Zinc finger transcription factors designed for bispecific coregulation of erbb2 and erbb3 receptors : insights into ErbB receptor biology. (2005 Oct)
Zinc finger transcription factors designed for bispecific coregulation of erbb2 and erbb3 receptors : insights into ErbB receptor biology . signaling through the ErbB family of tyrosine kinase receptors in normal and cancer derived cell lines contributes to cell growth and differentiation . In this work , we altered the levels of erbb2 and erbb3 receptors , individually and in combination , by using 6 finger and 12 finger synthetic zinc finger protein artificial transcription factors ( ATFs ) in an epidermoid squamous cell carcinoma line , A431 . We successfully designed 12 finger ATFs capable of coregulating erbb3 and ICAM 1 or erbb2 and erbb3 . With ATFs , the effects of changes in erbb2 and erbb3 receptor levels were evaluated by using cell proliferation , cell migration , and cell signaling assays . Cell proliferation was increased when erbb2 and erbb3 were both overexpressed . Cell migration on collagen was decreased when erbb2 was down regulated , yet migration on laminin was significantly increased with erbb3 overexpression . erbb2 and erbb3 overexpression also stimulated the phosphatidylinositol 3 kinase and mitogen activated protein kinase pathways . Our ATF approach has elucidated differences in ErbB receptor mediated proliferation , migration , and intracellular signaling that cannot be explained merely by the presence or absence of particular ErbB receptors and emphasizes the dynamic nature of the ErbB signaling system . The transcription factor approach developed here provides a gene economical route to the regulation of multiple genes and may be important …

Mizip , a highly conserved , vertebrate specific melanin concentrating hormone receptor 1 interacting zinc finger protein. (2002 Sep)
mizip , a highly conserved , vertebrate specific melanin concentrating hormone receptor 1 interacting zinc finger protein . using the yeast two hybrid system a novel protein was identified from human brain that interacts with the C terminus of melanin concentrating hormone receptor 1 ( MCH R1 ) . This protein , characterized by a myeloid translocation protein 8 , nervy , deaf1 proteins ( MYND ) zinc finger domain , is termed MCH R1 interacting zinc finger protein , mizip . It is fully conserved in man , rat , mouse and highly conserved in xenopus and zebrafish , but not detectable in invertebrates . mizip gene organization in human ( six exons on chromosome 9q34 . 3 ) and mouse is highly conserved , yet in rodents an additional exon is generated giving rise to alternatively spliced mrnas . mizip is expressed in brain , testis and stomach , where expression of MCH and MCH R1 was previously reported . mizip interaction with MCH R1 was verified by overlay and pull down assays as well as by co transfection experiments in human embryonic kidney 293 cells . mizip is cytoplasmically localized but gets recruited to the plasma membrane when cells are co transfected with MCH R1 supporting the notion that mizip is involved in the function of MCH R1 .

CDNA cloning , DNA binding , and evolution of mammalian transcription factor IIIA. (2002 Jan)
cDNA cloning , DNA binding , and evolution of mammalian transcription factor IIIA . cDNA for rat transcription factor IIIA ( tfiiia ) was cloned by degenerate PCR and rapid amplification of cDNA ends . This cDNA coded for a protein with nine Cys ( 2 ) His ( 2 ) zinc fingers and a non finger C terminal tail ; 63 amino acid ( aa ) sequence identity was observed with the xenopus tfiiia zinc finger region . recombinant rat protein containing only the nine fingers afforded dnase I protection of the identical nucleotides protected by xenopus laevis native tfiiia on the xenopus 5S RNA gene internal control region . A putative mouse tfiiia clone was identified in an expressed sequence tag database by sequence similarity to rat tfiiia . recombinant nine finger protein from this clone afforded dnase I protection of the xenopus 5S rRNA gene like the native frog protein as did a recombinant nine finger form of a putative human tfiiia clone . these DNA binding results demonstrate that these clones code for the respective mammalian tfiiias . rodent and human tfiiias share about 87 aa sequence identity in their zinc finger regions and have evolved to about the same extent as X . laevis and xenopus borealis tfiiias . A monoclonal antibody against human p53 tumor suppressor bound to rat and mouse tfiiia but not to human tfiiia in western blots . The N terminal regions of rodent and human tfiiia do not contain the …

