Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain

The yeast regulatory protein ADR1 binds in a zinc-dependent manner to the upstream activating sequence of ADH2

The yeast ADR1 protein contains two zinc finger domains that are essential for its role in transcriptional activation of alcohol dehydrogenase (ADH2). These domains are thought to function as DNA-binding structures. An ADR1-beta-galactosidase fusion protein made in Escherichia coli and containing the finger domains of ADR1 binds in vitro in a zinc-dependent manner to DNA fragments containing the two ADH2 upstream activation sequences. The strongest binding is to upstream activation sequence 1, a 22-base-pair palindrome.

Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology

Two cDNAs encoding new DNA-binding proteins (Dbps) have been cloned using a human placenta lambda gt11 recombinant cDNA library and DNA fragments as probes. Hybrid proteins expressed by the lambda gt11 cDNA library were blotted onto nitrocellulose filters, and incubated with three different radio-labeled DNA probes containing the human epidermal growth factor (EGF) receptor enhancer or the human c-erbB-2 promoter. Two kinds of clones, named dbpA and dbpB, showed high affinities for the DNA probes. The comparison of the nucleotide and the deduced amino acid (aa) sequences between these two cDNAs indicated that 100 of 109 aa located in the central region of these two Dbps were identical. The dbpA and dbpB-coded proteins also had an affinity for other cDNA probes such as the human c-ski gene, but not for poly(dI-dC).poly(dI-dC), suggesting that the sequence(s) recognized by the dbpA and dbpB-coded proteins may occur frequently, or that these proteins bind to DNA non-specifically in a different manner from that of histones. A simple method, described in this paper, can be used to isolate cDNA clones encoding Dbps. Strategies used for the detection of sequence-specific and non-specific Dbps are discussed.

Distinct regions of Sp1 modulate DNA binding and transcriptional activation

Sp1 is a sequence-specific DNA binding protein that activates RNA polymerase II transcription from promoters that contain properly positioned GC boxes. A series of deletion mutants of Sp1 were expressed in Escherichia coli and used to identify separate regions of the protein that are important for three different biochemical activities. The sequence-specificity of DNA binding was conferred by Zn(II) fingers, whereas a different region of Sp1 appeared to regulate the affinity of DNA binding. The E. coli-synthesized Sp1 was able to stimulate initiation of RNA synthesis in vitro, and at least two distinct segments of the protein contributed to its transcriptional activity.

Xenopus transcription factor IIIA forms a complex of covalent character with 5S DNA

The 5S gene-specific transcription factor TFIIIA forms an exceptionally stable complex with the internal promoter of the 5S RNA gene. Approximately 1 to 5% of TFIIIA-DNA or deoxyoligonucleotide complexes are stable to harsh denaturation conditions and can be resolved by electrophoresis in the presence of SDS. These complexes are resistant to acidic conditions (0.1 N HCl, 55 degrees C, 2h) suggesting that the interaction may be through a covalent bond. Complex formation does not result in DNA strand scission and studies of the chemical sensitivity of the complex suggest that the TFIIIA-DNA linkage may be through a phosphoramidate bond. Covalent complexes are formed with both the noncoding (RNA-like) and coding strands of the internal control region. The predominant sites of TFIIIA-DNA adducts have been mapped to the 3' end of the 5S gene internal control region, the region previously shown to exhibit essential guanine and phosphate contacts with TFIIIA.

A human lymphoid-specific transcription factor that activates immunoglobulin genes is a homoeobox protein

The human lymphoid-specific transcription factor OTF-2 contains a homoeodomain that is required for DNA binding and binds specifically to DNA elements that are recognized by Drosophila homoeodomain proteins, suggesting coevolutionary relationships between mammalian and invertebrate homoeodomain proteins and their DNA recognition elements.

Analysis of Sp1 in vivo reveals multiple transcriptional domains, including a novel glutamine-rich activation motif

We have adopted Drosophila tissue culture cells as a host system for studying the structure and function of mammalian transcription factors. These cells provide an Sp1-deficient background and have been used in a complementation assay to identify functional domains of human transcription factor Sp1. The SV40 early promoter, which contains six Sp1 binding sites (GC boxes), is induced up to 500-fold in Drosophila cells by the expression of Sp1, whereas promoters with fewer sites are activated less efficiently. Analysis of Sp1 mutants reveals multiple distinct regions outside of the DNA binding domain that are responsible for mediating transcriptional activation. The two most active domains, which appear to be functionally redundant with one another, consist of an unusual structure with a very low charge density, but a strikingly high glutamine content. A number of other sequence-specific transcription factors, such as the Drosophila zeste protein and several homeodomain proteins, contain glutamine-rich stretches, and we propose that these glutamine-rich domains represent a novel structural motif for transcriptional activation.

Molecular analysis of the 60-kDa human Ro ribonucleoprotein

Ro, or Sjogren syndrome type A (SS-A), antigen is the most prevalent of the human systemic autoimmune specificities and exists as an inabundant ribonucleoprotein complex (RNP) composed of a 60,649-Da protein, as defined here by cDNA cloning, and the human Y RNAs. The recombinant 60-kDa Ro protein and human Y1 RNA were reconstituted in vitro, and the binding was enhanced by divalent cations. A region of the Ro amino acid sequence revealed a resemblance to the RNP consensus motif found in most RNA-binding proteins. In addition, Ro contained a potential "zinc-binding finger" motif that was distinct from the RNP consensus region and that may participate in the interaction with human Y RNAs or with other proteins. The recombinant Ro fusion protein also proved useful for the detection of autoantibodies in the sera of patients with autoimmune disorders. Possible functions of the Ro RNPs and their relationship to RNA polymerase III transcription are discussed.

