Transcription. Opening the gateway

Analysis of Giardia lamblia Nucleolus as Drug Target: A Review

Giardia lamblia (G. lamblia) is the main causative agent of diarrhea worldwide, affecting children and adults alike; in the former, it can be lethal, and in the latter a strong cause of morbidity. Despite being considered a predominant disease in low-income and developing countries, current migratory flows have caused an increase in giardiasis cases in high-income countries. Currently, there is a wide variety of chemotherapeutic treatments to combat this parasitosis, most of which have potentially serious side effects, such as genotoxic, carcinogenic, and teratogenic. The necessity to create novel treatments and discover new therapeutic targets to fight against this illness is evident. The current review centers around the controversial nucleolus of G. lamblia, providing a historical perspective that traces its apparent absence to the present evidence supporting its existence as a subnuclear compartment in this organism. Additionally, possible examples of ncRNAs and proteins ubiquitous to the nucleolus that can be used as targets of different therapeutic strategies are discussed. Finally, some examples of drugs under research that could be effective against G. lamblia are described.

Strong deformations of DNA: Effect on the persistence length

Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of many important biological processes. In this paper we review an approach to calculate the persistence length of the double helix by taking into account the formation of kinks of arbitrary configuration. The reviewed approach improves the Kratky-Porod model to determine the type and nature of kinks that occur in the double helix, by measuring a reduction of the persistence length of the kinkable DNA.

Modeling B-a transformations of the DNA double helix

An approach to the description of DNA conformational transformations of B-A type is presented. Due to the consideration of joint motions of DNA structural elements the model for DNA transformation is constructed in the two-component form. One component is the degree of freedom of the elastic rod, and another component - the effective coordinate of the conformational transformation. In the model the internal and external components are interrelated, as it is characteristic for DNA B-A rearrangements. It is demonstrated that kinetic energy of the double helix transformations of heterogeneous DNA can be put in homogeneous form. In the frame of the developed approach the possible localized excitations in a static state are found to compare with the experiments on DNA B-A deformability. The comparison shows good qualitative agreement between theory and experiment. The conclusion is made that the found excitations in the DNA structure may be classified as static conformational solitons, and that such localized excitations may play the key role in the mechanisms of DNA intrinsic bending.

Marked stepwise differences within a common kinetic mechanism characterize TATA-binding protein interactions with two consensus promoters

Binding of the TATA-binding protein (TBP) to promoter DNA bearing the TATA sequence is an obligatory initial step in RNA polymerase II transcription initiation. The interactions of Saccharomyces cerevisiae TBP with the E4 (TATATATA) and adenovirus major late (TATAAAAG) promoters have been modeled via global analysis of kinetic and thermodynamic data obtained using fluorescence resonance energy transfer. A linear two-intermediate kinetic mechanism describes the reaction of both of these consensus strong promoters with TBP. Qualitative features common to both interactions include tightly bound TBP-DNA complexes with similar solution geometries, simultaneous DNA binding and bending, and the presence of intermediate TBP-DNA conformers at high mole fraction throughout most of the reaction and at equilibrium. Despite very similar energetic changes overall, the stepwise entropic and enthalpic compensations along the two pathways differ markedly following the initial binding/bending event. Furthermore, TBP-E4 dissociation ensues from both replacement and displacement processes, in contrast to replacement alone for TBP-adenovirus major late promoter. A model is proposed that explicitly correlates these similarities and differences with the sequence-specific structural properties inherent to each promoter. This detailed mechanistic comparison of two strong promoters interacting with TBP provides a foundation for subsequent comparison between consensus and variant promoter sequences reacting with TBP.

Tetracycline repressor, tetR, rather than the tetR-mammalian cell transcription factor fusion derivatives, regulates inducible gene expression in mammalian cells

This article describes the first (to our knowledge) tetracycline-inducible regulatory system that demonstrates that the tetracycline repressor (tetR) alone, rather than tetR-mammalian cell transcription factor fusion derivatives, can function as a potent trans-modulator to regulate gene expression in mammalian cells. With proper positioning of tetracycline operators downstream of the TATA element and of human epidermal growth factor (hEGF) as a reporter, we show that gene expression from the tetracycline operator-bearing hCMV major immediate-early enhancer-promoter (pcmvtetO) can be regulated by tetR over three orders of magnitude in response to tetracycline when (1) the reporter was cotransfected with tetR-expressing plasmid in transient expression assays, and (2) the reporter unit was stably integrated into the chromosome of a tetR-expressing cell line. This level of tetR-mediated inducible gene regulation is significantly higher than that of other repression-based mammalian cell transcription switch systems. In an in vivo porcine wound model, close to 60-fold tetR-mediated regulatory effects were detected and it was reversed when tetracycline was administered. Collectively, this study provides a direct implementation of this tetracycline-inducible regulatory switch for controlling gene expression in vitro, in vivo, and in gene therapy.

