Multiple Protein Factors Research Articles

Redundant role of tissue-selective TAF(II)105 in B lymphocytes.

Regulated gene expression is a complex process achieved through the function of multiple protein factors acting in concert at a given promoter. The transcription factor TFIID is a central component of the machinery regulating mRNA synthesis by RNA polymerase II. This large multiprotein complex is composed of the TATA box binding protein (TBP) and several TBP-associated factors (TAF(II)s). The recent discovery of multiple TBP-related factors and tissue-specific TAF(II)s suggests the existence of specialized TFIID complexes that likely play a critical role in regulating transcription in a gene- and tissue-specific manner. The tissue-selective factor TAF(II)105 was originally identified as a component of TFIID derived from a human B-cell line. In this report we demonstrate the specific induction of TAF(II)105 in cultured B cells in response to bacterial lipopolysaccharide (LPS). To examine the in vivo role of TAF(II)105, we have generated TAF(II)105-null mice by homologous recombination. Here we show that B-lymphocyte development is largely unaffected by the absence of TAF(II)105. TAF(II)105-null B cells can proliferate in response to LPS, produce relatively normal levels of resting antibodies, and can mount an immune response by producing antigen-specific antibodies in response to immunization. Taken together, we conclude that the function of TAF(II)105 in B cells is likely redundant with the function of other TAF(II)105-related cellular proteins.

A Proximal Promoter Domain Containing a Homeodomain-Binding Core Motif Interacts with Multiple Transcription Factors, Including HoxA5 and Phox2 Proteins, and Critically Regulates Cell Type-Specific Transcription of the Human Norepinephrine Transporter Gene

Expression of the norepinephrine transporter (NET), which mediates the reuptake of norepinephrine into presynaptic nerve terminals, is restricted to noradrenergic (NA) neurons. We have demonstrated previously that the 9.0 kb upstream sequences and the first intron residing in the 5′ untranslated area are critical for high-level and NA cell-specific transcription. Here, using transient transfection assays, we show that 4.0 kb of the 5′ upstream sequences contains sufficient genetic information to drive reporter gene expression in an NA cell type-specific manner. Three functional domains appear to be potentially important for the regulation ofhuman NET(hNET) gene transcription: an upstream enhancer region at −4.0 to −3.1 kb, a proximal domain at −133 to −75 bp, and a middle silencer region between these two domains. DNase I footprinting analysis of the proximal promoter region shows that a subdomain at −128 to −80 bp is protected in a cell-specific manner. We provide evidence that multiple protein factors interact with the proximal promoter domain to critically regulate the transcriptional activity of thehNETgene. In the middle of this proximal subdomain resides a homeodomain (HD)-binding core motif, which interacts with HD factors, including Phox2a and HoxA5, in an NA-specific manner. Cotransfection analyses suggest that HoxA5 and Phox2a may transactivate thehNETgene promoter. Together with previous studies indicating direct activation of dopamine β-hydroxylase transcription by Phox2a/2b, the present results support a model whereby Phox2 proteins may coordinately regulate the phenotypic specification of NA neurons by activating both NA biosynthetic and reuptake genes.

A proximal promoter domain containing a homeodomain-binding core motif interacts with multiple transcription factors, including HoxA5 and Phox2 proteins, and critically regulates cell type-specific transcription of the human norepinephrine transporter gene.

Expression of the norepinephrine transporter (NET), which mediates the reuptake of norepinephrine into presynaptic nerve terminals, is restricted to noradrenergic (NA) neurons. We have demonstrated previously that the 9.0 kb upstream sequences and the first intron residing in the 5' untranslated area are critical for high-level and NA cell-specific transcription. Here, using transient transfection assays, we show that 4.0 kb of the 5' upstream sequences contains sufficient genetic information to drive reporter gene expression in an NA cell type-specific manner. Three functional domains appear to be potentially important for the regulation of human NET (hNET) gene transcription: an upstream enhancer region at -4.0 to -3.1 kb, a proximal domain at -133 to -75 bp, and a middle silencer region between these two domains. DNase I footprinting analysis of the proximal promoter region shows that a subdomain at -128 to -80 bp is protected in a cell-specific manner. We provide evidence that multiple protein factors interact with the proximal promoter domain to critically regulate the transcriptional activity of the hNET gene. In the middle of this proximal subdomain resides a homeodomain (HD)-binding core motif, which interacts with HD factors, including Phox2a and HoxA5, in an NA-specific manner. Cotransfection analyses suggest that HoxA5 and Phox2a may transactivate the hNET gene promoter. Together with previous studies indicating direct activation of dopamine beta-hydroxylase transcription by Phox2a/2b, the present results support a model whereby Phox2 proteins may coordinately regulate the phenotypic specification of NA neurons by activating both NA biosynthetic and reuptake genes.

