYFAAKSGRMAAEAIVEGSANGTKMCGEDAIRVYLDKWDRKYWTTYKVLD ILQKVFYRSNPAREAFVELCEDSYVQKMTFDSYLYKTVVPGNPLDDVKLLVRTVSSILRSNALRSVNSKSVNVSFGSKANEERVM AA

ChlG
Mass: 36.84kDa
Sequence:
MNQQATEEKSDTNSAARQMLGMKGAALETDIWKIRVQLTKPVTWIPLIWGVACGAAASGHYQWNNPTQIAQLLTCMMMSGPFLTGYTQTINDWYDREIDAINEPYRPIPS GRISERDVIVQIWVLLLGGIGLAYTLDQWAGHTTPVMLQLTIFGSFISYIYSAPPLKLKQSGWAGNYALGSSYIALPWWAGQALFGTLTLDVMALTIAYSLAGLGIAIVNDFKSI EGDRQ MGLQSLPVAFGVDTAKWICVSTIDVTQLGVAAYLAWGLHEELYGAVLLALILPQIYFQYKYFLPDPIANDVKYQASAQPFLVFGLLTAGLACGHHVNAVAA AASAAGAL

References

[1] Hollingshead S, Kopečná J, Jackson PJ, Canniffe DP, Davison PA, Dickman MJ, Sobotka R, Hunter CN. Conserved chloroplast open-reading frame ycf54 is required for activity of the magnesium protoporphyrin monomethylester oxidative cyclase in Synechocystis PCC 6803. Journal of Biological Chemistry. 2012 Aug 10;287(33):27823-33.

[2] Alawady A, Reski R, Yaronskaya E, Grimm B. Cloning and expression of the tobacco CHLM sequence encoding Mg protoporphyrin IX methyltransferase and its interaction with Mg chelatase. Plant molecular biology. 2005 Mar 1;57(5):679-91.

[3] Shepherd M, McLean S, Hunter CN. Kinetic basis for linking the first two enzymes of chlorophyll biosynthesis. FEBS Journal. 2005 Sep 1;272(17):4532-9.

[4] Meinecke L, Alawady A, Schroda M, Willows R, Kobayashi MC, Niyogi KK, Grimm B, Beck CF. Chlorophyll-deficient mutants of Chlamydomonas reinhardtii that accumulate magnesium protoporphyrin IX. Plant molecular biology. 2010 Apr 1;72(6):643-58.

[5] Fujita Y. Protochlorophyllide reduction: a key step in the greening of plants. Plant and cell physiology. 1996 Jun 1;37(4):411-21.

[6] Darrah PM, Kay SA, Teakle GR, Griffiths WT. Cloning and sequencing of protochlorophyllide reductase. Biochemical Journal. 1990 Feb 1;265(3):789-98.

[7] Griffiths WT. Characterization of the terminal stages of chlorophyll (ide) synthesis in etioplast membrane preparations. Biochemical Journal. 1975 Dec 1;152(3):623-55.

[8] Davies K, editor. Annual plant reviews, plant pigments and their manipulation. John Wiley & Sons; 2009 Feb 12.

[9] Shpilyov AV, Zinchenko VV, Shestakov SV, Grimm B, Lokstein H. Inactivation of the geranylgeranyl reductase (ChlP) gene in the cyanobacterium Synechocystis sp. PCC 6803. Biochimica et Biophysica Acta (BBA)-Bioenergetics. 2005 Feb 17;1706(3):195-203.

[10] Tamiaki H, Shibata R, Mizoguchi T. The 17‐Propionate Function of (Bacterio) chlorophylls: Biological Implication of Their Long Esterifying Chains in Photosynthetic Systems. Photochemistry and photobiology. 2007 Jan 1;83(1):152-62.

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