Evidence for DNA bending at the T7 RNA polymerase promoter

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections

Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally. To address this gap, we developed CHiTA (Cleavage High-Throughput Assay), a high-throughput pipeline utilizing massively parallel oligonucleotide synthesis and next-generation sequencing to test putative ribozymes en masse in a scarless fashion. As proof of principle, we applied CHiTA to a small set of known active and mutant ribozymes. We then used CHiTA to test two large sets of naturally occurring twister ribozymes: over 1, 600 previously reported putative twisters and ∼1, 000 new candidate twisters. The new candidates were identified computationally in ∼1, 000 organisms, representing a massive increase in the number of ribozyme-harboring organisms. Approximately 94% of the twisters we tested were active and cleaved site-specifically. Analysis of their structural features revealed that many substitutions and helical imperfections can be tolerated. We repeated our computational search with structural descriptors updated from this analysis, whereupon we identified and confirmed the first intrinsically active twister ribozyme in mammals. CHiTA broadly expands the number of active twister ribozymes found in nature and provides a powerful method for functional analyses of other RNAs.

GRAPHICAL ABSTRACT

Understanding the impact of in vitro transcription byproducts and contaminants

The success of messenger (m)RNA-based vaccines against SARS-CoV-2 during the COVID-19 pandemic has led to rapid growth and innovation in the field of mRNA-based therapeutics. However, mRNA production, whether in small amounts for research or large-scale GMP-grade for biopharmaceutics, is still based on the In Vitro Transcription (IVT) reaction developed in the early 1980s. The IVT reaction exploits phage RNA polymerase to catalyze the formation of an engineered mRNA that depends on a linearized DNA template, nucleotide building blocks, as well as pH, temperature, and reaction time. But depending on the IVT conditions and subsequent purification steps, diverse byproducts such as dsRNA, abortive RNAs and RNA:DNA hybrids might form. Unwanted byproducts, if not removed, could be formulated together with the full-length mRNA and cause an immune response in cells by activating host pattern recognition receptors. In this review, we summarize the potential types of IVT byproducts, their known biological activity, and how they can impact the efficacy and safety of mRNA therapeutics. In addition, we briefly overview non-nucleotide-based contaminants such as RNases, endotoxin and metal ions that, when present in the IVT reaction, can also influence the activity of mRNA-based drugs. We further discuss current approaches aimed at adjusting the IVT reaction conditions or improving mRNA purification to achieve optimal performance for medical applications.

Flanking Sequence Cotranscriptionally Regulates Twister Ribozyme Activity

Small nucleolytic ribozymes are RNAs that cleave their own phosphodiester backbone. While proteinaceous enzymes are regulated by a variety of known mechanisms, methods of regulation for ribozymes remain unclear. Twister is one ribozyme class for which many structural and catalytic properties have been elucidated. However, few studies have analyzed the activity of twister ribozymes in the context of a native flanking sequence, even though ribozymes as transcribed in nature do not exist in isolation. Interactions between the ribozyme and its neighboring sequences can induce conformational changes that inhibit self-cleavage, providing a regulatory mechanism that could naturally determine ribozyme activity in vivo and in synthetic applications. To date, eight twister ribozymes have been identified within the staple crop rice (Oryza sativa). Herein, we select several twister ribozymes from rice and show that they are differentially regulated by their flanking sequence using published RNA-seq data sets, structure probing, and cotranscriptional cleavage assays. We found that the Osa 1-2 ribozyme does not interact with its flanking sequences. However, sequences flanking the Osa 1-3 and Osa 1-8 ribozymes form inactive conformations, referred to here as "ribozymogens", that attenuate ribozyme self-cleavage activity. For the Osa 1-3 ribozyme, we show that activity can be rescued upon addition of a complementary antisense oligonucleotide, suggesting ribozymogens can be controlled via external signals. In all, our data provide a plausible mechanism wherein flanking sequence differentially regulates ribozyme activity in vivo. More broadly, the ability to regulate ribozyme behavior locally has potential applications in control of gene expression and synthetic biology.

