Cloning the cDNA for a new human zinc finger protein defines a group of closely related krüppel like transcription factors. (1998 Nov)
cloning the cDNA for a new human zinc finger protein defines a group of closely related krüppel like transcription factors . We have identified a novel zinc finger protein that has been named ubiquitous krüppel like factor ( UKLF ) based on structural considerations and the pattern of gene expression . UKLF was isolated by the polymerase chain reaction approach using degenerate oligonucleotides corresponding to the DNA binding domain of erythroid krüppel like factor ( EKLF ) and cDNA prepared from human vascular endothelial cells . The carboxyl terminal portion of UKLF contains three zinc fingers of the Cys2 His2 type and binds in vitro to the caccc motif of the beta globin promoter and to the Sp1 recognition sequence . The amino terminal portion of UKLF consists of a hydrophobic region rich in serines and a negatively charged segment with several glutamic acid residues . The first 47 amino acids of the acidic region are nearly identical to the amino terminal portion of another krüppel like factor , the so called core promoter binding protein ( CPBP ) or Zf9 . Like CPBP / Zf9 , UKLF can function as a transcription activator in co transfection assays . however , this activity is lost when the highly conserved amino terminal segment is deleted . these findings indicate that UKLF and CPBP / Zf9 represent a distinct subgroup of closely related krüppel like activators of transcription . mapping of the UKLF gene to chromosome 2 suggested that UKLF and CPBP …

Identification of a novel krueppel related zinc finger gene ( znf184 ) mapping to 6p21. (1997 May)
identification of a novel krueppel related zinc finger gene ( znf184 ) mapping to 6p21 . 3 . cDNA selection and exon trapping were performed on cosmids mapping to a region 3 Mb distal to HLA A . analysis of resulting fragments indicated the presence of two zinc finger transcripts , and one of these was used to isolate a partial cDNA ( znf184 ) from a placental library . The second transcript contained additional sequence of the 5 end of the gene , extending the sequence to 2678 bp . sequence analysis indicates that znf184 is a classical krueppel zinc finger with 19 highly conserved zinc finger motifs at the C terminus and a krueppel associated box at the N terminus of the protein . This gene encodes a 3 . 2 kb transcript that is highly expressed in testis and expressed at a moderate to low level in all other tissues tested . This zinc finger gene maps to a region approximately 200 kb distal to the microsatellite marker d6s105 and approximately 300 kb proximal to d6s1260 .

The biology of the mammalian krüppel like family of transcription factors. (2001 Jan)
The biology of the mammalian krüppel like family of transcription factors . recent advances in molecular cloning have led to the identification of a large number of mammalian zinc finger containing transcription factors that exhibit homology to the drosophila melanogaster protein , krüppel . although the amino acid sequences in the zinc finger domains of these krüppel like factors ( KLFs ) are closely related to one another , the regions outside the zinc fingers of the proteins are usually unique . KLFs display seemingly different and broad biological properties with each functioning as an activator of transcription , a repressor or both . This review article provides a current phylogenetic classification of the identified KLFs to date . More importantly , the currently known biological activities of the KLFs in regulating transcription , cell proliferation , differentiation and development are summarized and compared . further characterization of this interesting protein family should provide additional insights into the their respective regulatory role in various important biological processes .

Transcriptional activation by the papillomavirus E6 zinc finger oncoprotein. (1990 Jul)
transcriptional activation by the papillomavirus E6 zinc finger oncoprotein . The introduction of the bovine ( BPV ) or human papillomavirus E6 gene into susceptible cells can result in their transformation , but there are few clues to the mechanism of action of the E6 gene . The characteristic features of E6 proteins are their small size ( approximately 150 amino acids ) and the potential to form two large zinc fingers . To determine if E6 can function as a transcription factor , the BPV E6 gene was fused to the sequence specific DNA binding peptide encoded by the BPV E2 gene . This chimeric E6 E2 protein trans activated promoters that incorporated E2 binding elements in both rodent cells and saccharomyces cerevisiae . In the absence of E6 E2 localization to the target promoter , trans activation did not occur . alteration of the cysteine residues at the base of each finger abrogated the transcriptional activity of the E6 E2 hybrids . these data demonstrated that the BPV E6 gene encodes a transcription activation domain and imply that a specific structure of the protein , most likely the zinc fingers , is critical for this function . since these cysteine mutants are also transformation defective , E6 transcriptional functions may be required for its oncogenic activity .