A sequence based computational identification of a Drosophila developmentally regulated TATA-less RNA polymerase II promoter and its experimental validation

Many RNA polymerase II promoters lack the characteristic TATA box sequence located -25/-30 nucleotides upstream from the transcription start. In Drosophila, half of the promoters identified so far are TATA-deficient. The yemanuclein-alpha gene whose promoter activity is restricted to oogenesis, falls in this class. A number of upstream and downstream promoter elements have been identified for some TATA-less promoters. The yem-alpha promoter contains none of the consensus elements identified so far. Our work was based on the assumption that the physical parameters of the DNA could be used to predict the location of the yem-alpha promoter. A sequence based computational analysis allowed us to determine the characteristic changes of DNA curvature and helix stability in the presumptive regulatory region. Our experimental data were in good agreement with the computational analysis. We have started to investigate the general value of this approach by analyzing other promoters.

The role of the Ikaros gene in lymphocyte development and homeostasis

The Ikaros gene, which encodes a family of hemopoietic-specific zinc finger proteins, is described as a central regulator of lymphocyte differentiation. During fetal development, it is required at the earliest stage of T cell and B cell specification. In the adult, however, lymphoid lineages rely on Ikaros at distinct phases of their development. Its activity is essential for the generation of B cell but not of T cell precursors, although the differentiation of the latter is not normal. A significant increase in CD4 thymocytes and their immediate precursors is detected, and because these cells lack markers that correlate with positive selection, a deregulation in their maturation process is suggested. Furthermore, Ikaros-null thymocytes hyperproliferate in response to T cell receptor (TCR) signaling; within days after their appearance in the thymus, clonally expanding populations are detected. Deregulated TCR-mediated responses and the fast kinetics of tumor development in these mutant thymocytes implicate Ikaros as a central tumor suppressor gene for the T cell lineage. In addition, lack of natural killer cells and selective defects in gamma delta T cells and dendritic antigen-presenting cells point to Ikaros as an essential factor for the establishment of early branchpoints of the T cell pathway. The dominant interference activity of Ikaros isoforms unable to bind DNA and their effects in lymphocyte development suggest that Ikaros works in concert with other factors. The role of Aiolos, a lymphoid-restricted and structurally related gene, in lymphoid differentiation is discussed. A model is proposed that defines Ikaros as the backbone of a complex regulatory protein network that controls cell fate decisions and regulates homeostasis in the hemo-lymphoid system. Changes in this regulatory network may reflect differentiation and proliferation adjustments made in hemo-lymphoid progenitors and precursors as they give rise to the cells of our immune system.

The transcriptional apparatus required for mRNA encoding genes in the yeast Saccharomyces cerevisiae emerges from a jigsaw puzzle of transcription factors

The number of identified yeast factors involved in transcription has dramatically increased in recent years and the understanding of the interplay between the different factors has become more and more puzzling. Transcription initiation at the core promoter of mRNA encoding genes consisting of upstream, TATA and initiator elements requires an approximately ribosome-sized complex of more than 50 polypeptides. The recent identification and isolation of an RNA polymerase holoenzyme which seems to be preassembled before interacting with a promoter allowed a better understanding of the roles, assignments and interplays of the various constituents of the basal transcription machinery. Recruitment of this complex to the promoter is achieved by numerous interactions with a variety of DNA-bound proteins. These interactions can be direct or mediated by additional adaptor proteins. Other proteins negatively affect transcription by interrupting the recruitment process through protein-protein or protein-DNA interactions. Some basic features of cis-acting elements, the transcriptional apparatus and various trans-acting factors involved in the initiation of mRNA synthesis in yeast are summarized.