DNA sequence, physics, and promoter function: Analysis of high-throughput data On T7 promoter variants activity

RNA polymerase/promoter recognition represents a basic problem of molecular biology. Decades-long efforts were made in the area, and yet certain challenges persist. The usage of certain most suitable model subjects is pivotal for the research. System of T7 bacteriophage RNA-polymerase/T7 native promoter represents an exceptional example for the purpose. Moreover, it has been studied the most and successfully applied to aims of biotechnology and bioengineering. Both structural simplicity and high specificity of this molecular duo are the reason for this. Despite highly similar sequences of distinct T7 native promoters, the T7 RNA-polymerase enzyme is capable of binding respective promoter in a highly specific and adjustable manner. One explanation here is that the process relies primarily on DNA physical properties rather than nucleotide sequence. Here, we address the issue by analyzing massive data recently published by Komura and colleagues. This initial study employed Next Generation Sequencing (NGS) in order to quantify activity of promoter variants including ones with multiple substitutions. As a result of our work substantial bias in simultaneous occurrence of single-nucleotide sequence alterations was found: the highest rate of co-occurrence was evidenced within specificity loop of binding region while the lowest - in initiation region of promoter. If both location and a kind of nucleotides involved in replacement (both initial and resulting) are taken into consideration, one can easily note that N to A substitutions are most preferred ones across the whole 19 b.p.-long sequence. At the same time, N to C are tolerated only at crucial position in recognition loop of binding region, and N to G are uniformly least tolerable. Later in this work the complete set of variants was split into groups with mutations (1) exclusively in binding region; (2) exclusively in melting region; (3) in both regions. Among these three groups second comprises extremely few variants (at triple-digit rate lesser than in two other groups, 46 versus over one and six thousand). Yet these are all promoter with substantial to high activity. This group two appeared heterogenous by primary sequence; indeed, upon further subdivision into above versus below average activity subgroups first one was found to comprise promoters with negligible conservation at -2 position of melting region; the second was hardly conserved in this region at all. This draws our attention to perfect consensus sequence of class III T7 promoter with -2 nucleotide randomized (all four are present by one to several copies in the previously published source dataset), the picture becomes even more pronounced. We therefore suggest that mutations at the position therefore do not cause significant changes in terms of promoter activity. At the same time, such modifications dramatically change DNA physical properties which were calculated in our study (namely electrostatic potential and propensity to bend). One possible suggestion here is that -2 nucleotide might function as a generic switch; if so, substitution -2A to -2T has important regulatory consequences. The fact that that -2 b.p. is the most evidently different nucleotide between class II versus class III promoters of T7 genome and that it also distinguishes the class III promoter in T7 genome versus promoters of its relative but reproductively isolated bacteriophage T3. In other words, it appears feasible that mutation at -2 nucleotide does not impede promoter activity yet alter its physical properties thus affecting differential RNA polymerase/promoter interaction.

Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by Escherichia coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex

FRET (fluorescence resonance energy transfer) between far-upstream (-100) and downstream (+14) cyanine dyes (Cy3, Cy5) showed extensive bending and wrapping of λP_R promoter DNA on Escherichia coli RNA polymerase (RNAP) in closed and open complexes (CC and OC, respectively). Here we determine the kinetics and mechanism of DNA bending and wrapping by FRET and of formation of RNAP contacts with -100 and +14 DNA by single-dye protein-induced fluorescence enhancement (PIFE). FRET and PIFE kinetics exhibit two phases: rapidly reversible steps forming a CC ensemble ({CC}) of four intermediates [initial (RP_C), early (I_1E), mid (I_1M), and late (I_1L)], followed by conversion of {CC} to OC via I_1L. FRET and PIFE are first observed for I_1E, not RP_c. FRET and PIFE together reveal large-scale bending and wrapping of upstream and downstream DNA as RP_C advances to I_1E, decreasing the Cy3-Cy5 distance to ∼75 Å and making RNAP-DNA contacts at -100 and +14. We propose that far-upstream DNA wraps on the upper β'-clamp while downstream DNA contacts the top of the β-pincer in I_1E. Converting I_1E to I_1M (∼1 s time scale) reduces FRET efficiency with little change in -100 or +14 PIFE, interpreted as clamp opening that moves far-upstream DNA (on β') away from downstream DNA (on β) to increase the Cy3-Cy5 distance by ∼14 Å. FRET increases greatly in converting I_1M to I_1L, indicating bending of downstream duplex DNA into the clamp and clamp closing to reduce the Cy3-Cy5 distance by ∼21 Å. In the subsequent rate-determining DNA-opening step, in which the clamp may also open, I_1L is converted to the initial unstable OC (I₂). Implications for facilitation of CC-to-OC isomerization by upstream DNA and upstream binding, DNA-bending transcription activators are discussed.