Identification of DNA recognition sequences and protein interaction domains of the multiple Zn finger protein Roaz. (1998 Nov)
identification of DNA recognition sequences and protein interaction domains of the multiple Zn finger protein Roaz . Roaz , a rat C2H2 zinc finger protein , plays a role in the regulation of olfactory neuronal differentiation through its interaction with the Olf 1 / EBF transcription factor family . An additional role for the Roaz / Olf 1 / EBF heterodimeric protein is suggested by its ability to regulate gene activation at a distinct promoter lacking Olf 1 / EBF binding sites . using an in vitro binding site selection assay ( selex ) , we demonstrate that Roaz protein binds to novel inverted perfect or imperfect repeats of gcaccc separated by 2 bp . We show that Roaz is capable of binding to a canonical consensus recognition sequence with high affinity ( Kd 3 nM ) . analysis of the structural requirement for protein dimerization and DNA binding by Roaz reveals the role of specific zinc finger motifs in the Roaz protein for homodimerization and heterodimerization with the Olf 1 / EBF transcription factor . The DNA binding domain of Roaz is mapped to the N terminal 277 amino acids , containing the first seven zinc finger motifs , which confers weak monomeric binding to a single half site and a stronger dimeric binding to the inverted repeat in a binding site dependent manner . Full length protein can form dimers on both the inverted repeat and direct repeat but not on a single half site . these findings …

The transactivation domain within cysteine / histidine rich region 1 of CBP comprises two novel zinc binding modules. (2000 Jun)
The transactivation domain within cysteine / histidine rich region 1 of CBP comprises two novel zinc binding modules . cAMP response element binding protein binding protein ( CBP ) is a transcriptional coactivator that interacts with a number of DNA binding proteins and cofactor proteins involved in the regulation of transcription . relatively little is known about the structure of CBP , but it has been noted that it contains three domains that are rich in cysteine and histidine ( CH1 , CH2 , and CH3 ) . The sequence of CH2 conforms to that of a leukemia associated protein domain ( PHD finger ) , and it has been postulated that this and both CH1 and CH3 may be zinc finger domains . This has not , however , been demonstrated experimentally . We have studied CH1 and show that it is composed of two novel zinc binding modules , which we term zinc bundles . Each bundle contains the sequence Cys X ( 4 ) Cys X ( 8 ) His X ( 3 ) Cys , and we show that a synthetic peptide comprising one zinc bundle from CH1 can fold in a zinc dependent manner . CH3 also appears to contain two zinc bundles , one with the variant sequence Cys X ( 2 ) Cys X ( 9 ) His X ( 3 ) Cys , and we demonstrate that this variant motif also undergoes Zn ( II ) induced folding . CH1 acts as …

A novel human striated muscle RING zinc finger protein , SMRZ , interacts with smt3b via its RING domain. (2001 Jun)
A novel human striated muscle RING zinc finger protein , SMRZ , interacts with smt3b via its RING domain . The RING domain is a conserved zinc finger motif , which serves as a protein protein interaction interface . searches of a human heart expressed sequence tag data base for genes encoding the RING domain identified a novel cDNA , named striated muscle RING zinc finger protein ( SMRZ ) . The SMRZ cDNA is 1 . 9 kilobase pairs in length and encodes a polypeptide of 288 amino acid residues ; analysis of the peptide sequence demonstrated an N terminal RING domain . fluorescence in situ hybridization localized SMRZ to chromosome 1p33 34 . northern blots demonstrated that SMRZ is expressed exclusively in striated muscle . In the cardiovascular system , SMRZ is more highly expressed in the fetal heart than in the adult heart ( slightly higher expression in the ventricle than in the atrium ) , suggesting that SMRZ is developmentally regulated . SMRZ was found to interact with smt3b , a ubiquitin like protein , through the SMRZ RING domain . This interaction was abolished by mutagenesis of conserved RING domain residues . transient transfection of SMRZ into c2c12 myoblasts showed localization of SMRZ to the nucleus . these data suggest that SMRZ may play an important role in striated muscle cell embryonic development and perhaps in cell cycle regulation .

