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 …

Anionic mechanisms of zinc uptake across the human red cell membrane. (1990 Jul)
anionic mechanisms of zinc uptake across the human red cell membrane . 1 . Zinc is taken up into human red cells by two mechanisms that depend upon the presence of anions . One of these requires bicarbonate ions , is inhibited by 4 , 4 diisothiocyanatostilbene 2 , 2 disulphonic acid ( DIDS ) and appears to be catalysed by the anion exchanger . The second occurs in the presence of thiocyanate or salicylate ions and may represent transport of a neutral complex with Zn2 . 2 . The initial rate of Zn2 uptake via the anion exchanger is 64 / 13 mumol ( 10 ( 13 ) cells x h ) 1 microm 1 external Zn2 , in the presence of 5 mM bicarbonate at pH 7 . 4 and 37 degrees C ( / S . D . ) . This is about 1 / 250 of the corresponding rate of Pb2 uptake by the anion exchanger . 3 . The variation of transport with Zn2 concentration , HCO3 concentration and pH suggests that the transported species may be znco3cl or Zn ( HCO3 ) Cl . OH . 4 . Zinc efflux could not be observed by either of the above routes . This observation suggests that the intracellular free Zn2 concentration is below 3 nM .

Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins. (1997 Jul)
variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins . The prosite pattern Zinc finger C2H2 was extended to permit the detection of all C2H2 zinc fingers and their parent proteins in the recently completed sequence of the yeast genome . additionally , a new computer program was written that extracts other zinc binding motifs ( non C2H2 fingers ) , overlapping with the classical zinc finger pattern , from the found set of yeast C2H2 fingers . The complete and correct detection of all fingers is a prerequisite for the classification of the yeast zinc finger proteins in functional terms . The detected 53 yeast C2H2 zinc finger proteins do not contain finger clusters with 10 or more repeats , as is frequently found in higher eukaryotes . Only three proteins contain four or more fingers in a cluster . moreover , nearly all 27 yeast proteins with tandem arrays of two or three finger domains can be classified into nine subgroups with high sequence conservation in their finger clusters , in particular of their DNA recognition helices . these results and application of the recently elaborated finger / DNA recognition rules suggest that the yeast proteins belonging to the same subgroup may recognize identical or very similar DNA sites .

Zinc finger proteins in oncogenesis : DNA binding and Gene regulation. (1993 Jul)
Zinc finger proteins in oncogenesis : DNA binding and Gene regulation . conference proceedings . noordwijkerhout , The netherlands , september 6 9 , 1992 .

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 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 .

Putative transcription activator with alternative isoforms encoded by human ZFX gene. (1990 Jan)
putative transcription activator with alternative isoforms encoded by human ZFX gene . The ZFY gene in the sex determining region of the human Y chromosome encodes a protein with 13 zinc fingers , and may determine whether an embryo develops as a male or female . ZFX , a related gene on the human X chromosome , may also function in sex determination ; it encodes a protein with a very similar zinc finger domain and escapes X inactivation . ZFY and ZFX diverged from a common ancestral gene before the radiation of placental mammals , and retain a similar genomic organization . analysis of complementary DNAs from the mouse Y chromosomal homologues of ZFY indicates that these genes encode probable transcription activators . Here , we report that ZFX encodes a protein composed of a highly acidic amino terminal domain , a basic putative nuclear localization signal , and a carboxy terminal zinc finger domain . This combination of features , also found in the ZFY gene product , is typical of transcription activators . alternative splicing generates ZFX transcripts encoding isoforms of 575 and 804 amino acids . these ZFX protein isoforms differ in the length of their acidic domains and may be functionally distinct .

The krüppel associated box ( KRAB ) zinc finger protein Kid 1 and the wilms tumor protein WT1 , two … (1997 Dec)
The krüppel associated box ( KRAB ) zinc finger protein Kid 1 and the wilms tumor protein WT1 , two transcriptional repressor proteins , bind to heteroduplex DNA . Zinc finger proteins of the cys2his2 class represent a large group of DNA binding proteins . A major subfamily of those proteins , the krüppel associated box ( KRAB ) domain containing cys2his2 zinc finger proteins , have been described as potent transcriptional repressors . So far , however , no DNA binding sites for KRAB domain containing zinc finger proteins have been isolated . using a polymerase chain reaction based selection strategy with double and single stranded DNA , we failed to reveal a binding site for Kid 1 , one member of KRAB zinc finger proteins . binding of Kid 1 both to single and homoduplex double stranded DNA was negligible . We now present evidence that Kid 1 binds to heteroduplex DNA . similar to Kid 1 , the non KRAB zinc finger protein WT1 also bound avidly to heteroduplex DNA ( both the KTS and KTS splice variant of WT1 ) , whereas the POU domain protein Oct 6 , the ets domain protein Ets 1 and the RING finger of BRCA 1 did not bind to heteroduplex DNA . binding of WT1 to heteroduplex DNA was markedly reduced in naturally occurring mutants . The recognition of certain DNA structures by transcriptional repressor proteins may therefore represent a more common phenomenon than previously thought .