Analysis of co-crystal structures to identify the stereochemical determinants of the orientation of TBP on the TATA box

Possible stereochemical determinants of the orientation of TBP on the TATA box are discussed using the crystal coordinates of TBP-TATA complexes, which have been determined by other groups. The C-terminal half of the TBP beta-sheet interacts with the TATA site of the DNA, and the N-terminal half with the A-rich site, so that the two sites with distinct curvatures produce a unique fit. Although chemical contacts take place between one side of the beta-sheet and the DNA minor groove, the interaction seems to be facilitated indirectly by the characteristics of the other side of the beta-sheet and the DNA major groove. Thus, Ala71, Leu162 and Pro190 differentiate the curvature of the beta-sheet in the N- and C-halves. The methyl positions in the DNA major groove modulate the bendability of the two DNA sites by using differences in the rolling capacity of TA and AT compared with PyT, and in the shifting capacity of AT compared with TT. The deformations of the first steps (TA and PyT) in the two sites are the largest and thus are important for the overall bending of the DNA. The differences between the two DNA sites are greatest at the second steps (AT and TT) and so these are important for determining the orientation of TBP.

TATA elements direct bi-directional transcription by RNA polymerases II and III

Eukaryotic promoter elements specify the direction and efficiency of transcription, as well as the type of RNA polymerase to be used. One such element, the TATA box, is thought to participate in determining the direction of transcription and can function within promoters for RNA polymerase II or III, depending on the sequence context. In this report the ability of four different TATA boxes to support transcription in vitro was determined. It was found that TATA elements are not directional. However, they support transcription by RNA polymerases II and III. An upstream activating sequence was found to stimulate downstream transcription by RNA polymerase II and to inhibit upstream transcription by RNA polymerases II and III. Thus a promoter necessarily consists of a TATA element and upstream sequences in order to specify the direction of transcription and the type of polymerase to be used.

Role of base-backbone and base-base interactions in alternating DNA conformations

Sequence-specific conformational differences between dinucleotide steps are characterised using published crystal coordinates with special attention to steric hindrance of the methyl group of a T base to the neighbouring base, and, more importantly, to the sugar-phosphate backbone. The TT step is inflexible and B-like, as it has two methyl groups which interlock with each other and with the sugar-phosphate backbones. AT slides, or overtwists, so that the methyl groups move away from the backbones, both lead the step towards the A-conformation. TA is most flexible as it does not have such restriction. These characteristics are observed with other pyrimidine-pyrimidine, pyrimidine-purine, purine-pyrimidine steps, respectively, but to less extent, depending on the number of non-A:T basepairs in the steps.

A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein

The structure of the TATA-box bound to the TATA-binding protein revealed a new and unexpected deformation of the double helix leading to a sharp change in the DNA trajectory. Here we show that the deformation imposed upon the TATA-box represents a novel form of the double helix--named TA-DNA--which differs from A-DNA by a single conformational parameter, namely the rotation around the glycosidic bond. This rotation causes a 50 degrees inclination of the base pairs in the TATA-box which in turn results in abrupt change in the trajectory of the flanking B-DNA segments. The observation that the TATA sequence can assume an A-DNA conformation coupled to the simplicity of the transition from A-DNA to TA-DNA may be the reason for the presence of the TATA sequence in a wide range of promoters.

Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays

The structural polymorphism of DNA is a vital aspect of its biological function. However, it has become increasingly apparent in recent years that DNA polymorphism is a complicated, multidimensional phenomenon that includes not only static sequence-directed structures but dynamic effects as well, including influences of counterions and sequence context. In order to address some of these additional factors that govern DNA conformation, we have used T4 ligase-mediated cyclization to investigate bending in a series of DNA sequences containing the GGGCCC.GGGCCC motif in different sequence contexts including various helical phasings with (A)5-tracts. We present evidence for curvature in GGGCCC.GGGCCC and (A)5-tract motifs in the presence of physiological levels of Mg2+ and show that these motifs curve through similar but oppositely directed bending angles under these ionic strength conditions. Although these two sequence motifs appear to bend similarly, our results suggest significant differences in stiffness and stability of curvature between them. We also show that under the same experimental conditions, the CTAG-CTAG sequence element possesses unusual torsional flexibility and that this appears to be associated with the central TA.TA dinucleotide. The results underscore the need to include sequence context and specific ion effects as well as a dynamic basis in more complete predictive models for functionally related DNA polymorphism.