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution

We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies. Real-time monitoring of abortive cycling using three-probe analysis showed that the initiation events are stochastically branched into productive and failed transcription. The abortive products are generated primarily from initiation events that fail to progress to elongation, and a majority of the productive events transit to elongation without making abortive products.

Fluorescent methods to study transcription initiation and transition into elongation

The DNA-dependent RNA polymerases induce specific conformational changes in the promoter DNA during transcription initiation. Fluorescence spectroscopy sensitively monitors these DNA conformational changes in real time and at equilibrium providing powerful ways to estimate interactions in transcriptional complexes and to assess how transcription is regulated by the promoter DNA sequence, transcription factors, and small ligands. Ensemble fluorescence methods described here probe the individual steps of promoter binding, bending, opening, and transition into the elongation using T7 phage and mitochondrial transcriptional systems as examples.

Probing allostery through DNA

Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which-together with molecular dynamics simulations-suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.

Differential scanning calorimetric approach to study the effect of melting region upon transcription initiation by T7 RNA polymerase and role of high affinity GTP binding

Transcription initiation by T7 RNA polymerase is a multistep process consisting of the transition from closed to open complex. The promoters of bacteriophage T7 share a consensus sequence of 23 base pairs, from -17 to +6, relative to transcription start site (+1). In the present study, we have characterized T7 RNA polymerase-promoter complexes by means of fluorescence spectroscopy and differential scanning calorimetry. We have examined the effect of high affinity GTP binding upon the equilibrium of the transition from closed to open complex. We have employed the promoter containing 23 base pair consensus sequence and two variants containing Adenine-Thymine and Guanine-Cytosine stretches in the melting region of the promoter sequence. Variation in the nucleotide sequence of melting region does not have any effect upon the affinity of promoter-T7 RNAP complex. On the other hand, alteration of the base sequence in the melting region of the promoter affects the isomerization process among the closed and open complexes. When the initiating nucleotide GTP is prebound to T7 RNA Polymerase, the isomerization process is affected only in case of the promoter with consensus sequence.

Conservation of promoter melting mechanisms in divergent regions of the single-subunit RNA polymerases

The single-subunit RNA polymerases make up a widespread family of proteins found in phage, mitochondria, and chloroplasts. Unlike the phage RNAPs, the eukaryotic RNAPs require accessory factors to melt their promoters and diverge from the phage RNAPs in the regions where functions associated with promoter melting in the latter have been mapped, suggesting that promoter melting mechanisms in the eukaryotic RNAPs diverge from those in the phage enzymes. However, here we show that an element in the yeast mitochondrial RNAP, identified by sequence alignment with the T7 phage RNAP, fulfills a role in promoter melting similar to that filled by the T7RNAP "intercalating hairpin". The yeast mitochondrial RNAP intercalating hairpin appears to be as important in promoter melting as the mitochondrial transcription factor, MTF1, and both a structurally integral hairpin and MTF1 are required to achieve high levels of transcription on a duplex promoter. Deletions from the hairpin also relieve MTF1 inhibition of promoter escape on premelted promoters, likely because such deletions disrupt interactions with the upstream edge of the transcription bubble. These results are consistent with recent structural and functional studies of human mitochondrial RNAP and further reveal the surprising extent of mechanistic conservation between the eukaryotic and phage-encoded members of the single-subunit RNAP family.