Molecular cloning of a zinc finger protein which binds to the heptamer of the signal sequence for V ( D … (1994 Jan)
molecular cloning of a zinc finger protein which binds to the heptamer of the signal sequence for V ( D ) J recombination . The somatic V ( D ) J recombination for the assembly of the Ig and TCR genes is mediated by the recombination signal sequences ( Rss ) and the V ( D ) J recombinase . A cDNA clone was isolated from a lambda gt11 expression library made from mouse thymocyte poly ( A ) RNA , using the Rss as a ligand . The deduced amino acid sequence of the putative protein , designated recognition component ( Rc ) , reveals a pair of Cys2 His2 zinc fingers followed by a Glu and Asp rich acidic domain . In addition , there are five copies of the Ser / Thr Pro X Arg / Lys sequence , which are putative DNA binding units . The zinc finger acidic domain structures present in Rc are also found in several enhancer binding proteins , such as those for the kappa B motif of the Ig kappa light chain enhancer or related sequences . bacterial fusion proteins for Rc bind preferentially to the Rss heptamer and to the kappa B motif . The dual affinities of Rc for the Rss heptamer and the kappa B motif suggest a possible link between Ig transcription and somatic recombination . The formation of multiple gel shifted DNA protein complexes for Rc and its DNA ligand suggests that these complexes tend to …

Genomic organisation and characterisation of the neural sex determination gene fruitless ( fru ) in the hawaiian species drosophila heteroneura. (2000 May)
genomic organisation and characterisation of the neural sex determination gene fruitless ( fru ) in the hawaiian species drosophila heteroneura . there are several mechanisms for the determination of sex . sexual behaviour is part of the sex determination cascade , and in drosophila melanogaster male courtship is controlled in part by the fruitless gene . As part of a study of sexual behaviour in hawaiian drosophila , we have cloned the neural sex determination gene fru from the hawaiian picture wing species drosophila heteroneura . The fru gene has at least seven exons covering a region of 18kb and encodes three transcripts , fruA , fruB and fruC . Each transcript encodes a single ORF of 841 , 678 and 691aa , respectively . The FRUA and FRUB proteins have a BTB protein protein binding domain and two zinc finger like domains and are well conserved with the D . melanogaster proteins . The FRUC protein has a BTB domain but no zinc finger like domains . The fru gene is expressed in 1 7 day old adult males as a 5 . 1kb transcript . This transcript is not seen in adult females , so the fru gene has a different pattern of sex differential expression in the hawaiian drosophila compared with D . melanogaster .

The arabidopsis jagged gene encodes a zinc finger protein that promotes leaf tissue development. (2004 Feb)
The arabidopsis jagged gene encodes a zinc finger protein that promotes leaf tissue development . important goals in understanding leaf development are to identify genes involved in pattern specification , and also genes that translate this information into cell types and tissue structure . Loss of function mutations at the jagged ( JAG ) locus result in arabidopsis plants with abnormally shaped lateral organs including serrated leaves , narrow floral organs , and petals that contain fewer but more elongate cells . jag mutations also suppress bract formation in leafy , apetala1 and apetala2 mutant backgrounds . The JAG gene was identified by map based cloning to be a member of the zinc finger family of plant transcription factors and encodes a protein similar in structure to superman with a single C ( 2 ) H ( 2 ) type zinc finger , a proline rich motif and a short leucine rich repressor motif . JAG mRNA is localized to lateral organ primordia throughout the plant but is not found in the shoot apical meristem . misexpression of JAG results in leaf fusion and the development of ectopic leaf like outgrowth from both vegetative and floral tissues . Thus , JAG is necessary for proper lateral organ shape and is sufficient to induce the proliferation of lateral organ tissue .

The RIM / NIM family of neuronal C2 domain proteins. (2000 Aug)
The RIM / NIM family of neuronal C2 domain proteins . interactions with Rab3 and a new class of Src homology 3 domain proteins . RIM1 is a putative effector protein for rab3s , synaptic GTP binding proteins . RIM1 is localized close to the active zone at the synapse , where it interacts in a GTP dependent manner with Rab3 located on synaptic vesicles . We now describe a second RIM protein , called RIM2 , that is highly homologous to RIM1 and also expressed primarily in brain . Like RIM1 , RIM2 contains an N terminal zinc finger domain that binds to Rab3 as a function of GTP , a central PDZ domain , and two C terminal C ( 2 ) domains that are separated by long alternatively spliced sequences . unexpectedly , the 3 end of the RIM2 gene produces an independent mRNA that encodes a smaller protein referred as NIM2 . NIM2 is composed of a unique N terminal sequence followed by the C terminal part of RIM2 . Data bank searches identified a third RIM / NIM related gene , which encodes a NIM isoform referred to as NIM3 ; no RIM transcript from this gene was detected . To test if NIMs , like RIMs , may function in secretion , we investigated the effect of NIM3 on calcium triggered exocytosis in PC12 cells . NIM3 induced a dramatic increase in calcium evoked exocytosis ( 50 ) , with no significant effect on …

