Team:Debrecen-Hungary/parts

From 2010.igem.org








Contents

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)

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). Go to the official parts registry page for this part

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. Go to the official parts registry page for this part

Nuclear hormone receptor 8 (C. Elegans)

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. Go to the official parts registry page for this part

Nuclear hormone receptor 23 (C. Elegans)

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. The expression of nhr-23 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. Furthermore NHR-23 binds the DRS-type hormone response sequence in vitro. Go to the official parts registry page for this part

Nuclear hormone receptor 25 (C. Elegans)

The 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. The nhr-25 is expressed in gonads and loaded into embryos as a maternal transcript. The 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. Go to the official parts registry page for this part

Nuclear hormone receptor 31 (C. Elegans)

The nhr-31 encodes one of over 200 C. elegans nuclear receptors. The 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. Go to the official parts registry page for this part

Nuclear hormone receptor 64(C. Elegans)

The nhr-64 encodes a conserved nuclear receptor that is a member of the NR2 subfamily of nuclear receptors that contains Drosophila and human HNF4 (mutations in human HNF4A are associated with Type I MODY (maturity-onset diabetes of the young)). By homology, NHR-64 is predicted to function as a transcription factor that may activate or repress transcription in response to a hormonal signal. However, as loss of nhr-64 activity via RNAi does not result in any obvious abnormalities, the precise role of NHR-64 in C. elegans development and/or behavior is not yet known. The nhr-64 is broadly expressed and detected in anterior and posterior neurons, the ventral nerve cord, the pharynx, gut, and hypodermis. Go to the official parts registry page for this part

Nuclear hormone receptor 80 (C. Elegans)

The 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. The nhr-80 is specific to nematodes, being a divergent ortholog of HNF4 with many paralogs in C. elegans. Go to the official parts registry page for this part

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. Go to the official parts registry page for this part

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. Go to the official parts registry page for this part

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. Go to the official parts registry page for this part



DNA binding domains - Basic Parts

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. Go to the official parts registry page for this part

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. Go to the official parts registry page for this part

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. Go to the official parts registry page for this part



Other Basic Parts

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. Go to the official parts registry page for this part

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. Go to the official parts registry page for this part

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. Go to the official parts registry page for this part

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). Go to the official parts registry page for this part

Chimeric Nuclear Receptors - Composite Parts

Gal4-DAF12 Chimeric nuclear receptor

Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans nuclear receptor LBD (Ligand Binding Domain) DAF-12.

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. Go to the official parts registry page for this part

Gal4-NHR8 Chimeric nuclear receptor

Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding 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. Go to the official parts registry page for this part

Gal4-NHR23 Chimeric nuclear receptor

Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding 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. Go to the official parts registry page for this part

Gal4-NHR31 Chimeric nuclear receptor

Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding 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. Go to the official parts registry page for this part

Gal4-NHR80 Chimeric nuclear receptor

Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding 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. Go to the official parts registry page for this part

Gal4-PXR Chimeric nuclear receptor

Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and H. sapiens nuclear receptor LBD (Ligand Binding 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. Go to the official parts registry page for this part

Gal4-EcR Chimeric nuclear receptor

Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and D. Melanogaster nuclear receptor LBD (Ligand Binding 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. Go to the official parts registry page for this part

Gal4-ER Chimeric nuclear receptor

Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and H. Sapiens nuclear receptor LBD (Ligand Binding 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. Go to the official parts registry page for this part

ER DBD-VDR hinge-ER LBD Chimeric nuclear receptor

Artificial eukaryotic TF made of Estrogen receptor's DBD (DNA Binding Domain), a vitamin D3 receptor hinge domain and H. sapiens nuclear receptor LBD (Ligand Binding 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. Go to the official parts registry page for this part



Eukaryotic expression vectors - Composite Parts

TRE-PolyA (intermediate part of the expression vector)

Tetracycline Response Element - minimal CMV promoter - PolyA tail which is a fusion of two regulators. It is not possible to fuse coding sequences between them because of scar formation after the ligation but it can be a negative control for the expression vectors made by standard BioBrick parts from pSB1A3 (BBa_K364332, BBa_K364333). Go to the official parts registry page for this part

TRE-Gal4-PXR-PolyA in PSB1A3 (expression vector)

Expression vector from standard BioBrick parts, expressing Gal4 - human Pregnane X receptor LBD composite part.

The Gal4-PXR Chimeric nuclear receptor is an artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and H. sapiens nuclear hormone receptor LBD (Ligand Binding Domain) which can be expressed by this expression vector.

The minimal CMV promoter ensures a continuous expression of the chimeric construct, but furthermore it can be expressed in an inducible form using the Tetracyclin-controlled transcriptional activation system. Go to the official parts registry page for this part

TRE-Gal4-EcR-PolyA in PSB1A3 (expression vector)

Expression vector from standard BioBrick parts, expressing Gal4 - Ecdysone receptor LBD composite part.

The Gal4-EcR Chimeric nuclear receptor is an artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and D. Melanogaster nuclear hormone receptor LBD (Ligand Binding Domain) which can be expressed by this expression vector.

The minimal CMV promoter ensures a continuous expression of the chimeric construct, but furthermore it can be expressed in an inducible form using the Tetracyclin-controlled transcriptional activation system. Go to the official parts registry page for this part