NMR structure of the single qalggh zinc finger domain from the arabidopsis thaliana superman protein. (2003 Mar)
NMR structure of the single qalggh zinc finger domain from the arabidopsis thaliana superman protein . Zinc finger domains of the classical type represent the most abundant DNA binding domains in eukaryotic transcription factors . plant proteins contain from one to four zinc finger domains , which are characterized by high conservation of the sequence qalggh , shown to be critical for DNA binding activity . The arabidopsis thaliana superman protein , which contains a single qalggh zinc finger , is necessary for proper spatial development of reproductive floral tissues and has been shown to specifically bind to DNA . Here , we report the synthesis and UV and NMR spectroscopic structural characterization of a 37 amino acid superman region complexed to a Zn ( 2 ) ion ( Zn sup37 ) and present the first high resolution structure of a classical zinc finger domain from a plant protein . The NMR structure of the superman zinc finger domain consists of a very well defined betabetaalpha motif , typical of all other Cys ( 2 ) His ( 2 ) zinc fingers structurally characterized . As a consequence , the highly conserved qalggh sequence is located at the N terminus of the alpha helix . This region of the domain of animal zinc finger proteins consists of hypervariable residues that are responsible for recognizing the DNA bases . therefore , we propose a peculiar DNA recognition code for the qalggh zinc finger domain that includes all or some of the …

Specific DNA RNA hybrid binding by zinc finger proteins. (1995 May)
specific DNA RNA hybrid binding by zinc finger proteins . Zinc finger proteins of the cys2his2 type represent a large class of proteins that have been assumed to function by means of specific interactions with DNA . experiments motivated by structural characteristics of zinc finger protein DNA complexes revealed that certain zinc finger proteins bound DNA RNA hybrids with affinities comparable to or greater than those for DNA duplexes . The interactions between the zinc finger proteins and the DNA RNA hybrids were dependent on which strand was RNA and were sequence specific . Thus , interactions with DNA RNA hybrids should be considered with regard to the biological roles of zinc finger proteins .

A search for a mammalian homologue of the drosophila photoreceptor development gene glass yields zfp64 , a zinc finger encoding … (1997 Mar)
A search for a mammalian homologue of the drosophila photoreceptor development gene glass yields zfp64 , a zinc finger encoding gene which maps to the distal end of mouse chromosome 2 . whilst searching for a mammalian homologue of the drosophila glass gene we cloned a mouse cDNA whose deduced sequence encodes a 614 amino acid ( aa ) protein with ten Cys2 His2 ( C2H2 ) zinc finger ( Zf ) motifs . zfp64 is expressed in all developing and mature mouse tissues examined , except the mouse erythroleukemia ( MEL ) cell line . zfp64 maps to the distal region of mouse chromosome 2 close to lens opacity 4 ( Lop4 ) , a semidominant cataract mutation . sequence analysis shows that zfp64 has multiple potential phosphorylation sites for casein kinase II ( CK II ) , protein kinase C ( PKC ) , tyrosine kinase ( TK ) and c AMP and c GMP dependent protein kinase ( cA / gmpdpk ) .

Transcriptional activation by the PHD finger is inhibited through an adjacent leucine zipper that binds 14 3 3 proteins. (2000 Sep)
transcriptional activation by the PHD finger is inhibited through an adjacent leucine zipper that binds 14 3 3 proteins . The PHD finger , a Cys ( 4 ) His Cys ( 3 ) zinc finger , is found in many regulatory proteins from plants or animals which are frequently associated with chromatin mediated transcriptional regulation . We show here that the PHD finger activates transcription in yeast , plant and animal cells . In plant homeodomain transcription factors the PHD finger is combined with an upstream leucine zipper . Both domains together form a highly conserved 180 amino acid region called the ZIP / PHDf motif and transcriptional activity of the PHD finger is masked when embedded in this motif . Our results indicate that the ZIP / PHDf domain is a potential regulatory domain of PHDf HD proteins . The leucine zipper upstream of the PHD finger interacts with 14 3 3gf14 mu from arabidopsis thaliana and 14 3 3gf14 12 from maize via a leucine zipper conserved in helix 4 of various 14 3 3 proteins from plants and animals . PHD type plant homeodomain proteins consequently may represent potential targets of 14 3 3 signalling .