Complex protein interactions within the human polyadenylation machinery identify a novel component.

Polyadenylation of mRNA precursors is a two-step reaction requiring multiple protein factors. Cleavage stimulation factor (CstF) is a heterotrimer necessary for the first step, endonucleolytic cleavage, and it plays an important role in determining the efficiency of polyadenylation. Although a considerable amount is known about the RNA binding properties of CstF, the protein-protein interactions required for its assembly and function are poorly understood. We therefore first identified regions of the CstF subunits, CstF-77, CstF-64, and CstF-50, required for interaction with each other. Unexpectedly, small regions of two of the subunits participate in multiple interactions. In CstF-77, a proline-rich domain is necessary not only for binding both other subunits but also for self-association, an interaction consistent with genetic studies in Drosophila. In CstF-64, a small region, highly conserved in metazoa, is responsible for interactions with two proteins, CstF-77 and symplekin, a nuclear protein of previously unknown function. Intriguingly, symplekin has significant similarity to a yeast protein, PTA1, that is a component of the yeast polyadenylation machinery. We show that multiple factors, including CstF, cleavage-polyadenylation specificity factor, and symplekin, can be isolated from cells as part of a large complex. These and other data suggest that symplekin may function in assembly of the polyadenylation machinery.

Multiple elements and protein factors coordinate the basal and cyclic adenosine 3',5'-monophosphate-induced transcription of the lutropin receptor gene in rat granulosa cells.

The expression of the lutropin receptor (LHR) in granulosa cells is a complex phenomenon under the hormonal control of FSH and estradiol. Using primary cultures of granulosa cells from immature female rats pretreated with diethylstilbestrol (a compound with estrogen-like activity), the role of FSH in LHR induction was studied. Previous studies from our laboratory have shown that FSH or 8-bromo-cAMP addition to these cells causes a marked increase in the rate of transcription of the rat LHR (rLHR) gene. The present studies were undertaken to compare the properties of the rLHR gene in undifferentiated vs. differentiated rat granulosa cells as a means of determining those elements that confer basal activity and cAMP responsiveness. Our studies show that the proximal 155 bp (relative to the translational initiation codon) of the 5'-flanking region of rLHR gene represent a minimal promoter that accounts for the basal expression of this receptor in rat granulosa cells. A major domain located between nucleotides (nt) -90 and -120, with another one possibly being between nt -120 and -155, induced activation of basal transcriptional activity. An inhibitory domain was observed to lie between nt -186 and -1375. Our data further show that multiple elements within the 2.1 kb of the 5'-flanking region of the rLHR gene are involved in the 8-bromo-cAMP-induced expression of the LHR gene. Of these, the three Sp1-binding sites within the proximal portion of the 5'-flanking region appear to be important for both basal as well as cAMP-induced rLHR gene transcription.

Multiple Elements and Protein Factors Coordinate the Basal and Cyclic Adenosine 3',5'-Monophosphate-Induced Transcription of the Lutropin Receptor Gene in Rat Granulosa Cells

Multiple Elements and Protein Factors Coordinate the Basal and Cyclic Adenosine 3',5'-Monophosphate-Induced Transcription of the Lutropin Receptor Gene in Rat Granulosa Cells

Multiple Protein Factors Interact with the cis-Regulatory Elements of the Proximal Promoter in a Cell-Specific Manner and Reg\ ulate Transcription of the Dopamine b-Hydroxylase Gene