Activation of the zinc finger encoding gene krox 20 in adult rat brain : comparison with zif268. (1992 Jun)
activation of the zinc finger encoding gene krox 20 in adult rat brain : comparison with zif268 . zif268 and krox 20 are transcription regulatory factors that contain highly homologous zinc finger DNA binding domains . recent studies have demonstrated that zif268 expression is rapidly regulated in brain by neuronal stimulation . We now report that , like zif268 , krox 20 is rapidly and transiently activated by electroconvulsive shock treatment ( ECT ) , D1 dopamine receptor activation , and opiate withdrawal . these studies indicate that , as found for the leucine zipper family of transcription factors , multiple members of the zinc finger family of transcription factors are induced by neuronal stimulation .

Why zinc fingers prefer zinc : ligand field symmetry and the hidden thermodynamics of metal ion selectivity. (2004 Nov)
Why zinc fingers prefer zinc : ligand field symmetry and the hidden thermodynamics of metal ion selectivity . The zinc finger , a motif of protein nucleic acid recognition broadly conserved among eukaryotes , is a globular minidomain containing a tetrahedral metal binding site . preferential coordination of Zn ( 2 ) ( relative to Co ( 2 ) ) is proposed to reflect differences in ligand field stabilization energies ( lfses ) due to complete or incomplete occupancy of d orbitals . LFSE predicts that the preference for Zn ( 2 ) should be purely enthalpic in accord with calorimetric studies of a high affinity consensus peptide ( CP 1 ; blasie , C . A . , and Berg , J . ( 2002 ) biochemistry 41 , 15068 73 ) . despite its elegance , the general predominance of LFSE is unclear as ( i ) the magnitude by which CP 1 prefers Zn ( 2 ) is greater than that expected and ( ii ) the analogous metal ion selectivity of a zinc metalloenzyme ( carbonic anhydrase ) is driven by changes in entropy rather than enthalpy . because CP 1 was designed to optimize zinc binding , we have investigated the NMR structure and metal ion selectivity of a natural finger of lower stability derived from human tumor suppressor protein WT1 . raman spectroscopy suggests that the structure of the WT1 domain is unaffected by interchange of Zn ( 2 ) and Co ( 2 …

Synthetic zinc finger peptides : old and novel applications. (2004 Jul)
synthetic zinc finger peptides : old and novel applications . In the last decade , the efforts in clarifying the interaction between zinc finger proteins and DNA targets strongly stimulated the creativity of scientists in the field of protein engineering . In particular , the versatility and the modularity of zinc finger ( ZF ) motives make these domains optimal building blocks for generating artificial zinc finger peptides ( ZFPs ) . ZFPs can act as transcription modulators potentially able to control the expression of any desired gene , when fused to an appropriate effector domain . artificial ZFPs open the possibility to re program the expression of specific genes at will and can represent a powerful tool in basic science , biotechnology and gene therapy . In this review we will focus on old , novel and possible future applications of artificial ZFPs .

Specific interactions of the autoantigen L7 with multi zinc finger protein ZNF7 and ribosomal protein S7. (1997 Oct)
specific interactions of the autoantigen L7 with multi zinc finger protein ZNF7 and ribosomal protein S7 . The eucaryotic protein L7 , which associates with the large subunit of ribosomes , has been shown to be a major autoantigen in systemic autoimmune arthritis . The N terminus carries a sequence motif that is similar to the leucine zipper domain of eucaryotic transcription factors . This domain promotes the homodimerization of protein L7 through alpha helical coiled coil formation and binds to distinct mrnas , thereby inhibiting their cell free translation . using a yeast two hybrid selection , we have identified from a jurkat T lymphoma cDNA library ribosomal protein S7 and the multi zinc finger protein ZNF7 as proteins that interact with protein L7 . A fragment of L7 carrying the leucine zipper like domain is fully sufficient to mediate these interactions . their potential biological significance is indicated by low apparent dissociation constants of S7 L7 ( 15 x 10 ( 9 ) M ) and , respectively , ZNF7 L7 ( 2 x 10 ( 9 ) M ) complexes and co immunoprecipitation of proteins S7 , ZNF7 , and L7 from a cell lysate with an anti L7 antibody . We also show that ZNF7 like L7 and S7 can exist in a ribosome bound form . This study provides further evidence suggesting that L7 is involved in translational regulation through interactions with components of the translational apparatus .

