Specific protein-DNA Interactions Research Articles

The 48 bp centromeric repeat is a functionally conserved motif in great apes and man showing protein-binding properties.

The centromere-kinetochore complex is a chromosomal assembly site including repeat motifs and protein binding properties thus mediating chromosome motility and mitotic regulation. Next to the alpha-satellite DNA family as well as human satellite III DNA, contribution of other repetitive sequences has to be strongly considered in centromere function. Here, we report the identification of centromeric 48 bp motifs, isolated from chimpanzee and orang-utan using an orthologous human DNA probe. Applying Southern hybridization we show that these sequences are restricted to hominoid species. Diminishing hybrid formation in gibbons suggested that the 48 bp repeat originated approximately 25-20 million years ago. Consistently, both chimpanzee as well as human repeat probes failed to generate any hybridization signal with the monkey species Cercopithecus aethiops and Aotes trivirgatus. Sequence deviations from the consensus of human repeat monomers of 6% and 10.4% in chimpanzee and orang-utan, respectively, were found within a 16 bp region of the 48 bp repeat units. Gel mobility shift assays using chimpanzee repeat dimers as probes revealed peptide-binding properties with human and chimpanzee nuclear extracts. Species-specific DNA-protein complexes remained unaffected by competition studies and indicated the presence of at least one novel interacting protein consisting of two subunits with 90 and 95 kDa. Our data suggest that the 48 bp repeat, next to alpha-satellite DNA, provides essential sequence information for specific DNA-protein interaction and they imply phylogenetic conservation of these binding properties in primates. The complex is likely involved in the proper formation and/or function of mammalian centromeres.

Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.

Restriction-modification (RM) systems comprise two opposing enzymatic activities: a restriction endonuclease, that targets specific DNA sequences and performs endonucleolytic cleavage, and a modification methyltransferase that renders these sequences resistant to cleavage. Studies on molecular genetics and biochemistry of RM systems have been carried out over the past four decades, laying foundations for modern molecular biology and providing important models for mechanisms of highly specific protein-DNA interactions. Although the number of known, relevant sequences 3D structures of RM proteins is growing steadily, we do not fully understand their functional diversities from an evolutionary perspective and we are not yet able to engineer new sequence specificities based on rational approaches. Recent findings on the evolution of RM systems and on their structures and mechanisms of action have led to a picture in which conserved modules with defined function are shared between different RM proteins and other enzymes involved in nucleic acid biochemistry. On the other hand, it has been realized that some of the modules have been replaced in the evolution by unrelated domains exerting similar function. The aim of this review is to give a survey on the recent progress in the field of structural phylogeny of RM enzymes with special emphasis on studies of sequence-structure-function relationships and emerging potential applications in biotechnology.

Characterization of human cathepsin L promoter and identification of binding sites for NF-Y, Sp1 and Sp3 that are essential for its activity

Cathepsin L is a cysteine protease whose overexpression in human melanoma cells increases their tumorigenicity and switches their phenotype from non-metastatic to highly metastatic. Regulation of the transcription of the gene encoding human cathepsin L has not been yet studied and only preliminary data exist on the promoter regulation of the gene encoding rodent cathepsin L. In the present study we identified molecular elements involved in the transcriptional regulation of human cathepsin L in melanoma cells. The sequence of the 5′-flanking region of the gene encoding human cathepsin L was determined up to 3263bp upstream of the translation start site. The major transcription intiation site was located. Three mRNA splice variants, differing in their 5′ untranslated ends, were identified. Regulatory regions crucial for cathepsin L promoter activity were characterized between −1489 and −1646bp. In this region, two GC boxes (−1590/−1595 and −1545/−1550) and a CCAAT motif (−1571/−1575) were involved in specific DNA–protein interactions. An electrophoretic mobility-shift assay demonstrated that Sp1 and Sp3 transcription factors bound to these GC boxes, and only the transcription factor nuclear factor Y (NF-Y) bound to the CCAAT motif. Mutagenesis studies demonstrated that these binding sites contributed at least 85% of cathepsin L promoter activity. Thus structural and functional analysis demonstrated that binding sites for NF-Y, Sp1 and Sp3 are essential for transcription of the gene encoding human cathepsin L in melanoma cells.

Characterization of human cathepsin L promoter and identification of binding sites for NF-Y, Sp1 and Sp3 that are essential for its activity.