Detection of a nuclear protein that interacts with a metal regulatory element of the mouse metallothionein 1 gene

Metallothionein (MT) genes contain multiple metal regulatory elements (MREs) that are responsible for metal induction. A protein blotting procedure and a synthetic oligonucleotide have been used to identify nuclear factors interacting with a MRE (MREd) of the mouse MT-1 gene. We report the specific binding of the probe to a protein of apparent Mr 108,000 (p108). The specificity of the interaction was demonstrated by mutation analysis and competition experiments. Furthermore, the probe contains the Sp1 consensus binding sequence 5'CCGCCC3', in addition to the MRE consensus sequence, 5'TGCAC3', and we show that a Simian Virus 40 DNA fragment which contains six Sp1 binding sites did not bind p108 nor did it compete for the protein(s) interacting with MREd in a DNA footprinting assay. These results show that a metal regulatory element of the mouse MT-1 gene interacts specifically with a nuclear protein of Mr 108,000 and that this protein is distinct from the transcription factor Sp1.

CYP1 (HAP1) regulator of oxygen-dependent gene expression in yeast. I. Overall organization of the protein sequence displays several novel structural domains

In the yeast Saccharomyces cerevisiae the CYP1 gene that modulates the expression of iso1-(CYC1) and iso2-cytochrome c (CYP3) structural genes gives rise to two classes of mutated alleles; one class, represented by CYP1-18, has opposite effects on CYC1 and CYP3, it reduces the expression of CYC1 while it stimulates that of CYP3. The other class, represented by cyp1-23 or the related allele hap1-1, reduces the expression of both CYC1 and CYP3 genes. Genetic data suggested that the CYP1 product is a positive regulator of the cytochrome c genes. The CYP1-18 allele has been cloned. We show here that the iso2 overproducer function of CYP1-18 is included in a 5300 base XhoI-PstI fragment. The sequence of this fragment reveals a unique, long, uninterrupted open reading frame of 4449 nucleotides able to encode a protein of 1483 amino acid residues. The predicted product of this open reading frame contains several interesting features. The N-terminal part of the protein resembles a nucleic acid-binding domain, in which two domains can be distinguished. The first is similar to a "finger" DNA binding motif, as found in TFIIIA and other regulatory proteins. The second consists of seven tandemly repeated sequences with a KCPVDH motif. Because of its structure, it is tempting to speculate that this region may act as a "redox sensor" folded around a metal atom or heme and involved in recognition of respiratory effectors. These two domains are separated by an "opa" sequence of 13 Gln residues. Implication of these domains for the function of CYP1-18 is discussed.

Properties of a 19-kDa Zn2+-binding protein and sequence of the Zn2+-binding domains

A novel 19-kDa protein has been described recently [Brand, I.A. and Söling, H.-D. (1986) J. Biol. Chem. 261, 5895-5900] which is able to inactivate 6-phosphofructo-1-kinase reversibly in a Zn2+-dependent manner. We present now additional biochemical and physicochemical data concerning this protein. It is extremely acidic with 40% glutamic and 15% aspartic acid residues. It contains no sulfur, aromatic amino acids, histidine or isoleucine. The protein has four binding sites for Zn2+ with an apparent Kd of about 6 microM. Two of these binding sites are called unspecific as Zn2+ is displaced from these binding sites at physiological concentrations of free Mg2+ (0.75 mM) and at high salt concentrations (100 mM NaCl). Whereas Mg2+-binding to the two other so-called specific Zn2+-binding sites occurs only at Mg2+ concentrations at about 5 mM. The four Zn2+-binding sites were detected on a tryptic peptide (T8) of 43 amino acid residues, which still possessed biological activity. This peptide has been sequenced and is characterized by four clusters of acidic amino acids separated by only a few neutral amino acids. The two specific Zn2+-binding sites could be detected in the C-terminal portion of T8, the two unspecific Zn2+-binding sites must therefore be located at the N-terminal portion. The Zn2+-binding domains of the 19-kDa Zn2+-binding protein described here are completely different from those of the 'zinc finger' discovered in several DNA-binding proteins.

Specific and ubiquitous expression of different Zn finger protein genes in the mouse

Zinc finger proteins (Zfp) are members of a multigene family encoding Zn mediated nucleic acid binding proteins. They have been isolated from various organisms including yeast, Drosophila, Xenopus mouse and human. All Zfp share the 28-30 amino acid long finger repeats containing conserved residues at specific positions. Some of these proteins have been identified as transcriptional regulatory factors. In this paper, we describe the isolation, DNA sequence determination and the expression pattern in developing embryos and adult tissues of 3 new members of the mouse Zfp. All of them are expressed as multiple transcripts. Unaltered level of mkr5 expression could be detected in 10-15 day whole embryo RNAs but its level started to decrease from day 16. In the adult animal, predominant expression was detected only in the ovary. In contrast, mkr3 and 4 were expressed at a constant level in all embryos and tissues tested. These data suggest the presence of both tissue specific and ubiquitious Zfp in the mouse.

The binding of in vitro synthesized adenovirus DNA binding protein to single-stranded DNA is stimulated by zinc ions

We have synthesized wild type DNA binding protein (DBP) of adenovirus type 5 (Ad5) and several truncated forms of this protein by a combination of in vitro transcription and translation. The proteins obtained were tested for binding to a single-stranded DNA-cellulose column. It could be shown that for binding of in vitro synthesized wild type DBP, it is necessary to add zinc ions to the in vitro translation system. Binding studies with the truncated proteins revealed that deletion of the carboxyl-terminal 46 amino acids abolishes DNA binding.

