[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2010&group=Debrecen-Hungary Our parts]
Our lipid detecting tool kit comprosis of 19 basic parts (11 ligand binding domains, 3 DNA binding domains and 5 other basic parts),9 composite chimeric receptors and 3 plasmid expression vectors and associated intermediates. Amongst our kit, parts of various speicies of the animalia kingdom may be found. The composite receptors are proof of concept that the basic parts acctually work. The bulk of the data (sequance, sub domains, 3d structure, ligand affinity and more..) can be found in the parts registry.
Ligand binding domains - Basic Parts
(click here to read more about LBD's)
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364310 Ecdysone Receptor Ligand Binding Domain (D. Melanogaster)]
The ecdysone receptor is a nuclear receptor found in arthropods, where it controls development and contributes to other processes such as reproduction. The receptor is a non-covalent heterodimer of two proteins, the EcR protein and ultraspiracle protein (USP). It binds to and is activated by ecdysteroids. Pulses of 20-hydroxyecdysone occur during insect development, whereupon this hormone binds to the ecdysone receptor, a ligand-activated transcription factor found in the nuclei of insect cells. This in turn leads to the activation of many other genes, which ultimately causes physiological changes that result in ecdysis (moulting). [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364310 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364303 DAF 12 Nuclear Receptor(C. Elegans)]
The nuclear hormone receptor DAF-12 from Caenorhabditis elegans is activated by dafachronic acids, which derive from sterols upon oxidation by DAF-9, a cytochrome P450. DAF-12 activation is a critical checkpoint in C. elegans for acquisition of reproductive competence and for entry into adulthood rather than dauer diapause.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364303 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364314 Nuclear hormone receptor 8 (C. Elegans)]
Nuclear hormone receptor family member nhr-8 The nhr-8 gene encodes a nuclear hormone receptor homolog; nhr-8(ok186) mutants have abnormally low resistance to the toxins colchicine and chloroquine. NHR-8 functions in the nematode xenobiotic defense system.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364314 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364315 Nuclear hormone receptor 23 (C. Elegans)]
Nuclear hormone receptor family member nhr-23. The nhr-23 gene encodes a nuclear hormone receptor homolog that is required in all larval molts; NHR-23 is highly similar to Drosophila DHR3, an ecdysone-inducible gene product involved in metamorphosis. The NHR-23 protein is nuclear, and is present in all blastomeres during early embryogenesis; during later stages of morphogenesis, NHR-23 is restricted to epidermal cells. nhr-23 expression cycles between stages of larval development; during each intermolt period, levels of nhr-23 transcripts are 2-5 times greater than levels at each molt. NHR-23 binds the DRS-type hormone response sequence in vitro
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364315 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364316 Nuclear hormone receptor 25 (C. Elegans)]
Nuclear hormone receptor family member nhr-25. nhr-25 encodes a nuclear hormone receptor orthologous to Drosophila Ftz-F1; NHR-25 is required for embryogenesis, molting, vulval and gonadal development, and hypodermal expression of acn-1; nhr-25 is expressed in gonads and loaded into embryos as a maternal transcript; nhr-25 is zygotically expressed in progeny of the E cell, and then in hypodermis and gut; the role of NHR-25 in molting may be evolutionarily conserved between nematodes and arthopods.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364316 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364317 Nuclear hormone receptor 31 (C. Elegans)]
Nuclear hormone receptor family member nhr-31 nhr-31 encodes one of over 200 C. elegans nuclear receptors; nhr-31 activity is required for proper growth, development, and function of the excretory cell; in regulating excretory cell development, NHR-31 appears to function by controlling the expression of genes encoding subunits of the vacuolar ATPase; an nhr-31::gfp promoter fusion is expressed at high levels in the excretory cell beginning at embryogenesis and continuing through adulthood, with lower levels of expression seen in the intestine and unidentified tail cells.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364317 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364321 Nuclear hormone receptor 64(C. Elegans)]
NHR-64 functions in the nematode xenobiotic defense system.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364321 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364318 Nuclear hormone receptor 80 (C. Elegans)]
NHR-80 encodes a nuclear hormone receptor, expressed in the intestine, that regulates expression of the delta-9 desaturases FAT-5/-6/-7, and thus regulates fatty acid metabolism. nhr-80 is specific to nematodes, being a divergent ortholog of HNF4 with many paralogs in C. elegans