Cathepsin L is a cysteine protease whose overexpression in human melanoma cells increases their tumorigenicity and switches their phenotype from non-metastatic to highly metastatic. Regulation of the transcription of the gene encoding human cathepsin L has not been yet studied and only preliminary data exist on the promoter regulation of the gene encoding rodent cathepsin L. In the present study we identified molecular elements involved in the transcriptional regulation of human cathepsin L in melanoma cells. The sequence of the 5'-flanking region of the gene encoding human cathepsin L was determined up to 3263 bp upstream of the translation start site. The major transcription intiation site was located. Three mRNA splice variants, differing in their 5' untranslated ends, were identified. Regulatory regions crucial for cathepsin L promoter activity were characterized between -1489 and -1646 bp. In this region, two GC boxes (-1590/-1595 and -1545/-1550) and a CCAAT motif (-1571/-1575) were involved in specific DNA-protein interactions. An electrophoretic mobility-shift assay demonstrated that Sp1 and Sp3 transcription factors bound to these GC boxes, and only the transcription factor nuclear factor Y (NF-Y) bound to the CCAAT motif. Mutagenesis studies demonstrated that these binding sites contributed at least 85% of cathepsin L promoter activity. Thus structural and functional analysis demonstrated that binding sites for NF-Y, Sp1 and Sp3 are essential for transcription of the gene encoding human cathepsin L in melanoma cells.

A New Analytical Scale DNA Affinity Binding Assay for Analyses of Specific Protein–DNA Interactions

We describe a rapid analytical assay for identification of proteins binding to specific DNA sequences. The DAPSTER assay (DNA affinity preincubation specificity test of recognition assay) is a DNA affinity chromatography-based microassay that can discriminate between specific and nonspecific protein–DNA interactions. The assay is sensitive and can detect protein–DNA interactions and larger multicomponent complexes that can be missed by other analytical methods. Here we describe in detail the optimization and utilization of the DAPSTER assay to isolate AP-1 complexes and associated proteins in multimeric complexes bound to the AP-1 DNA element.

Functional analysis of promoter sequences of cephalosporin C biosynthesis genes from Acremonium chrysogenum: specific DNA-protein interactions and characterization of the transcription factor PACC.

An analysis of the pcbC promoter from the cephalosporin C-producing filamentous fungus Acremonium chrysogenum was performed using fungal transformants carrying reporter gene fusions. By investigating sequential deletion derivatives of the pcbC promoter region, a DNA fragment was identified, which is responsible for transcriptional activation of the pcbC gene. Sequence analysis of this fragment revealed a consensus binding site for the fungal transcription factor PACC. Gel-retardation experiments with crude extracts of A. chrysogenum confirmed the specific binding of a protein to the PACC binding site. The subsequent cloning of the pacC homolog from A. chrysogenum allowed the identification of an ORF of 621 amino acids encoded by four exons. The polypeptide shows about 35% sequence identity to other fungal PACC proteins. A PACC protein fragment synthesized in E. coli was used for in vitro binding assays, and specific binding of the zinc-finger transcription factor to its consensus binding sites in the promoter regions of four cephalosporin C biosynthesis genes could be demonstrated. The bi-directional promoters of the genes pcbAB-pcbC and cefEF-cefG contain two PACC binding sites each. The data obtained strongly suggest that, in A. chrysogenum, the zinc-finger transcription factor PACC is involved in the transcriptional regulation of the genes involved in cephalosporin C biosynthesis.

Binding Assays by the Genome

In the cell, proteins bind to DNA elements to regulate such processes as transcription, replication, and chromosome condensation and cohesion. Many recent studies have tried to elucidate the various mechanisms involved in these processes, including specific protein-DNA interactions. For these analyses, researchers have widely used the techniques of chromatin immunoprecipitation analysis and DNA microarrays to examine protein-DNA interactions and gene expression levels, respectively. Ren et al. have now combined these two methods to monitor in vivo protein-DNA interactions across the entire yeast genome. This genome-wide location analysis method was used to characterize two transcriptional activators Gal4 and Ste12. These techniques should allow for a more detailed understanding of global regulatory networks. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T.L., Wilson, C.J., Bell, S.P., and Young, R.A. (2000) Genome-wide location and function of DNA binding proteins. Science 290 : 2306-2309. [Abstract] [Full Text]

Electrophoretic mobility shift assays for the analysis of DNA-protein interactions.