The pituitary-specific transcription factor GHF-1 is a homeobox-containing protein

Growth hormone factor 1 (GHF-1) is a pituitary-specific transcription factor that plays a critical role in cell type-specific expression of the growth hormone (GH) gene. Here, we describe the isolation of bovine and rat GHF-1 cDNA clones. These cDNAs encode proteins whose molecular mass, 33K, is identical to purified GHF-1 and whose sequence agrees with a partial GHF-1 peptide sequence. The predicted GHF-1 sequence contains a region, near its C-terminus, that exhibits considerable similarity to a homeobox consensus sequence. DNAase I footprinting with bacterially expressed fusion protein containing a fragment of GHF-1 encompassing the homeobox indicates that this region of the protein functions as its DNA binding domain. Expression of GHF-1 is restricted to cells of the somatotropic lineage in the pituitary. This remarkable specificity of GHF-1 expression correlates with the selective transcription of its target, the GH gene. Other mammalian homeobox-containing proteins may function similarly as transcription factors controlling cell type-specific expression in other locations.

A tissue-specific transcription factor containing a homeodomain specifies a pituitary phenotype

Multiple related cis-active elements required for cell-specific activation of the rat prolactin gene appear to bind a pituitary-specific positive transcription factor(s), referred to as Pit-1. DNA complementary to Pit-1 mRNA, cloned on the basis of specific binding to AT-rich cell-specific elements in the rat prolactin and growth hormone genes, encodes a 33 kd protein with significant similarity at its carboxyl terminus to the homeodomains encoded by Drosophila developmental genes. Pit-1 mRNA is expressed exclusively in the anterior pituitary gland in both somatotroph and lactotroph cell types, which produce growth hormone and prolactin, respectively. Pit-1 expression in heterologous cells (HeLa) selectively activates prolactin and growth hormone fusion gene expression, suggesting that Pit-1 is sufficient to confer a characteristic pituitary phenotype. The structure of Pit-1 and its recognition elements suggests that metazoan tissue phenotype is controlled by a family of transcription factors that bind to related cis-active elements and contain several highly conserved domains.

GAL11 protein, an auxiliary transcription activator for genes encoding galactose-metabolizing enzymes in Saccharomyces cerevisiae

Normal function of the GAL11 gene is required for maximum production of the enzymes encoded by GAL1, GAL7, and GAL10 (collectively termed GAL1,7,10) in Saccharomyces cerevisiae. Strains bearing a gal11 mutation synthesize these enzymes at 10 to 30% of the wild-type level in the induced state. In a DNA-RNA hybridization experiment, the gal11 effect was shown to be exerted at the transcription level. Yeast cells bearing the gal11 mutation were shown to grow on glycerol plus lactate more slowly than the wild type. We isolated recombinant plasmids carrying the GAL11 gene by complementation of the gal11 mutation. When the GAL11 locus was disrupted by insertion of the URA3 gene, the resulting yeast cells (gal11::URA3) exhibited phenotypes almost identical to those of the gal11 strains, with respect to both galactose utilization and growth on nonfermentable carbon sources. Deficiency of Gal4, the major transcription activator for GAL1,7,10, was epistatic over the gal11 defect. The Gal11 deficiency lowered the expression of GAL2 but not that of MEL1 or GAL80; expression of these genes is also known to be dependent on GAL4 function. We determined the nucleotide sequence of GAL11, which is predicted to encode a 107-kilodalton protein with stretches of polyglutamine and poly(glutamine-alanine). An alpha-helix-beta-turn-alpha-helix structure was found in a distal part of the predicted amino acid sequence. A possible role of the GAL11 product in the regulation of galactose-inducible genes is discussed.

Fine mapping of the latency-related gene of herpes simplex virus type 1: alternative splicing produces distinct latency-related RNAs containing open reading frames

The latency-related (LR) gene of herpes simplex virus type 1 (HSV-1) is transcriptionally active during HSV-1 latency, producing at least two LR-RNAs. The LR gene partially overlaps the immediate-early gene ICP0 and is transcribed in the opposite direction from ICP0, producing LR-RNAs that are complementary (antisense) to ICP0 mRNA. The LR gene is thought to be involved in HSV-1 latency. We report here the fine mapping and partial sequence analysis of this HSV-1 LR gene. 32P-labeled genomic DNA restriction fragments and synthetic oligonucleotides were used as probes for in situ hybridizations and Northern (RNA) blot hybridizations of RNA from trigeminal ganglia of rabbits latently infected with HSV-1. The two most abundant LR-RNAs appeared to share their 5' and 3' ends and to be produced by alternative splicing. These LR-RNAs were approximately 2 and 1.3 to 1.5 kilobases in length and were designated LR-RNA 1 and LR-RNA 2, respectively. Their 5' ends started approximately 1,210 nucleotides downstream from the 3' end of the ICP0 mRNA. Their 3' ends overlapped ICP0 by nearly 1,000 nucleotides. LR-RNA 1 appeared to have at least one intron removed, while LR-RNA 2 appeared to have at least two introns removed. The LR-RNAs contained two potential long open reading frames, suggesting the possibility that one or more of the LR-RNAs may be a functional mRNA.