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364318 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364306 Constitutive Androstane Receptor Ligand Binding Domain (H. Sapiens)]
The constitutive androstane receptor (CAR) also known as nuclear receptor subfamily 1, group I, member 3 is a protein that in humans is encoded by the NR1I3 gene.[1] CAR is a member of the nuclear receptor superfamily and along with PXR functions as a sensor of endobiotic and xenobiotic substances and in response upregulates the expression of proteins responsible for the metabolism and excretion of these substances.[2] Hence CAR (and PXR) are important in the detoxification of foreign substances such as drugs.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364306 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364308 Pregnane X receptor Ligand Binding Domain (H. Sapiens)]
PXR is a xenobiotic-activated member of the nuclear receptor superfamily of transcription factors. PXR is involved in transcriptional induction of hepatic xenobiotic-catabolizing cytochrome 3A enzymes, playing a fundamental role in protecting body tissues from toxic bile acids. PXR is almost exlcusively expressed in the gastrointestinal system (stomach, duodenum, jejunum, ileum, colon and gall bladder) and liver, with lower levels in the kidney and ovary. PXR dysfunction is associated with immune disorders (sclerosing cholangitis, inflammatory bowel disease) and biliary primary cirrhosis.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364308 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364309 Estrogen Receptor Ligand Binding Domain (H. Sapiens)]
ER-α is a 17β-estradiol-activated steroid receptor member of the nuclear receptor superfamily of transcription factors. It has a variety of central physiological roles, including those involved in maintenance of the reproductive, cardiovascular, musculoskeletal and central nervous systems. ER-α is expressed at low to moderate levels in major physiological systems (central nervous system (CNS), endocrine, metabolic, gastrointestinal, immune, reproductive, cardiovascular, respiratory and structural), with peaks of expression in the pituitary, ovary, uterus and vas deferens. ER-α dysfunction is associated with cancer, cardiovascular system defects, hematological system defects, immune and inflammation diseases, metabolic defects, reproductive defects.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364309 Go to the official parts registry page for this part]
DNA binding domains - Basic Parts
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364319 Gal 4 DNA binding Domain (S. cerevisiae)]
This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which encode for the enzymes used to convert galactose to glucose. This protein contains a fungal Zn(2)-Cys(6) binuclear cluster domain. Our Gal4 is flanked by RFC 25 Prefix and Suffix, and thus can be used for assembly of in frame composite parts. [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364319 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364201 Retinoid X Receptor DNA binding Domain (H.Sapiens)]
RXRα is a member of the nuclear receptor superfamily that mediates signaling by 9-cis retinoic acid, a vitamin A (retinol) derivative. Along with other members of the RXR family, RXRα plays roles in a variety of processes including embryonic patterning and organogenesis, cell proliferation and differentiation. RXRs commonly function as heterodimers with other members of the nuclear receptor superfamily. RXR-α is expressed in mulitple organs in many major physiological systems (central nervous system (CNS), endocrine, metabolic, gastrointestinal, reproductive and cardiopulmonary), with particularly high levels in the liver, preputial gland, skeletal muscle and skin. RXR-α variants have been associated with psychiatric (schizophrenia, autism, alcoholism, bipolar disorder and attention deficit hyperactivity disorder (ADHD)) and immune (psoriasis) disorders. [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364201 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364307 Estrogen Receptor DNA Binding Domain (H.Sapiens)]
Estrogen receptor refers to a group of receptors that are activated by the hormone 17β-estradiol[1] (estrogen) , which is a member of the nuclear hormone family of intracellular receptors. The main function of the estrogen receptor is as a DNA-binding transcription factor that regulates gene expression.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364307 Go to the official parts registry page for this part]
Other Basic Parts
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364312 Vitamin D3 Receptor hinge region (H. Sapiens)]
The VDR is a 1,25 dihydroxyvitamin D3-activated member of the nuclear receptor superfamily of transcription factors. It plays critical roles in calcium homeostasis, bone development and mineralization, as well as control of cell growth and differentiation. Upon activation by vitamin D, the VDR forms a heterodimer with the retinoid-X receptor and binds to hormone response elements on DNA resulting in expression or transrepression of specific geneproducts. Hinge region: Thought to be a flexible domain that connects the DBD with the LBD. Influences intracellular trafficking and subcellular distribution.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364312 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364304 Tetracyclin responsive DNA element in a CMV protmoter (TRE-CMV)]