AbstractSeveral nuclear mechanisms involve specific DNA-protein interactions. The electrophoretic mobility shift assay (EMSA, also known as the gel mobility shift or gel retardation assay), first described almost two decades ago (1,2), provides a simple, efficient and widely used method to study such interactions. Its ease of use, its versatility, and especially its high sensitivity (10−18 mol of DNA [2]) make it a powerful method that has been successfully used in a variety of situations not only in gene regulation analyzes but also in studies of DNA replication, repair, and recombination. Although very useful for qualitative purposes, EMSA has the added advantage of being suitable for quantitative and kinetic analyzes (3). Furthermore, because of its very high sensitivity, EMSA makes it possible to resolve complexes of different protein or DNA stoichiometry (4) and even to detect conformational changes.KeywordsElectrophoretic Mobility Shift AssayLabel ProbeDialysis TubingPlastic WrapCalf Intestinal Alkaline PhosphataseThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Interaction of CBFα/AML/PEBP2α Transcription Factors with Nucleosomes Containing Promoter Sequences Requires Flexibility in the Translational Positioning of the Histone Octamer and Exposure of the CBFα Site

Chromatin remodeling at eukaryotic gene promoter sequences accompanies transcriptional activation. Both molecular events rely on specific protein-DNA interactions that occur within these promoter sequences. Binding of CBFalpha/AML/PEBP2alpha (core binding factor alpha/acute myelogenous leukemia/polyoma enhancer binding protein 2alpha) proteins is a key event in both tissue-specific and developmentally regulated osteocalcin (OC) promoter activity. To address linkage between chromatin organization and transcription factor binding, we reconstituted segments of the rat OC gene proximal promoter into mononucleosomes and studied binding of CBFalpha proteins. We analyzed binding of bacterially produced Cbfalpha2Alpha and Cbfalpha2B, two splice variants of the human CBFalpha2 gene, and determined the effect of heterodimerization with the Cbfbeta subunit on binding activity. Our results indicate that binding of the truncated Cbfalpha2A protein to naked DNA is independent of Cbfbeta whereas Cbfalpha2A binding to nucleosomal DNA was enhanced by Cbfbeta. In contrast, the Cbfalpha2B interaction with either naked or nucleosomal DNA was strongly dependent on heterodimerization with the Cbfbeta subunit. Additionally, our results demonstrate that both Cbfalpha2A alone and Cbfalpha2B complexed with Cbfbeta can interact with nucleosomal DNA only if there is a degree of flexibility in the positioning of the histone octamer on the DNA fragment and exposure of the CBFalpha site. This situation was achieved with a DNA segment of 182 bp from the rat OC promoter that preferentially positions mononucleosomes upstream of the CBFalpha binding site and leaves this element partially exposed. Taken together, these results suggest that nucleosomal translational positioning is a major determinant of the binding of CBFalpha factors to nucleosomal DNA.

Structure and function of the HMGI(Y) family of architectural transcription factors.

The three known members of the HMGI(Y) family of high-mobility group (HMG) mammalian nonhistone nuclear proteins (HMG-I, HMG-Y, and HMGI-C) are thought to participate in numerous biological processes (transcription, replication, retroviral integration, genetic recombination, etc.) by virtue of their ability to recognize and alter the structure of both DNA and chromatin substrates. In vitro and in vivo the HMGI(Y) proteins preferentially bind to the narrow minor groove of stretches of AT-rich DNA by means of highly conserved peptide motifs called AT hooks. In vitro the HMGI(Y) proteins also have the ability to selectively bind to distorted DNA structures and to bend, unwind, and supercoil DNA substrates. Additionally, the HMGI(Y) proteins have the ability to interact with various protein transcription factors both in vitro and in vivo. Specific protein-DNA and protein-protein interactions permit the HMGI(Y) proteins to function as architectural transcription factors that regulate gene expression in vivo by controlling the formation of stereospecific multiprotein complexes on the AT-rich regions of certain gene promoters. Transcriptional overexpression of the HMGI(Y) genes is highly correlated with both cancerous transformation and increased metastatic potential of a number of different cancers, and chromosomal rearrangements involving AT-hook motifs have been associated with various types of benign human mesenchymal tumors. The levels of HMGI(Y) proteins in human cells have been proposed to be sensitive diagnostic indicators of both neoplastic transformation and metastatic progression. Drugs based on the AT-hook motif offer the potential for development of new tumor therapeutic reagents.