Point mutants of Moloney murine leukemia virus that fail to package viral RNA: evidence for specific RNA recognition by a "zinc finger-like" protein sequence

All retroviruses encode a nucleic acid-binding or nucleocapsid protein that is believed to be associated with RNA in the virion. Further, all retroviral nucleocapsid proteins contain either one or two copies of the sequence Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys. The conservation of this sequence suggested that it is important for virus replication, and its resemblance to the "zinc-finger" sequences found in eukaryotic transcription factors raised the possibility that it recognizes specific sequences in viral RNA during retrovirus assembly. We used oligonucleotide-directed mutagenesis to generate a series of mutations in the nucleocapsid protein-coding region of Moloney murine leukemia virus. These mutations changed single amino acids, including each of the cysteines, to serine. The mutant viral genomes direct the synthesis of virus particles; these particles lack detectable viral RNA but do contain significant levels of cellular RNAs. Thus it appears that the mutations have destroyed the ability of the viral proteins to specifically package viral RNA during virus assembly. We propose that the conserved sequence in retroviral nucleocapsid proteins functions in RNA sequence recognition and suggest that it is evolutionarily related to the zinc fingers that recognize specific sequences in double-stranded DNA.

Transcriptional activation by the pseudorabies virus immediate early protein requires the TATA box element in the adenovirus 2 E1B promoter

The adenovirus E1A protein and immediately early (IE) protein of pseudorabies virus stimulate transcription from many promoters. It has been postulated that these proteins function via cellular intermediates. We analyzed the transcription of adenovirus E1B promoter mutants in response to the stimulatory effect of IE protein in comparison with E1A. Far upstream deletions and precise Sp1 and TATA box substitution mutations were examined. Only mutations affecting the TATA box element interfered with transactivation by IE protein. This result is similar to observations for E1A transactivation (L. Wu et al. Nature (London) 326, 512-515, 1987), suggesting that both E1A and IE proteins mediate transactivation of the E1B promoter through a common cellular intermediate which interacts with the TATA box.

A gene activated in mouse 3T3 cells by serum growth factors encodes a protein with "zinc finger" sequences

We have recently identified by cDNA cloning a set of genes that are rapidly activated in mouse 3T3 cells by serum or purified growth factors. Here we report that the cDNA (clone 268) derived from one of these immediate early genes (zif/268) encodes a protein with three tandem "zinc finger" sequences typical of a class of eukaryotic transcription factors. The mRNA of zif/268 is present in many organs and tissues of the mouse and is especially abundant in the brain and thymus tissue. The 5' genomic flanking sequence of zif/268 has sequences related to binding sites for known regulatory proteins, including four sequences that resemble the core of the serum response elements (SREs) upstream of the c-fos and actin genes. The SRE-like sequences could be responsible for the coordinate activation of zif/268 and fos after serum stimulation of 3T3 cells.

O-glycosylation of eukaryotic transcription factors: implications for mechanisms of transcriptional regulation

Glycosylation is often regarded as being restricted to proteins confined to the cell surface or within the lumen of intracellular organelles. Here we show that the human RNA polymerase II transcription factor Sp1 bears multiple O-linked N-acetylglucosamine (GlcNAc) monosaccharide residues. The lectin wheat germ agglutinin specifically inhibits the transcriptional activation but not the DNA binding function of Sp1. Furthermore, many other RNA polymerase II transcription factors also bear terminal GlcNAc residues, whereas most nuclear proteins, including RNA polymerase I and III transcription factors tested, do not. In some cases, only a subset of the polypeptide species within a particular family of closely related RNA polymerase II factors appears to be glycosylated. Our findings raise the possibility that O-linked GlcNAc residues play a role in the mechanism or regulation of transcriptional activation of RNA polymerase II.

Molecular cloning, sequencing, and mapping of EGR2, a human early growth response gene encoding a protein with "zinc-binding finger" structure

Early growth response gene-1 (Egr-1) is a mouse gene displaying fos-like induction kinetics in diverse cell types following mitogenic stimulation. Egr-1 encodes a protein with "zinc-binding finger" structure. Zinc fingers are a protein structural motif that serve as DNA-binding domains in several transcriptional regulatory proteins. Using low-stringency hybridization with an Egr-1 cDNA probe, we identified a distinct human cDNA (designated EGR2 for early growth response gene-2), which is coregulated with EGR1 by fibroblast and lymphocyte mitogens; however, several stimuli that induce Egr-1 mRNA in PC12 (rat pheochromocytoma) cells do not induce Egr-2 mRNA. The cDNA sequence predicts a protein of 406 amino acids, including three tandem zinc fingers of the Cys2-His2 class. Strikingly, the deduced amino acid sequences of human EGR2 and mouse Egr-1 are 92% identical in the zinc finger region but show no similarity elsewhere. EGR2 maps to human chromosome 10 at bands q21-22. Structure-function analysis of EGR2 and EGR1 proteins should provide insight into the mechanisms linking signal transduction and transcriptional regulation of gene expression.

Convulsant-induced increase in transcription factor messenger RNAs in rat brain

Administration of the convulsants pentylenetetrazole (Metrazole) or picrotoxin to rats caused a dramatic increase in mRNAs of four putative transcription factor genes, zif/268, c-jun, jun-B, and c-fos, in neurons of the hippocampus and dentate gyrus, as well as other areas of the cerebral cortex, including pyriform cortex and cingulate cortex. The increase in these mRNAs was rapid and transient: amounts peaked within 1 hr and returned to baseline within 2 hr. These results extend the observation made by Morgan et al. [Morgan, J. I., Cohen, D. R., Hempstead, J. L. & Curran, T. (1987) Science 237, 192-197] that c-fos mRNA and protein are induced in rat brain after seizures. We hypothesize that the increase of these putative transcription factor mRNAs in the brain is part of a programmed genomic response of neurons to intense stimulation, which is analogous to the genomic response of nonneuronal cells to growth factors.