Nucleolin modulates the subcellular localization of GDNF inducible zinc finger protein 1 and its roles in transcription and cell proliferation. (2007 Oct)
nucleolin modulates the subcellular localization of GDNF inducible zinc finger protein 1 and its roles in transcription and cell proliferation . GZF1 is a zinc finger protein induced by glial cell line derived neurotrophic factor ( GDNF ) . It is a sequence specific transcriptional repressor with a BTB / POZ ( broad complex , tramtrack , Bric a brac / poxvirus and zinc finger ) domain and ten zinc finger motifs . In the present study , we used immunoprecipitation and mass spectrometry to identify nucleolin as a GZF1 binding protein . deletion analysis revealed that zinc finger motifs 1 4 of GZF1 mediate its association with nucleolin . When zinc fingers 1 4 were deleted from GZF1 or nucleolin expression was knocked down by short interference RNA ( sirna ) , nuclear localization of GZF1 was impaired . these results suggest that nucleolin is involved in the proper subcellular distribution of GZF1 . In addition , overexpression of nucleolin moderately inhibited the transcriptional repressive activity of GZF1 whereas knockdown of nucleolin expression by sirna enhanced its activity . Thus , the repressive activity of GZF1 is modulated by the level at which nucleolin is expressed . finally , we found that knockdown of GZF1 and nucleolin expression markedly impaired cell proliferation . these findings suggest that the physiological functions of GZF1 may be regulated by the protein s association with nucleolin .

FYVE finger proteins as effectors of phosphatidylinositol 3 phosphate. (1999 Jun)
FYVE finger proteins as effectors of phosphatidylinositol 3 phosphate . phosphatidylinositol 3 phosphate ( ptdins ( 3 ) P ) , generated via the phosphorylation of phosphatidylinositol by phosphatidylinositol 3 kinase ( PI 3 kinase ) , plays an essential role in intracellular membrane traffic . The underlying mechanism is still not understood in detail , but the recent identification of the FYVE finger as a protein domain that binds specifically to ptdins ( 3 ) P provides a number of potential effectors for ptdins ( 3 ) P . The FYVE finger ( named after the first letter of the four proteins containing it ; fab1p , YOTB , vac1p and EEA1 ) is a double zinc binding domain that is conserved in more than 30 proteins from yeast to mammals . It is found in several proteins involved in intracellular traffic , and FYVE finger mutations that affect zinc binding are associated with the loss of function of several of these proteins . The interaction of FYVE fingers with ptdins ( 3 ) P may serve three alternative functions : first , to recruit cytosolic FYVE finger proteins to ptdins ( 3 ) P containing membranes ( in concert with accessory molecules ) ; second , to enrich for membrane bound FYVE finger proteins into ptdins ( 3 ) P containing microdomains within the membrane ; and third , to modulate the activity of membrane bound FYVE finger proteins .

From repression domains to designer zinc finger proteins : a novel strategy of intracellular immunization against HIV. (1996 Oct)
From repression domains to designer zinc finger proteins : a novel strategy of intracellular immunization against HIV . tissue specific gene regulation of eukaryotic organisms is to a large extent mediated by transcription factors that interact with genomic DNA sequences in a sequence specific manner . The purpose of this synopsis is to put forward the potential of designer zinc finger proteins in treating infections of human immunodeficiency virus ( HIV ) . artificial transcription factors containing designer zinc finger structures fused to activator or repressor domains have been designated transcription response modifiers ( TRMs ) . The principle of engineering TRMs has been derived from the analysis of human krüppel type zinc finger genes and their products . Our research efforts encompass two fascinating features that are displayed by the human krüppel type zinc finger protein KOX1 : 1 ) the krüppel type zinc finger domains display rules of sequence specific DNA recognition , and 2 ) the evolutionarily conserved krüppel associated box ( KRAB ) presents one of the strongest transcriptional repressors identified so far in mammalian organisms . The KRAB repressor activity is postulated to be mediated through co repressor molecules , such as silencing mediating protein 1 ( SMP 1 ) . Thus , the structural organization and functional analysis of zinc finger proteins revealed principles of zinc finger transcription factors that are applicable for reducing the viral load in individuals infected with HIV . In this article , a novel concept of generating therapeutic proteins …