Light forces the pace: optical manipulation for biophotonics

The biomedical sciences have benefited immensely from photonics technologies in the last 50 years. This includes the application of minute forces that enable the trapping and manipulation of cells and single molecules. In terms of the area of biophotonics, optical manipulation has made a seminal contribution to our understanding of the dynamics of single molecules and the microrheology of cells. Here we present a review of optical manipulation, emphasizing its impact on the areas of single-molecule studies and single-cell biology, and indicating some of the key experiments in the fields.

Mitochondrial transcription factor Mtf1 traps the unwound non-template strand to facilitate open complex formation

The catalytic subunit of the mitochondrial (mt) RNA polymerase (RNAP) is highly homologous to the bacteriophage T7/T3 RNAP. Unlike the phage RNAP, however, the mtRNAP relies on accessory proteins to initiate promoter-specific transcription. Rpo41, the catalytic subunit of the Saccharomyces cerevisiae mtRNAP, requires Mtf1 for opening the duplex promoter. To elucidate the role of Mtf1 in promoter-specific DNA opening, we have mapped the structural organization of the mtRNAP using site-specific protein-DNA photo-cross-linking studies. Both Mtf1 and Rpo41 cross-linked to distinct sites on the promoter DNA, but the dominant cross-links were those of the Mtf1, which indicates a direct role of Mtf1 in promoter-specific binding and initiation. Strikingly, Mtf1 cross-linked with a high efficiency to the melted region of the promoter DNA, based on which we suggest that Mtf1 facilitates DNA melting by trapping the non-template strand in the unwound conformation. Additional strong cross-links of the Mtf1 were observed with the -8 to -10 base-paired region of the promoter. The cross-linking results were incorporated into a structural model of the mtRNAP-DNA, created from a homology model of the C-terminal domain of Rpo41 and the available structure of Mtf1. The promoter DNA is sandwiched between Mtf1 and Rpo41 in the structural model, and Mtf1 closely associates mainly with one face of the promoter across the entire nona-nucleotide consensus sequence. Overall, the studies reveal that in many ways the role of Mtf1 is analogous to the transcription factors of the multisubunit RNAPs, which provides an intriguing link between single- and multisubunit RNAPs.

The role of SOS boxes in enteric bacteriocin regulation

Bacteriocins are a large and functionally diverse family of toxins found in all major lineages of Bacteria. Colicins, those bacteriocins produced by Escherichia coli, serve as a model system for investigations of bacteriocin structure-function relationships, genetic organization, and their ecological role and evolutionary history. Colicin expression is often dependent on host regulatory pathways (such as the SOS system), is usually confined to times of stress, and results in death of the producing cells. This study investigates the role of the SOS system in mediating this unique form of toxin expression. A comparison of all the sequenced enteric bacteriocin promoters reveals that over 75 % are regulated by dual, overlapping SOS boxes, which serve to bind two LexA repressor proteins. Furthermore, a highly conserved poly-A motif is present in both of the binding sites examined, indicating enhanced affinity of the LexA protein for the binding site. The use of gene expression analysis and deletion mutations further demonstrates that these unique LexA cooperative binding regions result in a fine tuning of bacteriocin production, limiting it to times of stress. These results suggest that the evolution of dual SOS boxes elegantly accomplishes the task of increasing the amount of toxin produced by a cell while decreasing the rate of uninduced production, effectively reducing the cost of colicin production. This hypothesis may explain why such a promoter motif is present at such high frequencies in natural populations of bacteriocin-producing enteric bacteria.

Transcription initiation in a single-subunit RNA polymerase proceeds through DNA scrunching and rotation of the N-terminal subdomains

Elucidating the mechanism of transcription initiation by RNA polymerases (RNAP) is essential for understanding gene transcription and regulation. Although several models, such as DNA scrunching, RNAP translation, and RNAP rotation, have been proposed, the mechanism of initiation by T7 RNAP has remained unclear. Using ensemble and single-molecule Förster resonance energy transfer (FRET) studies, we provide evidence for concerted DNA scrunching and rotation during initiation by T7 RNAP. A constant spatial distance between the upstream and downstream edges of initiation complexes making 4-7 nt RNA supports the DNA scrunching model, but not the RNAP translation or the pure rotation model. DNA scrunching is accompanied by moderate hinging motion (18 degrees +/- 4 degrees ) of the promoter toward the downstream DNA. The observed stepwise conformational changes provide a basis to understand abortive RNA synthesis during early stages of initiation and promoter escape during the later stages that allows transition to processive elongation.