The yeast regulatory protein ADR1 binds in a zinc-dependent manner to the upstream activating sequence of ADH2

The yeast ADR1 protein contains two zinc finger domains that are essential for its role in transcriptional activation of alcohol dehydrogenase (ADH2). These domains are thought to function as DNA-binding structures. An ADR1-beta-galactosidase fusion protein made in Escherichia coli and containing the finger domains of ADR1 binds in vitro in a zinc-dependent manner to DNA fragments containing the two ADH2 upstream activation sequences. The strongest binding is to upstream activation sequence 1, a 22-base-pair palindrome.

Functional domains required for tat-induced transcriptional activation of the HIV-1 long terminal repeat

The transcriptional regulation of the human immunodeficiency virus (HIV) type I involves the interaction of both viral and cellular proteins. The viral protein tat is important in increasing the amount of viral steady-state mRNA and may also play a role in regulating the translational efficiency of viral mRNA. To identify distinct functional domains of tat, oligonucleotide-directed mutagenesis of the tat gene was performed. Point mutations of cysteine residues in three of the four Cys-X-X-Cys sequences in the tat protein resulted in a marked decrease in transcriptional activation of the HIV long terminal repeat. Point mutations which altered the basic C-domain of the protein also resulted in decreases in transcriptional activity, as did a series of mutations that repositioned either the N or C termini of the protein. Conservative mutations of other amino acids in the cysteine-rich or basic regions and in a series of proline residues in the N terminus of the molecule resulted in minimal changes in tat activation. These results suggest that several domains of tat protein are involved in transcriptional activation with the cysteine-rich domain being required for complete activity of the tat protein.

Transient administration of estradiol-17 beta establishes an autoregulatory loop permanently inducing estrogen receptor mRNA

A single transient dose of estradiol-17 beta is sufficient to elicit the permanent induction of hepatic estrogen receptor mRNA, which is induced 18-fold (from 0.13 to 2.4 molecules per cell) and then remains fully induced for at least 125 days. In primary liver cultures, extremely low concentrations of estradiol-17 beta, which are below the Kd of the Xenopus laevis estrogen receptor, maintain persistent induction of estrogen receptor mRNA but not of estrogen-inducible vitellogenin mRNA. These data and the ability of the antiestrogen, hydroxytamoxifen, to reverse persistent induction of estrogen receptor mRNA, support a model in which transient doses of estradiol-17 beta induce the estrogen receptor and thereby establish an autoregulatory loop. The low levels of estradiol-17 beta normally circulating in male X. laevis and the elevated level of receptor provide sufficient hormone-receptor complex to permanently maintain the induced level of expression of the estrogen receptor gene. The permanent induction of the estrogen receptor may be the regulatory switch that results in the persistent expression of a recently identified class of proteins that exhibit long-term responses to estrogen.

Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box

The expression of HLA class II genes is regulated by a series of cis-acting elements and trans-acting factors. Several cis-acting elements have been identified and have been termed the Z box, X box, Y box, octamer, and "TATA" box. The Y box contains an inverted CCAAT box. By probing a phage lambda gt11 library with double-stranded oligonucleotides, we have directly isolated a cDNA encoding a Y box-binding protein designated YB-1. YB-1 binding has an absolute requirement for the CCAAT box and relative specificity for the Y box. It has a Mr of 35,414, contains 18% basic residues, and contains putative nuclear localization signals. An inverse correlation of YB-1 and HLA-DR beta chain mRNA levels suggests that YB-1 is a negative regulatory factor.

5' flanking sequence and genomic structure of Egr-1, a murine mitogen inducible zinc finger encoding gene

Egr-1 is a murine zinc finger encoding cDNA whose expression is modulated by a variety of ligand-receptor interactions and is often coregulated with c-fos (1). This study reports the isolation of a mouse Egr-1 genomic clone, its intron-exon structure, and 935 bp of 5' flanking sequence. The gene spans about 3.8 kb and consists of 2 exons and one 700 bp intron. S1 nuclease protection and primer extension analysis were used to define the transcription initiation site. "TATA" and "CCAAT" sequences were located at nucleotides -26 and -337 respectively. In addition, there exist five elements whose sequence is nearly identical to the inner core 10 nucleotide region (CCATATTAGG) of the c-fos serum response element, four Sp1 consensus sequences, two AP1 target sequence analogs, and two potential cAMP response elements. These results will ultimately lead to a detailed definition of the intracellular events regulating Egr-1 expression.

Isolation of the gene encoding the S. cerevisiae heat shock transcription factor

The yeast heat shock transcription factor gene, HSF1, has been isolated from an S. cerevisiae genomic expression library (in lambda gt11). The sequenced gene encodes an 833 amino acid protein having a mass of 93,218 daltons. Expression of specific DNA-binding activity in E. coli and of transcriptional activity in yeast confirmed the identity of the cloned gene. Southern analysis and gene-disruption experiments indicate that the heat shock transcription factor is encoded by a single-copy, essential gene. The DNA-binding domain was localized to a 118 amino acid region in the amino-terminal third of the protein. Inspection of the DNA-binding domain reveals no resemblance to any currently known secondary structural motifs implicated in DNA recognition and binding.