The dopamine beta-hydroxylase (DBH) gene is expressed selectively in noradrenergic and adrenergic neurons and neuroendocrine cells in the nervous system. A cAMP response element (CRE) residing at -181 to -174 bp from the transcription start site of the human DBH gene seems to be essential for DBH transcription. Potential cis-regulatory motifs such as AP1 and YY1 occur proximal to and overlap this CRE, endowing the area with a composite promoter structure. Using the DBH-expressing human neuroblastoma SK-N-BE(2)C and DBH-negative HeLa cell lines as model systems, we report here that this CRE/YY1/AP1 area interacts with multiple nuclear proteins, including CRE-binding protein (CREB) and transcription factor YY1 in a cell-specific manner. In support of the notion that multiple proteins bind to the CRE/YY1/AP1 area, DNase I foot-printing analysis has demonstrated that nuclear extracts protect an extended region (from -186 to -150 bp) relative to that protected by the purified CREB (from -186 to -171 bp). Site-directed mutational analysis has revealed differential roles of potential cis-regulatory motifs in regulation of DBH transcription. Strikingly, the YY1 element positively regulated basal DBH transcription while simultaneously regulating cAMP-mediated induction negatively, which is a novel mechanism of promoter function. Furthermore, three additional DNA-binding sites have been identified by DNase I footprint analysis in the upstream 260 bp promotor region of the human DBH gene, of which two sites are cell-specific. These results support a model whereby multiple proteins bind to the 5'-proximal area in a cell-specific manner and coordinately regulate the cell type-specific transcriptional activation of the DBH gene.

A polyadenylation factor subunit is the human homologue of the Drosophila suppressor of forked protein.

Polyadenylation of messenger RNA precursors is a complex process that requires multiple protein factors (for reviews, see refs 1, 2). Cleavage stimulation factor (CstF) is one of these, functioning together with cleavage-polyadenylation specificity factor, two cleavage factors, and poly(A)+ polymerase. CstF is composed of three subunits of M(r) 77, 64 and 50K. The 64K and 50K subunits contain, respectively, an RNP-type RNA-binding domain that contacts the pre-mRNA and transducin repeats characteristic of G-protein beta-subunits. Here we report the cloning and characterization of the 77K subunit of human CstF (referred to as 77K). We show that the 77K subunit is required for formation of active CstF and bridges the 64K and 50K subunits. Sequence analyses indicate that the 77K subunit is the homologue of the protein encoded by the Drosophila melanogaster suppressor of forked (su(f)) gene. Mutations in su(f) can enhance or suppress the effects of transposable element insertions, and our data indicate that this is due to changes in polyadenylation. Both the 77K subunit and the su(f) protein share homology with Saccharomyces cerevisiae RNA14, previously shown to be involved in mRNA metabolism. Our results thus also indicate that components of the complex polyadenylation machinery are conserved from yeast to man.

Analysis of the DNA binding proteins interacting with specific upstream sequences of the S. purpuratus CyI actin gene.

The CyI actin gene of the sea urchin, Strongylocentrotus purpuratus, is regulated temporally and spatially within the cells of the early embryo. In an effort to understand the molecular basis for the CyI actin pattern of expression, we have begun analyzing the protein-DNA interactions within regions previously shown to be of potential functional importance (Katula et al., 1987). Using DNase I footprinting, 10 protected regions were identified containing both conserved and apparently novel protein binding sites. Gel mobility shift competition assays confirmed the presence of multiple protein factors which specifically recognize CyI actin upstream sequences. Determination of a relative affinity constant value (Kr) indicated that most of the protein factors preferred their respective oligonucleotide sequences vs. a synthetic competitor DNA in a range of 10(4). The highest affinity binding was observed for proteins binding to the oligonucleotide probe containing the octamer element (Kr approximately 10(6)). Heterologous gel shift competition assays were carried out to investigate the interrelatedness of the protein factors. These studies, combined with other data, indicate there are both unique and redundant protein-DNA interactions in the region being examined. Possible alterations in CyI actin DNA binding proteins were investigated during the period of CyI transcriptional activation by gel mobility shift analysis. An increase in binding activity was observed for most of the factors, indicating that early transcriptional activity of CyI actin may involve a general increase in the amount or activity of specific transcription factors. In addition, qualitative changes, as seen by alterations in the shift patterns, were observed for some of the oligonucleotide probes.

Advances in RNA polymerase II transcription

Multiple protein factors are necessary to mediate transcription by RNA polymerase II. Recently, a number of advances have been made in our understanding of how general transcription factors collectively modulate basal transcription in the context of different promoter environments and how this process is activated and repressed by accessory components.

Advances in RNA polymerase II transcription

Multiple protein factors are necessary to mediate transcription by RNA polymerase II. Recently, a number of advances have been made in our understanding of how general transcription factors collectively modulate basal transcription in the context of different promoter environments and how this process is activated and repressed by accessory components.