An inverted TATA box directs downstream transcription of the bone sialoprotein gene

The orientation of the TATA box is thought to direct downstream transcription of eukaryotic genes by RNA polymerase II. However, the putative TATA box in the promoter of the bone sialoprotein (BSP) gene, which codes for a tissue-specific and developmentally regulated bone matrix protein, is inverted (5'-TTTATA-3') relative to the consensus TATA box sequence (5'-TATAAA-3') and is overlapped by a vitamin D3-response element. Here we show that the inverted TATA sequence in the rat BSP gene binds to recombinant TATA-box-binding protein (TBP) with an affinity similar to that observed with the consensus TATA box, and site-directed point mutations in the inverted TATA sequence (mutating TTTATA into TCTCTA) abrogate both TBP binding and BSP promoter activity. However, when the inverted TATA sequence is changed to a canonical TATAAA, the TBP- and vitamin D3 receptor-binding properties together with the BSP promoter activity are retained. In addition, we found that the TBP is required to reconstitute in vitro transcription driven by the BSP promoter. These studies, which have revealed a naturally occurring inverted TATA box that can bind TBP and direct downstream transcription, demonstrate that the orientation of the TATA box does not determine the direction of transcription in higher eukaryotic genes. Consequently, the inverted TATA box that is conserved in the human, rat and mouse BSP gene promoters will provide an excellent in vivo model to investigate the polarity of the transcription factor IID-DNA complex and its relation to downstream transcription.

TBP binding to the TATA box induces a specific downstream unwinding site that is targeted by pluramycin

BACKGROUND

The TATA-binding protein (TBP) is one of the major components of the human TFIID multiprotein complex. It is important in directing the initiation of RNA transcription at a site immediately downstream of the TATA sequence (TATA box) found in many eukaryotic promoters. The crystal structure of TBP complexed with an oligonucleotide containing the TATA box revealed a protein with an approximate two-fold symmetry which apparently has symmetrical interactions with DNA. It is not known how an asymmetric effect involving downstream activation can be produced by an apparent symmetric complex. We set out to examine the state of DNA in the TBP-DNA complex using pluramycin, a small molecular weight probe of DNA accessibility.

RESULTS

Binding of TBP to the TATA box facilitates intercalation of pluramycin at a defined site immediately downstream of the TATA sequence through an apparent transient unwinding of the DNA. Pluramycin adducts are detected by the production of DNA strand breakage products upon heating. Incubation of pluramycin with the TBP-DNA complex facilitates the trapping of the specific complex by intercalation. Gel mobility shift and circularization assays reveal that the binding of pluramycin on the 3'-side of the TATA box region considerably stabilizes the TBP-DNA complex.

CONCLUSIONS

We propose that the TBP-DNA-pluramycin ternary complex is a 'specific' binding mode in which TBP and pluramycin make compensatory alterations in DNA, accounting for the improved stability of the ternary complex. We also propose a model of the ternary complex that explains the observed asymmetric effect of TBP binding to the TATA box.

Gene regulatory proteins and their interaction with DNA

The selective expression of a gene is achieved through the interaction of protein transcription factors with characteristic DNA sequences located in the regulatory region of the gene, which is usually distinct from the coding region. These proteins contain domains that bind specifically to the DNA sites (or response elements). Some general principles in the design of these DNA-binding domains are described, followed by examples of the different structural classes discovered so far and how they recognize their binding sites.

Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II

The mechanisms that govern core promoter recognition and basal transcription efficiency remain poorly understood. Here, we have assessed the potential role of TAFs and the TFIID complex in directing basal promoter function. Reconstituted transcription reactions revealed the ability of TFIID versus TBP to discriminate between distinct core promoters. A comparison of different partial TBP-TAF assemblages established that a trimeric TBP-TAFII250-TAFII150 complex is minimally required for efficient utilization of the initiator and downstream promoter elements. Depending on the promoter structure, TAFs can increase or decrease the stability of TFIID-promoter interactions. These findings suggest that TAFs play a critical role in promoter selectivity and transcription regulation through direct contacts with core promoter elements.

Stereochemical basis of DNA bending by transcription factors

Superstructure-formation of DNA plays an important role in transcription regulation as well as in chromatin formation. To understand the stereochemical basis of DNA bending by proteins we analysed the structural characteristics of dinucleotide steps which occur at the site where DNA is bent upon binding a transcription factor. When DNA is considerably bent in a crystal structure the bending is not spread smoothly over a length, but the DNA is kinked at a pair of crucial steps which are highly rolled and untwisted. These rolled steps are spaced 6-10 bp apart and are predominantly occupied by pyrimidine-purine sequences. In association with another dinucleotide step at the centre, which combines 6 bp-spaced rolled steps towards the same side of the DNA, these produce two essentially different types of DNA bending.