The 289-amino acid E1A protein of adenovirus binds zinc in a region that is important for trans-activation

The E1A gene of adenovirus type 5 encodes two major proteins of 289 and 243 amino acid residues, which are identical except that the larger protein has an internal stretch of 46 amino acids required for efficient trans-activation of early viral promoters. This domain contains a consensus zinc finger motif (Cys-Xaa2-Cys-Xaa13-Cys-Xaa2-Cys) in which the cysteine residues serve as postulated ligands. Atomic absorption spectrophotometry applied to bacterially expressed E1A proteins revealed that the 289-amino acid protein binds one zinc ion, whereas the 243-amino acid protein binds no zinc. Replacing individual cysteine residues of the finger with other amino acids destroyed the trans-activating ability of the 289-amino acid protein, even when structurally or functionally conserved amino acids were substituted. These results strongly suggest that the zinc finger of the 46-amino acid domain is intimately linked to the ability of the large E1A protein to stimulate transcription of E1A-inducible promoters. Furthermore, zinc binding to one of the mutant finger proteins suggests either that only a precise finger structure formed by the tetrahedral coordination of zinc to the four consensus ligands is required for trans-activation or, possibly, that one of several neighboring histidine residues in various combinations with three of the consensus cysteine residues normally coordinates zinc. How the zinc finger in E1A might interact with DNA or protein to bring about trans-activation is discussed.

Sp1 transcription factor binds DNA and activates transcription even when the binding site is CpG methylated

In vertebrates, a negative correlation between gene activity and CpG methylation of DNA, notably in the promoter region, is well established. Therefore, it is conceivable that differential binding of transcription factors to methylated versus unmethylated binding sites is crucial for gene activity. Since the consensus binding site of transcription factor Sp1 contains a central CpG, we have investigated the binding of Sp1 factor to unmethylated and synthetically CpG-methylated DNA. A strong Sp1 binding site was methylated on both strands at two CpG positions, located in the center and at the periphery of the recognition sequence. Our studies show that neither binding in vitro, nor transcription in vivo and in vitro are affected by methylation of the Sp1 binding site. We discuss the possibility that binding of Sp1 factor, which is often associated with promoters of housekeeping genes, prevents CpG methylation.

Multiple elements are required for expression of an intermediate filament gene

The expression of vimentin is unique within the intermediate filament multigene family. It is the only member which deviates from its usual tissue-specific expression pattern and whose 5'-flanking region contains multiple GC boxes, the binding site for Sp1. The activity of vimentin 5'-end:CAT fusions has been compared in cells where vimentin is highly expressed (mouse L cells) or not expressed at all (MH1C1). In addition, CAT activity has been examined by microinjection into Xenopus oocytes. Both in vivo expression and in vitro binding studies implicate Sp1 as a general regulatory factor in vimentin gene expression. Increased expression of 5'-end:CAT fusions in mouse L cells suggests that a fibroblast-specific enhancer element resides in the region -321 to -160. Low transcriptional activity in MH1C1 cells may be due to either the lack of this positive transcription factor(s) or the presence of a repressor element. Here, we demonstrate that the unique and complex pattern of vimentin gene expression is controlled by multiple cis-acting elements.

The function and structure of the metal coordination sites within the glucocorticoid receptor DNA binding domain

The glucocorticoid receptor enhances or represses transcription by binding to specific DNA sequences termed glucocorticoid response elements, or GREs. Studies of cloned glucocorticoid receptors reveal that the protein is organized as functional domains, in an arrangement that appears to be common among members of the steroid receptor family. A segment near the centre of the gene specifies DNA binding activity in vitro and contains two sequence motifs similar to 'zinc fingers' found in Xenopus transcription factor IIIA (TFIIIA). Such sequence motifs have been identified in nucleic acid binding proteins from a wide range of organisms. Steroid receptor protein fingers are proposed to bind zinc through two pairs of conserved cysteine residues. We report here that a protein of relative molecular mass 19,000 (Mr = 19 K) encompassing the DNA-binding domain of the glucocorticoid receptor that has been overexpressed in Escherichia coli and purified to homogeneity reversibly ligates two Zn(II) or Cd(II) ions. We show that metal ions are required for specific DNA binding and proper folding. Using EXAFS (extended X-ray absorption fine structure) and visible light spectroscopies, we find that each Zn atom is coordinated in a tetrahedral arrangement by four cysteines.

Regulatory effect of a synthetic CRP recognition sequence placed downstream of a promoter

A series of plasmids were constructed in which a promoter was introduced into a lac-based operon fusion vector. A perfectly symmetrical oligonucleotide of 22-bp corresponding to an idealized binding site for cAMP receptor protein (CRP) of E. coli was chemically synthesized. The synthetic CRP site was placed between the promoter and the lacZ structural gene with varying distances from the promoter. Specific binding of cAMP-CRP complex to the synthetic CRP site was shown by a gel retardation and a DNase I footprinting assays. Plasmid constructs were transformed into crp+ and crp- cells carrying a chromosomal deletion of the lac genes. The regulatory effect of the inserted CRP site was examined by comparing the beta-galactosidase activity and the levels of RNA transcript in two cells harboring the plasmids. We found a strong inhibitory effect of the CRP site in the presence of cAMP and CRP when it was placed close to the promoter. When the CRP site was placed far downstream of the promoter, a moderate repression of transcription was observed.