The DNA ligase III zinc finger stimulates binding to DNA secondary structure and promotes end joining. (2000 Sep)
The DNA ligase III zinc finger stimulates binding to DNA secondary structure and promotes end joining . The ability to rejoin broken chromosomes is fundamental to the maintenance of genetic integrity . mammalian cells possess at least five DNA ligases , including three isoforms of DNA ligase III ( Lig 3 ) . Lig 3 proteins differ from other DNA ligases in the presence of an N terminal zinc finger ( Zn f ) motif that exhibits extensive homology with two zinc fingers in poly ( ADP ribose ) polymerase ( PARP ) . Here we report that the Zn f confers upon Lig 3 the ability to bind DNA duplexes harbouring a variety of DNA secondary structures , including single strand gaps and single strand flaps . moreover , the Zn f stimulates intermolecular end joining of duplexes that harbour these structures up to 16 fold . The Zn f also stimulates end joining between duplexes lacking secondary structure , but to a lesser extent ( up to 4 fold ) . We conclude that the Zn f may enable Lig 3 to rejoin chromosomal DNA strand breaks located at sites of clustered damage induced by ionising radiation or near to secondary structure intermediates of DNA metabolism .

Structure and expression of the gene encoding a broad complex homolog in the silkworm , bombyx mori. (2004 Sep)
structure and expression of the gene encoding a broad complex homolog in the silkworm , bombyx mori . The steroid hormone ecdysone ( 20 hydroxyexdysone ) initiates metamorphosis and also larval ecdysis in many insects by activating a cascade of genes that includes primary response genes ( early genes ) , most of which encode transcriptional regulators , and secondary response genes ( late genes ) regulated by the early genes . One of the early genes , broad complex ( BR C ) , a key regulator of the ecdysone cascade , shares a common amino terminal BTB domain which is fused by alternative splicing to one of four pairs of C ( 2 ) H ( 2 ) zinc finger domains ( Z1 , Z2 , Z3 , and Z4 ) . cdnas for BR C ( BmBR C ) were isolated from the silkworm bombyx mori . these genes showed 90 . 3 and 98 . 2 amino acid identity with the drosophila BR C and manduca BR C in the N terminal BTB domain ; 96 . 0 , 90 . 7 , and 85 . 2 identity with the three zinc finger domains of the drosophila Z1 , Z2 , and Z4 isoforms ; and 96 . 3 and 98 . 1 identity with the two zinc finger domains of the manduca Z2 and Z4 isoforms , respectively . partial genomic sequencing ( from the 3 region of the core sequence to the 3 region …

Alteration of zif268 zinc finger motifs gives rise to non native zinc co ordination sites but preserves wild type DNA … (1998 Aug)
alteration of zif268 zinc finger motifs gives rise to non native zinc co ordination sites but preserves wild type DNA recognition . Zinc fingers are among the major structural motifs found in proteins that are involved in eukaryotic gene regulation . Many of these zinc finger domains are involved in DNA binding . This study investigated whether the zinc co ordinating ( Cys ) 2 ( His ) 2 motif found in the three zinc fingers of zif268 could be replaced by a ( Cys ) 4 motif while still preserving DNA recognition . ( Cys ) 2 ( His ) 2 to ( Cys ) 4 mutations were generated in each of the three zinc fingers of zif268 individually , as well as in fingers 1 and 3 , and fingers 2 and 3 together . whereas finger 1 and finger 3 tolerate the switch , such an alteration in finger 2 renders the polypeptide incapable of DNA recognition . The protein DNA interaction was examined in greater detail by using a methylation interference assay . The mutant polypeptides containing the ( Cys ) 4 motif in fingers 1 or 3 recognize DNA in a manner identical to the wild type protein , suggesting that the ( Cys ) 4 motif appears to give rise to a properly folded finger . additional results indicate that a zif268 variant containing a ( Cys ) 2 ( His ) ( Ala ) arrangement in finger 1 is also capable of DNA …