Structural and Functional Characterization of Liver Cell-Specific Activity of the Human Sodium/Taurocholate Cotransporter

Bile salts are rapidly removed from the circulation by the liver-specific sodium/taurocholate cotransporter (SLC10A1). To understand factors controlling its liver-specific expression, we isolated human SLC10A1 from a YAC chromosomal clone. SLC10A1 spans ∼23 kb distributed over five exons. The major transcription start site is at 299 bp, and a minor start site is at 395 bp from the translational start site. A 1.2-kb portion of the 5′ flanking region was sequenced and shown to contain a number of liver-enriched elements, but no TATA box. Using secreted alkaline phosphatase reporter constructs liver-specific expression was examined. Transient transfection demonstrated that SLC10A1 promoter expression was selectively expressed eightfold in FAO and rat hepatocytes, while deletion mutants demonstrated liver-specific expression in a region extending from −5 to +198 bp, which contained putative sites for C/EBP and HNF3. Mutations of the C/EBP site resulted in loss of 77% of transcriptional activity. Cotransfection of C/EBP, but not other putative liver-enriched binding factors, increased SLC10A1 promoter activity. Electrophoretic mobility shift assays demonstrated specific protein–DNA interactions that involved C/EBPα and β. These studies demonstrate that the TATA-less human SLC10A1 promoter exhibits liver-specific activity and its regulatory elements contain binding sites for C/EBP, which contributes specifically to its transcriptional regulation.

Involvement of Sp1 and Microsatellite Repressor Sequences in the Transcriptional Control of the Human CD30 Gene

CD30, as a member of the tumor necrosis factor (TNF) receptor family, is expressed on the surface of activated lymphoid cells. CD30 overexpression is a characteristic of lymphoproliferative diseases such as Hodgkin's/non-Hodgkin's lymphomas, embryonal carcinoma, and a number of Th2-associated diseases. The CD30 gene has been mapped to a region of the murine genome that is involved in susceptibility to systemic lupus erythematosus. Functionally, CD30 may play a role in the deletion of autoreactive T cells. We were interested in determining the molecular nature of CD30 overexpression. Sequence comparison has revealed significant identity between the TATA-less human and murine CD30 promoters; they share a number of common consensus binding motifs. Transfection assays identified three regions of transcriptional importance; the region between position -1.2 kb and -336 bp, containing a CCAT microsatellite sequence, a conserved Sp1 site at positions -43 to -38, and a downstream promoter element (DPE) at positions +24 to +29. EMSA and DNase I footprinting showed specific DNA-protein interactions of the CD30 promoter with the Sp1 site and the CCAT repeat region. The DPE element was shown to be essential for start site selection. We conclude that the conserved Sp1 site at -43 to -38 is associated with maximum reporter gene activity, the DPE element is required for start site selection, and the CCAT tetranucleotide repeats act to repress transcription. We also have shown that the microsatellite is multiallelic, when we screened a random healthy population. Further studies are required to determine whether microsatellite instability in the repressor predisposes susceptible individuals to CD30 overexpression.

Characterization of Cre-loxP interaction in the major groove: Hint for structural distortion of mutant Cre and possible strategy for HIV-1 therapy

Although the crystal structure of Cre recombinase complexed with DNA, named loxA, was elucidated a couple of years ago, it has not yet been determined which amino acids of the protein are involved in the specific Cre-loxP interaction. Arg259 and Gln90 interact with DNA substrate in the major groove from which the specificity of protein-DNA interaction comes. In this study, we substituted these residues for other amino acids. Also, two mutated DNA substrates were constructed. In each mutant, one of the bases that interact with Arg259 or Gln90 was changed into another base. In vitro binding assays and recombination assays of variant lox sites with wild-type and mutant-type Cre revealed that Arg259 plays a key role in Cre-loxP binding but Gln90 does not. However, the recombination activity still remained intact, although the binding between Cre and DNA substrate was not ensured.

Interactions of mammalian proteins with cisplatin-damaged DNA

We have undertaken the systematic isolation and characterization of mammalian proteins which display an affinity for cisplatin-damaged DNA. Fractionation of human cell extracts has led to the identification of two classes of proteins. The first includes proteins that bind duplex DNA in the absence of cisplatin damage and retain their affinity for DNA in the presence of cisplatin–DNA adducts. The DNA-dependent protein kinase (DNA-PK) falls into this class. The inhibition of DNA-PK phosphorylation activity by cisplatin-damaged DNA has led to the hypothesis that cisplatin sensitization of mammalian cells to ionizing radiation may be mediated by DNA-PK. The second class of proteins identified are those which display a high relative affinity for cisplatin-damaged DNA and a low affinity for undamaged duplex DNA. Proteins that fall into this class include high mobility group 1 protein (HMG-1), replication protein A (RPA) and xeroderma pigmentosum group A protein (XPA). Each protein has been isolated and purified in the lab. The interaction of each protein with cisplatin-damaged DNA has been assessed in electrophoretic mobility shift assays. A series of DNA binding experiments suggests that RPA binds duplex DNA via denaturation and subsequent preferential binding to the undamaged DNA strand of the partial duplex. DNA substrates prepared with photo-reactive base analogs on either the damaged or undamaged DNA strand have also been employed to investigate the mechanism and specific protein–DNA interactions that occur as each protein binds to cisplatin-damaged DNA. Results suggest both damage and strand specificity for RPA and XPA binding cisplatin-damaged DNA.

