poison.gil

//This file should contain any source code related to the poison subconstruct


import "ExpressionLocation"

sequence construct
{
    TrojanHorseSaporin
}


sequence TrojanHorseSaporin
{
    /*
    This is one way we could do this. We use a special construct to make the saporin mRNA be produced in prokaryotes but only 
    translated in human cells. This way, the mRNA will build up and be ready as it's delivered into the human cell. This needs to
    be done to prevent the saporin from negatively affecting the bacteria delivering the toxin
    */
    ExpressionLocation:: .Bactofection
    {
        Saporin
    }
}



sequence DumbSaporin
{
    .DefaultPromoter
    {
        Saporin
    }
}

//Where you define sequences doesn't matter
sequence JustProduceCyanide
{
    //Just produce the cyanide synthase genes
    .DefaultPromoter
    {
        HcnA
    }

    .DefaultPromoter
    {
        HcnB
    }

    .DefaultPromoter
    {
        HcnC
    }
}


//_______________________________________________________________________________________________________________
// The raw genes
//_______________________________________________________________________________________________________________


//Cyanide stuff

//Pseudomonas aeruginosa cyanide synthase A subunit
sequence HcnA
{
    //Amino acids should be enclosed in @ symbols
    @MHLLERQHDIQPLSRADMTIHLNGQPVAAAAGETVLNVLNAVGLRRLARNDHGQASGAFCGMGVCHCCLVAIDGRPKRRACQTVVRPGMRVETESNRFDQEERP@
}

//Pseudomonas aeruginosa cyanide synthase B subunit
sequence HcnB
{
    @MNLRPVIVGGGSAGMAAAIELARRGVPCVLFDEASRPGGVVYRGPLRAGVDPAYLGARYTRMLEKLRRDFSACAGHIDLRLNSRVVGGDGQRLMVLDEAERLHEVEYSH
    LLLATGCHERSVPFPGWTLPGVMLLGGLQLQIKSGVVKPLGDTLIAGSGPLLPLVACQLHAAGVRVAGVYEACAFGRMARESLALLNKPQLFLDGLSMLGYLKLNGIPLH
    YGWGVVEASGDGELTEVTVAPYDEEWRPDLENARPVKASTLAVGYGFIPRTQLSQQLGLEHGFSDDGYLRAECNVWQQSSQPHIHLAGDMAGIRGGEAAMIGGRIAALSI
    LLQREAIAPAEAIERRESHLARLEAIKRFRAGVERYTQRGARQVELARADTVICRCEQVTRGDIERALEQGVQDIAGLKMRTRAGMGDCQGRMCIGYCSDRLRRATGRHD
    VGWLRPRFPIDPIPFSAFQNLGTEA@
}

//Pseudomonas aeruginosa cyanide synthase C subunit
sequence HcnC
{
    @MNRTYDIVIAGGGVIGASCAYQLSRRGNLRIAVVDDKRPGNATRASAGGLWAIGESVGLGCGVIFFRMMSSRNRREAQGAAVAVDASTPHILPPAFFDLALQSNALYPE
    LHRELIERHGMDFKFERTGLKYVIQDDEDRQYAEHIVAQIPHLAEQVRWLDREELRRAEPAVSHAAHGALEFLCDHQVSPFRLADAYLEAARQNGVELLPGTNVTGVLRQ
    GRRISGVRTDNAGVLHCRTLINAAGAWAAELSEMATGRRIPVKPVKGQIVLTERMPRLLNGCLTTSDCYMAQKDNGEILIGSTTEDKGFDVSNTFPEIAGLVQGAVRCVP
    ELQQVNLKRTWAGLRPGSPDELPILGPVAEVEGYLNACGHFRTGILTSAITGVLLDRLVHEETLPLDIAPFLAARFQPEPAAVAVAAC@
}


//Promoters (TBD)

//An operation is just a sequence with an implicit $InnerCode parameter. Call it using .OpName and put the innercode 
//in curly braces
operation DefaultPromoter
{
    //TBD
    $InnerCode
    //TBD
}

/*
I could have just wrote the following:
sequence DefaultPromoter($InnerCode)
{
    //TBD
    $InnerCode
    //TBD
}
*/


//_______________________________________________________________________________________________________________
// Saporin stuff
//_______________________________________________________________________________________________________________

sequence Saporin
{
    //I think this should work...
    @DPNLKYGGTDIAVIGPPSRDKFLRLNFQSSRGTVSLGLKRENLYVVAYLAMDNANVNRAY
    YFGTEITSAELTTLLPEATVANQKALEYTEDYQSIEKNAKITEGDKTRKELGLGINLLST
    LMDAVNKKARVVKNEARFLLIAIQMTAEAARFRYIQNLVTKNFPNKFNSEDKVIQFQVNW
    SKISKAIYGDAKNGVFNKDYDFGFGKVRQVKDLQMGLLMYLGTTPNNAADRYRAEL@
}