Self association of the erythroid transcription factor GATA 1 mediated by its zinc finger domains. (1995 Jun)
Self association of the erythroid transcription factor GATA 1 mediated by its zinc finger domains . GATA 1 , the founding member of a distinctive family of transcription factors , is expressed predominantly in erythroid cells and participates in the expression of numerous erythroid cell expressed genes . GATA binding sites are found in the promoters and enhancers of globin and nonglobin erythroid genes as well as in the alpha and beta globin locus control regions . To elucidate how GATA 1 may function in a variety of regulatory contexts , we have examined its protein protein interactions . Here we show that GATA 1 self associates in solution and in whole cell extracts and that the zinc finger region of the molecule is sufficient to mediate this interaction . This physical interaction can influence transcription , as GATA 1 self association is able to recruit a transcriptionally active but DNA binding defective derivative of GATA 1 to promoter bound GATA 1 and result in superactivation . through in vitro studies with bacterially expressed glutathione S transferase fusion proteins , we have localized the minimal domain required for GATA 1 self association to 40 amino acid residues within the C terminal zinc finger region . finally , we have detected physical interaction of GATA 1 with other GATA family members ( GATA 2 and GATA 3 ) also mediated through the zinc finger domain . these findings have broad implications for the involvement of GATA factors in transcriptional control . …

A xenopus zinc finger protein that specifically binds dsrna and RNA DNA hybrids. (1997 Sep)
A xenopus zinc finger protein that specifically binds dsrna and RNA DNA hybrids . proteins containing C2H2 type zinc finger motifs represent one of the largest classes of nucleic acid binding proteins found in nature . We describe a novel zinc finger protein , dsrbp ZFa , isolated by screening an expression library with dsrna . The dsrbp ZFa cDNA encodes a protein containing seven zinc finger motifs and an acidic C terminal domain . mobility shift experiments demonstrate that dsrbp ZFa binds dsrna and RNA DNA hybrids with nanomolar dissociation constants and in a sequence independent manner . We also show that DNA and single stranded RNA fail to compete with dsrna for binding suggesting dsrbp ZFa prefers to bind an A form helix . using western analyses we have localized dsrbp ZFa primarily to the nucleus of xenopus laevis oocytes . The identification of dsrbp ZFa provides the first example of a zinc finger protein that is specific for dsrna . In addition , dsrbp ZFa does not contain the previously described dsrna binding motif , suggesting certain zinc fingers may provide an alternative way to recognize the A form helix .

Nuclear transport and phosphorylation of the RNA binding xenopus zinc finger protein XFG 5 1. (1993 Mar)
nuclear transport and phosphorylation of the RNA binding xenopus zinc finger protein XFG 5 1 . XFG 5 1 is a krüppel type xenopus zinc finger protein with specific RNA homopolymer binding activity in vitro . In the oocyte , the protein is distributed between nucleus and cytoplasm ; the nuclear fraction , not the cytoplasm , contains phosphorylated isoform ( s ) of XFG 5 1 . In vitro phosphorylation by use of oocyte / egg extracts or purified casein kinase II is specific to the amino terminal portion of the protein . The carboxy terminal zinc finger domain contains a signal sufficient for nuclear transport . overexpression of either full length XFG 5 1 or of the carboxy terminal portion alone , which maintains RNA binding and nuclear import activities , was achieved in xenopus embryos by mRNA injection . This treatment did not result in impaired regulation of development , suggesting that XFG 5 1 functions in a way distinct from the mode of action exemplified in the drosophila zinc finger protein krüppel .