The GLI-Kruppel family of human genes

Previous characterization of GLI, a gene found to be amplified and expressed in a subset of human brain tumors, revealed the presence of five tandem zinc fingers related to those of Krüppel (Kr), a Drosophila segmentation gene of the gap class. We have used the GLI cDNA as a molecular probe to isolate related sequences from the human genome. Partial characterization of six related loci, including sequence determination, expression studies, and chromosome localization, revealed that each locus could encode a separate finger protein. The predicted proteins all had similar H-C links, i.e., a conserved stretch of 9 amino acids connecting the C-terminal histidine of one finger to the N-terminal cysteine of the next. On the basis of amino acid sequence and intron-exon organization, the genes could be placed into one of two subgroups: the GLI subgroup (with the consensus finger amino acid sequence [Y/F]XCX3GCX3[F/Y]X5LX2HX3-4H[T/S]GEKP) or the Kr subgroup (with the consensus finger amino acid sequence [Y/F]XCX2CX3FX5LX2HXRXHTGEKP). Unlike GLI or Kr, most of the newly isolated genes were expressed in many adult tissues. The predicted proteins probably control the expression of other genes and, by analogy with Kr and GLI, may be important in human development, tissue-specific differentiation, or neoplasia.

brlA is necessary and sufficient to direct conidiophore development in Aspergillus nidulans

The brlA gene of A. nidulans mediates the developmental switch from the indeterminate, apical growth pattern of vegetative cells to the budding growth pattern of conidiophores. brlA encodes a 432 amino acid polypeptide containing two directly repeated motifs resembling the Zn(II) coordination sites first recognized in Xenopus TFIIIA. Misscheduled expression of brlA in vegetative cells results in transcriptional activation of developmentally regulated genes, cessation of unidirectional hyphal growth, initiation of cellular transformations resembling those that occur during normal conidiophore development, and production of viable conidiospores. We propose that BRLA is a nucleic acid-binding protein whose expression in vegetative cells is sufficient to induce sporulation through its role in regulating expression of conidiation-specific genes.

A family of human CCAAT-box-binding proteins active in transcription and DNA replication: cloning and expression of multiple cDNAs

The CTF/NF-I group of cellular DNA binding proteins recognizes the sequence GCCAAT and is implicated in eukaryotic transcription as well as DNA replication. Molecular analysis of human CTF/NF-I complementary DNA clones reveals multiple messenger RNA species containing alternative coding regions, apparently as a result of differential splicing. Expression and functional analysis establish that individual gene products can bind to GCCAAT recognition sites and serve both as promoter-selective transcriptional activators and as initiation factors for DNA replication.

Finger proteins and DNA-specific recognition: distinct patterns of conserved amino acids suggest different evolutionary modes

Finger proteins, the first example of which was Xenopus TFIIIA, share Zn2+ finger-like folded domains capable of binding to nucleic acids. A large number of this type of protein have been characterised from diverse organisms, indicating a wide evolutionary spread of the DNA-binding fingers. At least two classes of finger proteins may be distinguished. Class I proteins contain variable numbers of the tandemly repeating TFIIIA-like finger motif, (Y/F-X-C-X2-4-C-X3-F-X5-L-X2-H-X3-H). Class II finger proteins display a single (C-X2-C-X13-C-X2-C) motif and a facultative second putative finger. The relation between the structure of finger proteins and their recognised DNA sequences is discussed.

Heavy metal ions in transcription factors from HeLa cells: Sp1, but not octamer transcription factor requires zinc for DNA binding and for activator function

Zinc is an important cofactor for many enzymes involved in nucleic acid metabolism such as DNA and RNA polymerases, reverse transcriptase and tRNA synthetases. We have developed an inducible in vitro transcription system using metal-depleted nuclear extracts to reveal the presence and functional relevance of heavy metal ions in transcription factors. Using protein-DNA binding assays (band shift and DNAase I footprint) we show that Sp1, a promoter-specific vertebrate transcription factor that binds to the "GC box" (Sequence in text), is reversibly inactivated by metal-depletion. Zinc is required for specific DNA binding in vitro and is also essential for Sp1 factor-directed transcription. In contrast, another factor from HeLa cells, the so-called octamer transcription factor (OTF) that binds to the sequence 5'-ATGCAAATNA, is not affected by metal-depletion and thus seems not to be a zinc metalloprotein.

An erythrocyte-specific protein that binds to the poly(dG) region of the chicken beta-globin gene promoter

The promoter region of the chicken adult beta-globin gene contains a sequence of 16 deoxyguanosine residues located at a nucleosome boundary in tissues where the gene is inactive. In definitive erythrocytes that express the beta-globin gene, the nucleosome is displaced, the G-string and adjacent sequences are occupied by sequence-specific DNA-binding proteins, and a nuclease hypersensitive domain is generated in this region. To gain insight into the role of the G-string in this series of events, we have examined the proteins that bind to it. Using the gel mobility shift assay and a monoclonal antibody that blocks specific binding to the G-string, we have identified a specific protein, BGP1, that is found only in chicken erythroid cells and appears at the same time, or shortly before, the changes in chromatin structure. The antibody interacts strongly with BGP1 and cross-reacts weakly with Sp1. Although both BGP1 and Sp1 require Zn2+ for their DNA-binding activity, these proteins differ in their binding-site specificities, chromatographic properties, and molecular weights. In contrast to Sp1, which is found in a wide variety of cell types, BGP1 is restricted to erythrocytes and is most abundant in definitive erythrocytes. Thus, its presence corresponds to the tissue- and stage-specific occupancy of the G-string in vivo.