An experiment illustrating DNA-protein interactions using nuclear extracts from chicken erythrocytes

The electrophoretic mobility shift assay is a simple and rapid method for visualizing the existence of specific DNA-protein interactions and is a useful teaching experiment. In the experiment described here the students prepare nuclear extracts, a DNA probe, and can successfully produce specific DNA-protein complexes and estimate physicochemical parameters characterizing the interaction. The system described is easy to perform. The synthesis of the oligonucleotides required and the labeled deoxyribonucleotide used for labeling the probe are the main costs of the experiment, but since the synthesized oligonucleotides can be used in several courses and the amount of labeled deoxyribonucleotide required for labeling the probe is small the experiment is relatively inexpensive to put on with a class.

Human Cdc5 controls mitotic entry through specific DNA-protein interactions and is regulated through a mitogen-activated pathway

Human Cdc5 controls mitotic entry through specific DNA-protein interactions and is regulated through a mitogen-activated pathway

Human Cdc5 Controls Mitotic Entry through Specific DNA-Protein Interactions

Human Cdc5 Controls Mitotic Entry through Specific DNA-Protein Interactions

5'-flanking motifs control cell-specific expression of trefoil factor genes (TFF).

A group of secreted peptides (trefoil factor family; TFF) is abundantly expressed at mucosal surfaces of the gastrointestinal tract and promote epithelial restitution. They are upregulated around areas of epithelial damage, ulceration and neoplasia. The transcriptional regulation of the three human TFF genes was assayed by multiplex RT-PCR and reporter gene analysis in 8 gastrointestinal carcinoma cell lines. The level of endogenous mRNA matched well the reporter gene activity of all TFFs, indicating that the cis-acting elements located less than 1,000 bp upstream of the TATAA box account for cell-specific gene expression. In HT-29, the endogenous TFF expression profile changed in relation to cell growth conditions. Deletion and mutation analysis of TFF promoter constructs revealed enhancing elements shared within the three TFF promoters that were shown to bind nuclear proteins. Thus such specific DNA-protein interaction may explain the TFF peptides' cell specific expression pattern and altered levels in pathological conditions.

Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex.

Many biochemical processes, including DNA packing, maintenance and control, rely on non-sequence specific protein-DNA interactions. Nonspecific DNA-binding proteins have evolved to tolerate a wide range of DNA sequences, yet bind with a respectable affinity. The nonspecific binding requirement is in contrast to that imposed on, for example, transcription factors and implies a different structural basis for the biomolecular recognition process. To address this issue, and the mechanism for archaeal DNA packing, we determined the structure of the Sso7d protein from Sulfolobus solfataricus in complex with DNA. Sso7d binds DNA by placing a triple-stranded beta-sheet across the DNA minor groove. The protein is anchored in this position by the insertion of hydrogen bond-donating side chains into the groove and additionally stabilized by electrostatic and non-polar interactions with the DNA backbone. This structure explains how strong binding can be achieved independent of DNA sequence. Sso7d binding also distorts the DNA conformation and introduces significant unwinding of the helix. This effect suggests a mechanism for DNA packing in Sulfolobus based on negative DNA supercoiling.

Regulation of Transcription of the TATA-less Human Complement Component C4 Gene

The 5'-sequences flanking the human complement component C4 genes (C4A and C4B) have been analyzed for their ability to direct expression of a reporter gene in cell lines that constitutively express or do not express C4. No difference in the level of reporter gene expression was detected in cells transfected with C4A- or C4B-specific constructs. A series of reporter constructs containing progressively truncated C4 promoter fragments transfected into the hepatocyte Hep G2 cell line, identified the sequence contained within the region -178 to -39 as that associated with maximal reporter gene expression. This region contains consensus binding motifs for nuclear factor 1 (-110 to -97), Sp1 (-57 to -49), and three basic helix-loop-helix (-137 to -132, -98 to -93, and -78 to -73)-like transcription factors. Electromobility shift assays and DNase I footprinting analysis showed specific DNA-protein interactions of the C4 promoter at the nuclear factor 1, two E box (-98 to -93 and -78 to -73), and Sp1 binding domains. Site-directed mutagenesis of the Sp1 binding site resulted in total abrogation of reporter gene expression and mutation of the E box (-78 to -73) resulted in a 8-fold reduction in expression. We conclude that the Sp1 binding site at position -57 to -49 is critical for accurately initiated, basal transcription of C4.