Zinc finger like structure in U1 specific protein C is essential for specific binding to U1 snrnp. (1991 May)
Zinc finger like structure in U1 specific protein C is essential for specific binding to U1 snrnp . The U1 small nuclear ribonucleoprotein ( snrnp ) contains three specific proteins denoted 70K , A and C , in addition to the common proteins . specific functions of these proteins are not known although recently protein C was shown to be involved in the binding of U1 snrnp to the 5 splice site of a pre mRNA . unlike proteins A and 70K , U1 C lacks an RNA binding domain ( RNP 80 motif ) and does not appear to bind directly to U1 snrna . however , at the amino terminal end protein C contains a zinc finger like structure of the CC HH type found in transcription factor TF IIIA . several lines of evidence indicate that the zinc finger like structure is essential for the binding of protein C to U1 snrnp particles : i ) deletion analysis of protein C showed that the N terminal 45 amino acids are sufficient for binding to U1 snrnps , ii ) modification of the cysteine residues in the N terminal domain with N ethylmaleimide and iii ) single point mutations of the cysteines and histidines contributing to the putative zinc finger abolished binding of protein C to U1 snrnps . interestingly , unlike the proteins U1 A and U1 70K the U1 C protein is unable to bind to naked U1 snrna . On the other hand it is …

Zinc fingers as protein recognition motifs : structural basis for the GATA 1 / friend of GATA interaction. (2005 Jan)
Zinc fingers as protein recognition motifs : structural basis for the GATA 1 / friend of GATA interaction . GATA 1 and friend of GATA ( FOG ) are zinc finger transcription factors that physically interact to play essential roles in erythroid and megakaryocytic development . several naturally occurring mutations in the GATA 1 gene that alter the FOG binding domain have been reported . The mutations are associated with familial anemias and thrombocytopenias of differing severity . To elucidate the molecular basis for the GATA 1 / FOG interaction , we have determined the three dimensional structure of a complex comprising the interaction domains of these proteins . The structure reveals how zinc fingers can act as protein recognition motifs . details of the architecture of the contact domains and their physical properties provide a molecular explanation for how the GATA 1 mutations contribute to distinct but related genetic diseases .

A conserved family of nuclear proteins containing structural elements of the finger protein encoded by krüppel , a drosophila segmentation … (1987 Jan)
A conserved family of nuclear proteins containing structural elements of the finger protein encoded by krüppel , a drosophila segmentation gene . krüppel ( Kr ) , a segmentation gene of drosophila , encodes a protein sharing structural features of the DNA binding finger motif of tfiiia , a xenopus transcription factor . Low stringency hybridization of the Kr finger coding sequence revealed multiple copies of homologous DNA sequences in the genomes of drosophila and other eukaryotes . molecular analysis of one Kr homologous DNA clone identified a developmentally regulated gene . Its product , a finger protein , relates to Kr by the invariant positioning of crucial amino acid residues within the finger repeats and by a stretch of seven amino acids connecting the finger loops , the H / C link . This H / C link is conserved in several nuclear and chromosome associated proteins of drosophila and other eukaryotic organisms including mammals . Our results demonstrate a new subfamily of evolutionarily conserved nuclear and possibly DNA binding proteins that again relate to a drosophila segmentation gene as in the case of the homeo domain .

A novel human zinc finger protein that interacts with the core promoter element of a TATA box less gene. (1997 May)
A novel human zinc finger protein that interacts with the core promoter element of a TATA box less gene . We describe a novel human cDNA isolated by target site screening of a placental expression library , using as a probe , an essential element of a TATA box less promoter corresponding to a pregnancy specific glycoprotein gene . The cDNA encoded a predicted protein of 290 amino acids , designated core promoter binding protein ( CPBP ) , which has three zinc fingers ( type Cys2 His2 ) at the end of its C terminal domain , a serine / threonine rich central region and an acidic domain lying within the N terminal region . additional sequence analysis and data base searches revealed that only the zinc finger domains are conserved ( 60 80 identity ) in other transcription factors . In cotransfection assays , CPBP increased the transcription from a minimal promoter containing its natural DNA binding site . moreover , a chimeric protein between CPBP and Gal4 DNA binding domain also increased the activity of an heterologous reporter gene containing Gal4 DNA binding sites . The tissue distribution analysis of CPBP mRNA revealed that it is differentially expressed with an apparent enrichment in placental cells . The DNA binding and transcriptional activity of CPBP , in conjunction with its expression pattern , strongly suggests that this protein may participate in the regulation and / or maintenance of the basal expression of PSG and possibly other TATA box …

Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus and plus strand transfer. (2000 Oct)
Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus and plus strand transfer . The nucleocapsid protein ( NC ) of human immunodeficiency virus type 1 ( HIV 1 ) has two zinc fingers , each containing the invariant metal ion binding residues CCHC . recent reports indicate that mutations in the CCHC motifs are deleterious for reverse transcription in vivo . To identify reverse transcriptase ( RT ) reactions affected by such changes , we have probed zinc finger functions in NC dependent RT catalyzed HIV 1 minus and plus strand transfer model systems . Our approach was to examine the activities of wild type NC and a mutant in which all six cysteine residues were replaced by serine ( SSHS NC ) ; this mutation severely disrupts zinc coordination . We find that the zinc fingers contribute to the role of NC in complete tRNA primer removal from minus strand DNA during plus strand transfer . annealing of the primer binding site sequences in plus strand strong stop DNA ( ) ssdna to its complement in minus strand acceptor DNA is not dependent on NC zinc fingers . In contrast , the rate of annealing of the complementary R regions in ( ) ssdna and 3 viral RNA during minus strand transfer is approximately eightfold lower when SSHS NC is used in place of wild type NC . moreover , unlike wild type NC , SSHS NC has only a small stimulatory …

Zinc fingers : DNA binding and protein protein interactions. (2000 Oct)
Zinc fingers : DNA binding and protein protein interactions . The zinc finger domain is a very ubiquitous structural element whose hallmark is the coordination of a zinc atom by several amino acid residues ( cysteines and histidines , and occasionally aspartate and glutamate ) . these structural elements are associated with protein nucleic acid recognition as well as protein protein interactions . The purpose of this review is to examine recent data on the DNA and protein binding properties of a few zinc fingers whose three dimensional structure is known .

Phosphorylation of A170 stress protein by casein kinase II like activity in macrophages. (1998 Jan)
phosphorylation of A170 stress protein by casein kinase II like activity in macrophages . A170 is an oxidative stress inducible protein having a Zinc finger domain , two PEST sequences , and many potential phosphorylation sites for serine / threonine kinases . these structural features suggest that the phosphorylation of A170 affects its function and degradation . We have found that A170 is phosphorylated in cultured murine peritoneal macrophages . In addition , using recombinant A170 proteins , we found two proteins of 40 and 44 kDa with kinase activity in cell extracts using an in gel kinase assay . We compared the properties of the intrinsic A170 kinases with those of mitogen activated protein kinase ( ERK 2 ) , protein kinase A ( PKA ) , casein kinase II ( CK II ) , and protein kinase C , since their catalytic subunits have molecular masses similar to A170 kinases . ERK 2 , CK II , and PKA phosphorylated recombinant A170 as a substrate . The 40 and 44 kDa kinases present in the macrophage extract were similar to alpha and alpha subunits of CK II in respect to substrate specificity , pharmacological properties , immuno reactivities , and ubiquitous expression in tissues .

Two short basic sequences surrounding the zinc finger of nucleocapsid protein ncp10 of moloney murine leukemia virus are critical for … (1993 Apr)
Two short basic sequences surrounding the zinc finger of nucleocapsid protein ncp10 of moloney murine leukemia virus are critical for RNA annealing activity . The 56 amino acid nucleocapsid protein ( ncp10 ) of moloney murine leukemia virus , contains a cysx2cysx4hisx4cys zinc finger flanked by basic residues . In vitro ncp10 promotes genomic RNA dimerization , a process most probably linked to genomic RNA packaging , and replication primer tRNA ( Pro ) annealing to the initiation site of reverse transcription . To characterize the amino acid sequences involved in the various functions of ncp10 , we have synthesized by solid phase method the native protein and a series of derived peptides shortened at the N or C terminus with or without the zinc finger domain . In the latter case , the two parts of the protein were linked by a glycine glycine spacer . The in vitro studies of these peptides show that nucleic acid annealing activities of ncp10 do not require a zinc finger but are critically dependent on the presence of specific sequences located on each side of the CCHC domain and containing proline and basic residues . Thus , deletion of 11R or 49prpqt , of the fully active 29 residue peptide 11rqggerrrsqldrdggkkprgprgprpqt53 leads to a complete loss of ncp10 activity . therefore it is proposed that in ncp10 , the zinc finger directs the spatial recognition of the target RNAs by the basic domains surrounding the zinc finger .