The Tetracycline Response Element (TRE) is recognized and bound by the Tetracycline repressor (TetR) protein. The TRE consists of 7 repeats separated by spacer sequences and placed upstream of CMV minimal promoter that has basal expession in the abscence of bound TetR. Tetracycline derivatives (e.g. doxycycline) bind TetR and render it incapable of binding to TRE, thereby forcing the expression of target genes.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364304 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364302 Poly A tail type terminator]
The PolyA tail of mRNA has multiple adenilates which is important for the nuclear export, translation and stability of mRNA in eukaryotes.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364302 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364202 BCL-2 Associated X protein (H. Sapiens)]
Coding sequence of Bax (Bcl-2-associated X) protein which is a pro-apoptotic member of the Bcl-2 protein family. It contains three BH (Bcl-2 homology) domains, can form homo- and heterodimers and plays essential role in the formation of MOMP (Mitochondrial outer membrane permeabilization) leading to apoptosis through cytochrome c release which is the most frequent type of PCD (Programmed cell death).
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364202 Go to the official parts registry page for this part]
Chimeric Nuclear Receptors - Composite Parts
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364328 Gal4-DAF12 Chimeric nuclear receptor]
Gal4 DBD - DAF12 C. elegans nuclear hormone receptor LBD
Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain)
DAF-12
The nuclear hormone receptor DAF-12 from Caenorhabditis elegans is activated by dafachronic acids, which derive from sterols upon oxidation by DAF-9, a cytochrome P450. DAF-12 activation is a critical checkpoint in C. elegans for acquisition of reproductive competence and for entry into adulthood rather than dauer diapause.
Gal4 DBD
This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which encode for the enzymes used to convert galactose to glucose. This protein contains a fungal Zn(2)-Cys(6) binuclear cluster domain.
This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator.
With this system NHR (Nuclear Hormone Receptor) ligands or NHR interacting partners can be screened.
The NHR: cofactor-VP interaction should be also broken by a potential ligand binding, this is why this setup is also suitable for ligand identification. The benefit of the cofactor-VP interaction test is that the dynamic range of the assay is much higher than the dynamic range of the normal Gal4-NHR ligand activation assay.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364328 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364320 Gal4-NHR8 Chimeric nuclear receptor]
Gal4 DBD - NHR 8 C. elagans LBD
Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain)
NHR-8 LBD
Nuclear hormone receptor family member nhr-8 The nhr-8 gene encodes a nuclear hormone receptor homolog; nhr-8(ok186) mutants have abnormally low resistance to the toxins colchicine and chloroquine. NHR-8 functions in the nematode xenobiotic defense system.
Gal4 DBD
This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which encode for the enzymes used to convert galactose to glucose. This protein contains a fungal Zn(2)-Cys(6) binuclear cluster domain.
This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator.
With this system NHR (Nuclear Hormone Receptor) ligands or NHR interacting partners can be screened.
The NHR: cofactor-VP interaction should be also broken by a potential ligand binding, this is why this setup is also suitable for ligand identification. The benefit of the cofactor-VP interaction test is that the dynamic range of the assay is much higher than the dynamic range of the normal Gal4-NHR ligand activation assay.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364320 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364322 Gal4-NHR23 Chimeric nuclear receptor]
Gal4 DBD - NHR 23 C. elagans LBD
Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain)
NHR-23
Nuclear hormone receptor family member nhr-23. The nhr-23 gene encodes a nuclear hormone receptor homolog that is required in all larval molts; NHR-23 is highly similar to Drosophila DHR3, an ecdysone-inducible gene product involved in metamorphosis. The NHR-23 protein is nuclear, and is present in all blastomeres during early embryogenesis; during later stages of morphogenesis, NHR-23 is restricted to epidermal cells. nhr-23 expression cycles between stages of larval development; during each intermolt period, levels of nhr-23 transcripts are 2-5 times greater than levels at each molt. NHR-23 binds the DRS-type hormone response sequence in vitro.