Imaging and analysis of transcription on large, surface-mounted single template DNA molecules

A surface-based approach is described for the transcriptional analysis of large, single DNA molecule templates and their imaged reaction products using RNA polymerase (RNAP). Results demonstrated that surfaces with a charge density supporting stretching of single DNA molecules to 70-80% of their full contour length were ideal for analysis of T7 RNAP transcription complexes on bound single template DNAs. Such DNA molecules were shown to sustain efficient transcription reactions and analysis, which enabled localization of transcription complexes on templates at kilobase resolution. Direct labeling of nascent RNA transcripts by the incorporation of a second fluorochrome into DNA templates promotes more robust and sensitive detection of punctates. Further characterization by RNase digestions, atomic force microscopy studies, and fluoro-immunolabeling revealed a "supercomplex" structure within a punctate where elongation complexes aggregate through entanglement of DNA and RNA strands from individual ternary elongation complexes. We have proposed mechanisms that underlie the supercomplex formation process. Whereas supercomplexes develop naturally in free solution, spatial constraints involved in a topologically limited system where template DNA is bound to the surface may facilitate the assembling process by stalling transcriptional elongation.

Twisted or shifted? Fluorescence measurements of late intermediates in transcription initiation by T7 RNA polymerase

T7 RNA polymerase undergoes dramatic structural rearrangements in the transition from initiation to elongation. Two models have been proposed for promoter-bound intermediates late in the transition. (i) A subset of promoter interactions are maintained through completion of the protein conformational (twist) change, and (ii) concerted movement (shift) of all promoter-binding elements away from the growing DNA-RNA hybrid leads to an open intermediate, with large-scale domain rotations deferred until after promoter release. Fluorescence resonance energy transfer measurements provide very strong support for the latter.

Structural confirmation of a bent and open model for the initiation complex of T7 RNA polymerase

T7 RNA polymerase is known to induce bending of its promoter DNA upon binding, as evidenced by gel-shift assays and by recent end-to-end fluorescence energy transfer distance measurements. Crystal structures of promoter-bound and initially transcribing complexes, however, lack downstream DNA, providing no information on the overall path of the DNA through the protein. Crystal structures of the elongation complex do include downstream DNA and provide valuable guidance in the design of models for the complete melted bubble structure at initiation. In the current study, we test a specific structural model for the initiation complex, obtained by alignment of the C-terminal regions of the protein structures from both initiation and elongation and then simple transferal of the downstream DNA from the elongation complex onto the initiation complex. Fluorescence resonance energy transfer measurement of distances from a point upstream on the promoter DNA to various points along the downstream helix reproduce the expected helical periodicity in the distances and support the model's orientation and phasing of the downstream DNA. The model also makes predictions about the extent of melting downstream of the active site. By monitoring fluorescent base analogues incorporated at various positions in the DNA, we have mapped the downstream edge of the bubble, confirming the model. The initially melted bubble, in the absence of substrate, encompasses 7-8 bases and is sufficient to allow synthesis of a three base transcript before further melting is required. The results demonstrate that despite massive changes in the N-terminal portion of the protein and in the DNA upstream of the active site, the DNA downstream of the active site is virtually identical in both initiation and elongation complexes.