The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides

Crystallographic, isotopic labeling nmr and transferred nuclear Overhauser effect studies have highlighted the extended conformation as a very important element of secondary structure at the binding site of many peptide/protein complexes including peptide inhibitors-enzymes, B-cell epitopes-antibodies, and T-cell epitopes-major histocompatibility complex (MHC) of class I and II complexes. This paper discusses the peptide ligand conformation consequences of these findings particularly in view of the identification of the PII conformation (left-handed extended polyproline II) in free solution.

Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators

We previously reported that transcriptional regulators can bind selected TAF subunits of the TFIID complex. However, the specificity and function of individual TAFs in mediating transcriptional activation remained unknown. Here we report the in vitro assembly and transcriptional properties of TBP-TAF complexes reconstituted from the nine recombinant subunits of Drosophila TFIID. A minimal complex containing TBP and TAFII250 directs basal but not activator-responsive transcription. By contrast, reconstituted holo-TFIID supports activation by an assortment of activators. The activator NTF-1, which binds TAFII150, stimulates transcription with a complex containing only TBP, TAFII250, and TAFII150, whereas Sp1 binds and additionally requires TAFII110 for activation. Interestingly, TAFII150 enhances Sp1 activation even though this subunit does not bind directly to Sp1. These results establish that specific subcomplexes of TFIID can mediate activation by different classes of activators and suggest that TAFs perform multiple functions during activation.

2.1 A resolution refined structure of a TATA box-binding protein (TBP)

The three-dimensional structure of a TATA box-binding protein (TBP2) from Arabidopsis thaliana has been refined at 2.1 A resolution. TBPs are general eukaryotic transcription factors that participate in initiation of RNA synthesis by all three eukaryotic RNA polymerases. The carboxy-terminal portion of TBP is a unique DNA-binding motif/protein fold, adopting a highly symmetric alpha/beta structure that resembles a molecular saddle with two stirrup-like loops. A ten-stranded, antiparallel beta-sheet provides a concave surface for recognizing class II nuclear gene promoters, while the four amphipathic alpha-helices on the convex surface are available for interaction with other transcription factors. The myriad interactions of TBP2 with components of the transcription machinery are discussed.

Transcription factors and the regulation of haemopoiesis: lessons from GATA and SCL proteins

One of the central issues of developmental biology concerns the molecular mechanisms whereby a multipotent cell gives rise to distinct differentiated progeny. Differences between specialised cell types reflect variations in their patterns of gene expression. The regulation of transcription initiation is an important control point for gene expression and it is, therefore, not surprising that transcription factors play a pivotal role in mammalian development and differentiation. Haemopoiesis offers a uniquely tractable system for the study of lineage commitment and differentiation. The importance of transcription factors in the normal regulation of haemopoiesis is underlined by the frequency with which transcription factors are targeted by leukaemogenic mutations. Studies of the function and regulation of haemopoietic transcription factors, especially those expressed in lineage-restricted patterns, should greatly increase our understanding of the molecular control of haemopoiesis. In this review we have focused on insights provided by recent studies of the GATA and SCL proteins.

TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs

In this report, we test the hypothesis that TBP binds DNA promiscuously due to its manner of recognition of the DNA minor groove. The experiment performed was to select TBP-binding sequences from a pool of random double stranded oligonucleotides. Sixty two clones from this pool were sequenced. Surprisingly, the results show that TBP has a marked preference for stably binding one sequence (TATATAA) over all others, yet only four classes of TATA box were selected. The features of the selected sequences allow definition of a binding consensus for TBP. The DNA binding properties of TBP to the four TATA variants was examined, the results being in accord with the observed selection frequencies. However, the nature of TBP-DNA binding is strongly affected by ionic strength. We infer that recognition of DNA via the minor groove can be highly selective even where A:T and T:A discrimination is required. Models for how this might be accomplished are discussed.

Co-chairman's remarks: protein designs for the specific recognition of DNA

The selective expression of a gene is achieved through the interaction of protein transcription factors with characteristic nucleotide sequences located in the regulatory region of the gene, which is usually distinct from the coding region. These proteins contain domains which bind specifically to the DNA sites (or response elements). Some general principles in the design of these DNA-binding domains are described, followed by examples of the different structural classes discovered so far and how they recognise their binding sites.