Isolation of multiple protein factors involved in ribosomal DNA transcription

Studies were made of the molecular mechanisms which regulate ribosomal gene transcription in response to changes in the growth rate of cells. Extracts prepared from exponentially growing Ehrlich ascites cells faithfully and efficiently transcribe cloned mouse rDNA, whereas extracts from growth-arrested cells are virtually inactive. In an attempt to identify and characterize functionally the proteins that mediate the accuracy and the control of transcription initiation, a fractionation procedure was developed which allows the purification of RNA polymerase I and four accessory factors that are required for transcription initiation at the ribosomal gene promoter. Starting from about 300 ml of cell extract, each of the individual factors and the polymerase was purified on at least four different chromatographic columns, including ion-exchange chromatography on DEAE-Sepharose, heparin-Ultrogel, Mono Q and Mono S, gel filtration and specific affinity chromatography. The resulting protein fractions are functionally active, as shown by reconstitution of specific rDNA transcription in the presence of purified polymerase and the additional factors.

Repression of the Drosophila fushi tarazu (ftz) segmentation gene.

The striped expression of the Drosophila segmentation gene fushi tarazu in alternate parasegments of the early embryo is controlled by the 740 bp zebra element. Among multiple protein factors that bind to the zebra element, FTZ-F2 behaves as a transcriptional repressor of ftz. Point mutations in the zebra element which disrupt FTZ-F2 binding to DNA cause ectopic expression of zebra-lacZ activity in transformed embryos. The mutant constructs are expressed from the zygotic genome in preblastoderm embryos as early as the third nuclear division cycle. This unprecedented early transcription suggests that ftz requires active repression during initial nuclear division cycles, a novel type of embryonic gene regulation. A putative FTZ-F2 cDNA clone isolated by recognition site screening of an expression library was found to be identical in sequence with the zinc finger protein tramtrack (Harrison and Travers, 1990).

The Regulation of γ‐Globin Gene Expression

In summary, our analysis indicates that important sequences for the proper initiation of fetal gene transcription in fetal cells are located in the gamma-globin [sequence: see text] promoter. These sequences are sufficient for tissue-specific expression but not induction in K562 cells. Sequences in the gamma-globin IVS-2 and the beta-globin 3' enhancer increase gamma beta and gamma-Neo transcripts when cells containing these genes undergo erythroid maturation as measured by induction with hemin. The mechanism by which these sequences exert their effect remains to be elucidated. [see text] Multiple protein factors bind to both the gamma promoter and the beta 3' enhancer. Both of these regions contain binding sites for the erythroid-specific factor NFE-1 and the octamer binding factor OTF-1. In the gamma upstream region, there may be a competition between OTF-1 binding and NFE-1 binding that affects gamma gene regulation. Our results indicate that the beta 3' enhancer interacts with the gamma gene promoter to permit increased gamma gene expression. We have developed a model for globin gene switching that takes into consideration the effect of cis-acting sequences on globin gene transcription. A similar model of hemoglobin switching in chickens has been proposed by Choi and Engel. In our model, competition for the beta-globin 3' enhancer is involved in stage-specific transcriptional activation of gamma-globin genes in fetal cells and beta-globin genes in adult cells. In adult cells the protein-protein interactions between adult cell-specific factors interacting with the beta-globin promoter and erythroid-specific factors interacting with the beta 3' enhancer would activate transcription of the beta-globin gene. In fetal cells protein-protein interactions between fetal cell-specific factors interacting with the gamma-globin promoter and erythroid-specific factors interacting with the beta 3' enhancer would activate the transcription of the gamma-globin genes.

Assembly of Xenopus transcription factor III A-5S RNA complex

The regulation of Xenopus 5S rRNA gene expression involves multiple protein factors, among which is transcription factor III A (TFIIIA). This factor can be isolated as a protein-RNA complex. The assembly behavior of this complex was studied by sedimentation velocity and gel electrophoresis at pH 7.5 and 23 degrees C. The reaction boundary was monitored by the absorbance at 260 nm; thus, the shape of the boundary reflects mainly RNA or RNA-containing complexes. Values for the weight-average sedimentation coefficient (S20,w) change with protein-RNA concentration. At low concentrations, values of S20,w increase with increasing concentration. The extrapolated value for S20,w at infinite dilution is 5.2 S, the same value for free Xenopus rRNA under the same experimentation conditions. Furthermore, the same value of S20,w at a specific RNA concentration can be obtained either by dilution of a concentrated sample or by concentrating a diluted one. These results indicate that complex formation can be described by a reversible process. When the data are analyzed by computer fitting, the simplest model that fits the sedimentation data is that TFIIIA and RNA form a 1:1 complex which self-aggregates to a dimer. The sedimentation coefficients (S020,w) of PR and (PR)2 are 7.5 and 10.6 S, respectively, where PR and (PR)2 are the 1:1 TFIIIA-RNA complex and its dimer, respectively. The protein-RNA interaction was also investigated by gel electrophoresis. The resolved components were identified by differential staining for protein and RNA on a single gel. One band corresponding to free 5S rRNA was detected in addition to two bands which stained for both protein and nucleic acids.(ABSTRACT TRUNCATED AT 250 WORDS)