Gal4 DBD
This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which encode for the enzymes used to convert galactose to glucose. This protein contains a fungal Zn(2)-Cys(6) binuclear cluster domain.
This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator.
With this system NHR (Nuclear Hormone Receptor) ligands or NHR interacting partners can be screened.
The NHR: cofactor-VP interaction should be also broken by a potential ligand binding, this is why this setup is also suitable for ligand identification. The benefit of the cofactor-VP interaction test is that the dynamic range of the assay is much higher than the dynamic range of the normal Gal4-NHR ligand activation assay.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364322 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364323 Gal4-NHR31 Chimeric nuclear receptor]
Gal4 DBD - NHR 31 C. elagans LBD
Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain)
NHR-31
Nuclear hormone receptor family member nhr-31 nhr-31 encodes one of over 200 C. elegans nuclear receptors; nhr-31 activity is required for proper growth, development, and function of the excretory cell; in regulating excretory cell development, NHR-31 appears to function by controlling the expression of genes encoding subunits of the vacuolar ATPase; an nhr-31::gfp promoter fusion is expressed at high levels in the excretory cell beginning at embryogenesis and continuing through adulthood, with lower levels of expression seen in the intestine and unidentified tail cells.
Gal4 DBD
This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which encode for the enzymes used to convert galactose to glucose. This protein contains a fungal Zn(2)-Cys(6) binuclear cluster domain.
This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator.
With this system NHR (Nuclear Hormone Receptor) ligands or NHR interacting partners can be screened.
The NHR: cofactor-VP interaction should be also broken by a potential ligand binding, this is why this setup is also suitable for ligand identification. The benefit of the cofactor-VP interaction test is that the dynamic range of the assay is much higher than the dynamic range of the normal Gal4-NHR ligand activation assay.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364323 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364324 Gal4-NHR80 Chimeric nuclear receptor]
Gal4 DBD - NHR 80 C. elagans LBD
Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain)
NHR-80
nhr-80 encodes a nuclear hormone receptor, expressed in the intestine, that regulates expression of the delta-9 desaturases FAT-5/-6/-7, and thus regulates fatty acid metabolism. nhr-80 is specific to nematodes, being a divergent ortholog of HNF4 with many paralogs in C. elegans Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain)
Gal4 DBD
This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which encode for the enzymes used to convert galactose to glucose. This protein contains a fungal Zn(2)-Cys(6) binuclear cluster domain.
This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator.
With this system NHR (Nuclear Hormone Receptor) ligands or NHR interacting partners can be screened.
The NHR: cofactor-VP interaction should be also broken by a potential ligand binding, this is why this setup is also suitable for ligand identification. The benefit of the cofactor-VP interaction test is that the dynamic range of the assay is much higher than the dynamic range of the normal Gal4-NHR ligand activation assay.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364324 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364325 Gal4-PXR Chimeric nuclear receptor]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364325 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364326 Gal4-EcR Chimeric nuclear receptor]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364326 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364327 Gal4-ER Chimeric nuclear receptor]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364327 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364329 ER DBD-VDR hinge-ER LBD Chimeric nuclear receptor]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364329 Go to the official parts registry page for this part]
Eukaryotic expression vectors - Composite Parts
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364330 TRE-PolyA (intermediate part of the expression vector)]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364330 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364332 TRE-Gal4-PXR-PolyA in PSB1A3 (expression vector)]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364332 Go to the official parts registry page for this part]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364333 TRE-Gal4-EcR-PolyA in PSB1A3 (expression vector)]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364333 Go to the official parts registry page for this part]
== Favorite Three parts ==
=== Part A ===
=== Part B ===
=== Part C ===
"
Team