Expression of dominant negative and mutant isoforms of the antileukemic transcription factor ikaros in infant acute lymphoblastic leukemia. (1999 Mar)
expression of dominant negative and mutant isoforms of the antileukemic transcription factor ikaros in infant acute lymphoblastic leukemia . ikaros , a zinc finger containing DNA binding protein , is required for normal lymphocyte development , and germline mutant mice that express only non DNA binding dominant negative leukemogenic ikaros isoforms lacking critical N terminal zinc fingers develop an aggressive form of lymphoblastic leukemia 3 6 months after birth . therefore , we sought to determine whether molecular abnormalities involving the ikaros gene could contribute to the development of acute lymphoblastic leukemia ( ALL ) in infants . primary leukemic cells were freshly obtained from 12 infants ( 1 year of age ) with newly diagnosed ALL . In leukemic cells from each of the 12 infants with ALL , we found high level expression of dominant negative isoforms of ikaros with abnormal subcellular compartmentalization patterns . PCR cloning and nucleotide sequencing were used to identify the specific ikaros isoforms and detect ikaros gene mutations in these cells . leukemic cells from seven of seven infants with ALL , including five of five MLL AF4 ( ) infants , expressed dominant negative ikaros isoforms Ik 4 , Ik 7 , and Ik 8 that lack critical N terminal zinc fingers . In six of seven patients , we detected a specific mutation leading to an in frame deletion of 10 amino acids ( delta kssmpqkflg ) upstream of the transcription activation domain adjacent to the C terminal zinc fingers of …

Zinc finger protein 278 , a potential oncogene in human colorectal cancer. (2008 Apr)
Zinc finger protein 278 , a potential oncogene in human colorectal cancer . Zinc finger protein 278 ( znf278 ) is a novel krueppel Cys2 His2 type zinc finger protein that is ubiquitously distributed in human tissues . whether znf278 is related to the development of colorectal cancer is still unclear . The transcriptional level of znf278 was studied in colorectal cancer by real time polymerase chain reaction . The results showed that znf278 expression was increased in 53 of colorectal cancer tissues compared to corresponding non cancerous tissues . The transcriptional down regulation of znf278 was detected in only three ( 6 ) human colorectal cancer tissues compared to corresponding non cancer tissues . No significant difference was detected in 19 ( 41 ) pairs of samples . however , we failed to find a significant association between the up regulation of znf278 transcription and age , sex , the degree of infiltration , or the tumor size of colorectal cancer . To study the function of znf278 in colorectal carcinogenesis , the colon cancer cell line sw1116 was stably transfected with a wild type znf278 plasmid to construct an overexpression system , and was transiently transfected with the small interfering RNA of znf278 to construct a znf278 knockdown system . Cell proliferation was assessed with 3 4 , 5 dimethylthiazol 2 yl 2 , 5 diphenyltetrazolium bromide dye and a cell counter . The results show that znf278 promotes cell growth , and its knockdown suppresses cell proliferation …

Binding of free and protein associated zinc to rat spermatozoa. (1991 Aug)
binding of free and protein associated zinc to rat spermatozoa . 1 . The zinc content of rat spermatozoa increases , upon ejaculation , from 0 . 035 to 1 . 055 micrograms / 10 ( 6 ) cells . 2 . The rat seminal plasma holds zinc both as free ion and as protein bound forms . 3 . Zinc free ions bind in vitro to rat epididymal spermatozoa . 4 . Zinc protein complexes can be isolated , by a chromatographic procedure , from the dorsolateral lobe of rat prostate . 5 . The isolated zinc protein complexes bind in vitro to rat epididymal spermatozoa .

Zinc dependent structure of a single finger domain of yeast ADR1. (1988 Oct)
Zinc dependent structure of a single finger domain of yeast ADR1 . In the proposed zinc finger DNA binding motif , each repeat unit binds a zinc metal ion through invariant Cys and His residues and this drives the folding of each 30 residue unit into an independent nucleic acid binding domain . To obtain structural information , we synthesized single and double zinc finger peptides from the yeast transcription activator ADR1 , and assessed the metal binding and DNA binding properties of these peptides , as well as the solution structure of the metal stabilized domains , with the use of a variety of spectroscopic techniques . A single zinc finger can exist as an independent structure sufficient for zinc dependent DNA binding . An experimentally determined model of the single finger is proposed that is consistent with circular dichroism , one and two dimensional nuclear magnetic resonance , and visual spectroscopy of the single finger peptide reconstituted in the presence of zinc .