Multiple protein factors bind to a rice glutelin promoter region

Our goal is to identify cis-acting elements in the regulatory region of the major seed storage protein gene in rice. A glutelin gene (pGL5-1) has been cloned by screening a rice genomic DNA library with synthetic oligonucleotides and with an amplified DNA fragment. A transient expression assay using immature rice seeds shows that its 5' flanking sequence can direct the synthesis of beta-glucuronidase (GUS) when fused upstream of the GUS coding region. Gel-retardation assays were performed to study protein-DNA interactions between putative regulatory sequences of pGL5-1 and nuclear proteins from immature rice seeds. We demonstrate that at least six protein-DNA complexes are formed between the 5' flanking sequence of pGL5-1 (-677 to -45) and nuclear protein factors. By subsequent DNase I-footprinting analyses we defined several protein-binding regions. Two of the protein-binding sequences contain the TGAGTCA motif, which is also present in the -300 element found in the 5' flanking sequences of several storage protein genes of other crop plants, and to which the transcription factors jun and GCN4 bind.

Resolution and partial characterization of factors required for in vitro transcription by mammalian RNA polymerase II.

Multiple protein factors from HeLa cells are necessary for the accurate initiation of transcription on minimal promoters in vitro. We have partially purified these factors by chromatographic methods. In addition to RNA polymerase II, six factors A-F (FA, FB, FC, FD, FE, and FF) necessary for initiation at the beta-globin promoter start site in vitro have been identified. Certain of these (FA, FC, and FE) have been purified to near homogeneity. The present purification scheme yields sufficient amounts of purified material for the more detailed characterization and cloning of the genes for these activities. Among these factors, FD and FF were required with template DNA at an early step of formation of the initiation complex, whereas FB, FA together with FC, and FE were effective when added at successively later stages in the process of complex formation.

Regulation of human fetal hemoglobin gene expression.

An understanding of the mechanism involved in the regulated expression of the human gamma and beta globin genes requires the detailed definition of the cis-acting DNA sequences and trans-acting protein factors responsible for their developmental stage specific expression. To determine the critical cis-acting elements, hybrid genes containing elements of the gamma and beta globin genes were transfected into K562 cells, a human erythroleukemia line. The regulated expression of the gamma and beta genes was also studied by transferring hybrid genes containing the gamma or beta promoters linked to the neomycin resistance gene (neoR) into erythroid (K562) cells and nonerythroid (Hela) cells. DNA sequences found to be important to the expression of the gamma gene were assayed for the presence of transacting factors by studying the binding of protein factors using the gel mobility shift assay. The results suggest that there are multiple cis-acting elements 5' and 3' to the gamma and beta genes, and perhaps within these genes contributing to their regulation. In addition, there are multiple trans-acting protein factors interacting with these regions which may determine their transcriptional regulation in erythroid cells.

Yeast GCN4 transcriptional activator protein interacts with RNA polymerase II in vitro.

Regulated transcription by eukaryotic RNA polymerase II (Pol II) requires the functional interaction of multiple protein factors, some of which presumably interact directly with the polymerase. One such factor, the yeast GCN4 activator protein, binds to the upstream promoter elements of many amino acid biosynthetic genes and induces their transcription. Through the use of affinity chromatography involving GCN4- or Pol II-Sepharose columns, we show that GCN4 interacts specifically with Pol II in vitro. Purified Pol II is retained on the GCN4-Sepharose column under conditions in which the vast majority of proteins flow through. Moreover, Pol II can be selectively isolated from more complex mixtures of proteins. Conversely, GCN4 protein, synthesized in vitro or in Escherichia coli, specifically binds to the Pol II-Sepharose column under equivalent conditions. Using deletion mutants, we also show that the DNA-binding domain of GCN4 is both necessary and sufficient for this interaction. We suggest the possibility that this GCN4-Pol II interaction may be important for transcription in vivo.