Two mouse genes encoding potential transcription factors with identical DNA-binding domains are activated by growth factors in cultured cells

We previously reported the identification of a mouse gene, Krox-20, encoding a protein with three "zinc fingers" (DNA-binding domains with coordinated zinc ions) whose expression is regulated during G0/G1 transition (cell-cycle reentry). We now have isolated cDNAs corresponding to a related gene, Krox-24. Krox-24 encodes a protein with zinc fingers nearly identical to those encoded by Krox-20 and similar to those of transcription factor Sp1. Similarity between Krox-20 and Krox-24 proteins also extends to several blocks of amino acid sequence located upstream of the finger region. Like Krox-20, Krox-24 is transiently activated in quiescent cells after treatment with fetal bovine serum or purified growth factors. The kinetics of activation are similar to those of the protooncogene c-fos. The induction does not require de novo protein synthesis, and cycloheximide treatment of the cells leads to superinduction due, at least in part, to mRNA stabilization. In the mouse, the two genes are expressed in a tissue-specific manner, with slightly different patterns. These properties suggest that Krox-20 and Krox-24 may encode transcription factors with identical DNA target sequences and that these factors may be involved in the modulation of cell proliferation and differentiation.

A sequence-specific single-strand-binding protein for the late-coding strand of the simian virus 40 control region

We have purified a protein from uninfected monkey CV1 cells that binds specifically in vitro to the late-coding simian virus 40 DNA strand in the region of transcription control without any detectable binding to the complementary single strand. Nuclease protection experiments detected two binding sites in the 21-base-pair repeat region. The protein did not bind to this region in the double-stranded form, nor did it bind to RNA synthesized in vitro by using either DNA strand as a template. This protein, and perhaps other DNA single-strand-sequence-specific proteins, may play a role in the control of gene expression in higher organisms.

The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins

A 30-amino-acid segment of C/EBP, a newly discovered enhancer binding protein, shares notable sequence similarity with a segment of the cellular Myc transforming protein. Display of these respective amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The periodic array of at least four leucines was also noted in the sequences of the Fos and Jun transforming proteins, as well as that of the yeast gene regulatory protein, GCN4. The polypeptide segments containing these periodic arrays of leucine residues are proposed to exist in an alpha-helical conformation, and the leucine side chains extending from one alpha helix interdigitate with those displayed from a similar alpha helix of a second polypeptide, facilitating dimerization. This hypothetical structure is referred to as the "leucine zipper," and it may represent a characteristic property of a new category of DNA binding proteins.

Xenopus laevis in developmental and molecular biology

Xenopus laevis is a prime system for the study of embryogenesis in vertebrates. Both prelocalized information in the egg and inductive interactions between cells contribute to the ordered increase in complexity during development. Embryonic induction, discovered in amphibians, is being studied intensely in Xenopus; recent work suggests a role for growth factors in this process. Contributions of the Xenopus system to the analysis of ribosomal and 5S RNA genes, and the diverse and highly productive applications of the oocyte injection technology, are also summarized.

Transcription factors that activate the Ultrabithorax promoter in developmentally staged extracts

We have initiated a biochemical analysis of factors that regulate the expression of the Ultrabithorax (Ubx) homeotic gene during embryogenesis. Transcriptionally active extracts have been prepared from Drosophila embryos at successive stages of development that recreate in vitro the temporal profile of Ubx gene expression during embryogenesis. Multiple sequence-specific transcription factors have been detected that bind to essential cis control elements located upstream and downstream of the Ubx mRNA cap site. The activity of some of these transcription factors varies during embryogenesis, and some are detected in embryonic extracts but not in Drosophila tissue culture cells. One factor, which binds to multiple GAGA DNA sequence motifs in the Ubx promoter, has been purified and shown to activate transcription from this promoter in a binding site-dependent manner. This in vitro analysis should help in understanding how Ubx expression is regulated and provide insight into the processes determining cellular fates during development.

Isolation of cDNAs encoding finger proteins and measurement of the corresponding mRNA levels during myeloid terminal differentiation

The finger motif is a tandemly repeated DNA-binding domain recently identified in the primary structure of several eukaryotic transcriptional regulatory proteins. It was first described for Xenopus TFIIIA, a factor required for transcription of 5S ribosomal genes and subsequently identified in regulatory proteins from other eukaryotic organisms including yeast, Drosophila and mammals. In this paper we report the isolation and characterization of two human cDNA clones both encoding for multifingered protein products. Transcriptional studies indicate that the two finger genes are expressed in a variety of human tissues. Moreover, upon in vitro induced terminal differentiation of human HL-60 and THP-1 myeloid cell lines the expression of both genes is drastically reduced. These data provide support for the existence of a human multigene family coding for regulatory finger proteins which are likely involved in the processes of cell differentiation and/or proliferation.

The human papillomavirus type 16 E7 gene encodes transactivation and transformation functions similar to those of adenovirus E1A

Clinical and epidemiological data have implicated the human papillomaviruses (HPVs) as having an etiologic role in some anogenital malignancies, with HPV-16 being most frequently (greater than 60%) detected in cervical carcinoma. HPV-16 is actively transcribed in the cancers; the most abundant transcripts map to the E6 and E7 early open reading frames. Evidence is presented that the HPV-16 E7 open reading frame encodes transcriptional transactivation and cellular transformation functions analogous to those of adenovirus E1A proteins. Specifically, the HPV-16 E7 gene product could transactivate the adenovirus E2 promoter and cooperate with an activated ras oncogene to transform primary baby rat kidney cells. The E7 transforming function differed somewhat from that of adenovirus E1A in that E7 was also able to transform established mouse cells. Examination of the amino acid sequence of HPV-16 E7 revealed striking similarities with conserved domains 1 and 2 of adenovirus E1A proteins.