Combining structure based design with phage display to create new Cys ( 2 ) His ( 2 ) zinc finger … (2000 Oct)
combining structure based design with phage display to create new Cys ( 2 ) His ( 2 ) zinc finger dimers . background : several strategies have been reported for the design and selection of novel DNA binding proteins . Most of these studies have used Cys ( 2 ) His ( 2 ) zinc finger proteins as a framework , and have focused on constructs that bind DNA in a manner similar to zif268 , with neighboring fingers connected by a canonical ( krüppel type ) linker . This linker does not seem ideal for larger constructs because only modest improvements in affinity are observed when more than three fingers are connected in this manner . Two strategies have been described that allow the productive assembly of more than three canonically linked fingers on a DNA site : connecting sets of fingers using linkers ( covalent ) , or assembling sets of fingers using dimerization domains ( non covalent ) . results : using a combination of structure based design and phage display , we have developed a new dimerization system for Cys ( 2 ) His ( 2 ) zinc fingers that allows the assembly of more than three fingers on a desired target site . Zinc finger constructs employing this new dimerization system have high affinity and good specificity for their target sites both in vitro and in vivo . constructs that recognize an asymmetric binding site as heterodimers can be obtained through substitutions in the zinc …

DNA target selectivity by the vitamin D3 receptor : mechanism of dimer binding to an asymmetric repeat element. (1993 Aug)
DNA target selectivity by the vitamin D3 receptor : mechanism of dimer binding to an asymmetric repeat element . The 1 , 25 dihydroxyvitamin D3 receptor , like other members of the nuclear receptor superfamily , forms dimers in solution that are probably stabilized by a dyad symmetrical interface formed by the ligand binding domain . This receptor , however , recognizes DNA targets that are not dyad symmetric but rather are organized as direct repeats of a hexameric sequence with a characteristic 3 bp spacing . using molecular modeling and site directed mutagenesis , we have identified regions within the vitamin D3 receptor zinc finger region that confer selectivity for direct repeats with appropriate spacing . reflecting the organization of the DNA target , these regions , mapping to the tip of the first zinc finger module and the N and C termini of the second finger module , direct asymmetrical protein protein contacts . A stereochemical model is proposed for these interactions .

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 .

Early hematopoietic zinc finger protein zinc finger protein 521 : a candidate regulator of diverse immature cells. (2008 Mar)
early hematopoietic zinc finger protein zinc finger protein 521 : a candidate regulator of diverse immature cells . The early hematopoietic zinc finger protein / zinc finger protein 521 ( EHZF / znf521 ) is a recently identified , 1131 amino acid long nuclear factor that contains 30 zinc fingers distributed in clusters throughout its sequence . A 13 AA motif , that binds to components of the nuclear remodelling and histone deacetylation ( NuRD ) complex and is conserved in several trascriptional co repressors , is located at the amino terminal end of the molecule . EHZF / znf521 expression is high in the most immature cells of the haematopoietic system and declines with differentiation . Its transcript is also abundant in brain , particularly in the cerebellum . Its murine counterpart , Evi3 / zfp521 , is enriched in haematopoietic and neural stem cells , in cerebellar granule neuron precursors and in the developing striatum . enforced expression of EHZF / znf521 in haematopoietic progenitors results in their expansion and in inhibition of differentiation . EHZF / znf521 is a member of the BMP signalling pathway and an inhibitor of the transcription factor OLF1 / EBF1 , implicated in the differentiation of neural progenitors and in the specification of the B cell lineage . EHZF expression is observed in most acute myelogenous leukaemias and is particularly high in those with rearrangements of the MLL gene , where EHZF may contribute to the leukaemic phenotype . EHZF / znf521 …

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 …

Metal and DNA binding properties and mutational analysis of the transcription activating factor , B , of coliphage 186 : … (1997 Aug)
metal and DNA binding properties and mutational analysis of the transcription activating factor , B , of coliphage 186 : a prokaryotic C4 zinc finger protein . coliphage 186 B is a 72 amino acid protein belonging to the Ogr family of analogous transcription factors present in P2 like phage , which contain a Cys X2 Cys X22 Cys X4 Cys presumptive zinc finger motif . The molecular characterization of these proteins has been hampered by their insolubility , a difficulty overcome in the present study by obtaining B as a soluble cadmium containing derivative ( CdB ) . atomic absorption spectroscopy showed the presence of one atom of cadmium per molecule of purified CdB . The UV absorption spectrum revealed a shoulder at 250 nm , characteristic of CysS Cd ( II ) ligand to metal charge transfer transitions , and the difference absorption coefficient after acidification ( delta epsilon 248 , 24 mM 1 cm 1 ) indicated the presence of a Cd ( Cys S ) 4 center . Gel mobility shift analysis of CdB with a 186 late promoter demonstrated specific DNA binding ( KD , app 3 4 microm ) and the protein was shown to activate transcription in vitro from a promoter reporter plasmid construct . The B DNA binding site was mapped by gel shift and dnaase I cleavage protection experiments to an area between 70 and 43 relative to the transcription start site , coincident with the consensus sequence , gttgt N8 …

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 …