T7 RNA polymerase-induced bending of promoter DNA is coupled to DNA opening

To initiate transcription, T7 RNA polymerase (RNAP) forms a specific complex with its promoter DNA and melts several base pairs near the initiation site to form an open complex. Previous gel electrophoresis studies have indicated that the promoter DNA in the initiation complex is bent [Ujvari, A., and Martin, C. T. (2000) J. Mol. Biol. 295, 1173-1184]. Here we use fluorescence resonance energy transfer (FRET) to investigate the conformation of promoter DNA in the closed and open complexes of T7 RNAP. We have used steady state and time-resolved fluorescence approaches to measure the FRET efficiency in a doubly dye-labeled duplex promoter and in a premelted bubble promoter. Changes in the FRET efficiency and hence the DNA end-to-end distance changes are small when the duplex promoter forms a complex with T7 RNAP. On the other hand, FRET changes are relatively larger when the bubble promoter binds T7 RNAP or when initiating nucleotides are added to the duplex promoter-T7 RNAP complex. The shortening of DNA end-to-end distances is indicative of DNA bending in the bubble DNA complex and in the duplex promoter complex with the initiating nucleotides. Our results are consistent with the model in which in the absence of initiating nucleotides there is a distribution of closed and open complexes, and the promoter DNA is bent slightly by <40 degrees in the closed complex but bent more sharply by 86 degrees in the open complex. The energetics of DNA bending suggests that a significant part of the available free energy from promoter and polymerase interactions is utilized in DNA bending and/or untwisting. We propose that promoter opening occurs spontaneously upon DNA bending and/or untwisting as free energy is gained through interactions of the melted promoter with the T7 RNAP active site.

Rapid binding of T7 RNA polymerase is followed by simultaneous bending and opening of the promoter DNA

To form a functional open complex, bacteriophage T7 RNA polymerase (RNAP) binds to its promoter DNA and induces DNA bending and opening. The objective of this study was to elucidate the temporal coupling in DNA binding, bending, and opening processes that occur during initiation. For this purpose, we conducted a combined measurement of stopped-flow fluorescence anisotropy, fluorescence resonance energy transfer (FRET), and 2-aminopurine fluorescence. Stopped-flow anisotropy measurements provided direct evidence of an intermediate resulting from rapid binding of the promoter to T7 RNA polymerase. Stopped-flow FRET measurements showed that promoter bending occurred at a rate constant that was slower than the initial DNA binding rate constant, indicating that the initial complex was not significantly bent. Similarly, stopped-flow 2-aminopurine fluorescence changes showed that promoter opening occurred at a rate constant that was slower than the initial DNA binding rate constant, indicating that the initial complex was not significantly melted. The indistinguishable observed rate constants of FRET and 2-aminopurine fluorescence changes indicate that DNA bending and opening processes are temporally coupled and these DNA conformational changes take place after the DNA binding step. The results in this paper are consistent with the mechanism in which the initial binding of T7 RNAP to the promoter results in a closed complex, which is then converted into an open complex in which the promoter is both sharply bent and melted.

Topological measurement of an A-tract bend angle: effect of magnesium

Sequences of four to six adenine residues, termed A-tracts, have been shown to produce curvature in the DNA double helix. A-tracts have been used extensively as reference standards to quantify bending induced by other sequences as well as by DNA binding proteins when they bind to their sites. However, the ability of an A-tract to serve as such a standard is hampered by the wide variation of values reported for the amount of bend conferred by an A-tract. One experimental condition that differs in these studies is the presence of divalent cation. To evaluate this effect, a new application of a topological method, termed rotational variant analysis, is used here to measure for the first time the effect of the presence of magnesium ion on the bend angle conferred by an A-tract. This method, which has the unique ability to measure a bend angle in the presence or absence of magnesium ion, demonstrates that magnesium ion markedly increases the bend angle. For example, when measured in a commonly used gel electrophoretic buffer, the bend angle conferred by a tract of six adenine residues increases from about 7 degrees in the absence of magnesium ion to 19 degrees in the presence of 3.9 mM magnesium ion. This quantitative demonstration of substantial magnesium ion dependence has several important implications. First, it explains discrepancies among bend values reported in various previous studies, particularly those employing gel electrophoretic versus other solution methods. In addition, these findings necessitate substantial revisions of the conclusions in a large number of studies that have used A-tract DNA as the bend angle reference standard in comparison measurements. Finally, any such future studies employing this comparison methodology will need to use the same sequence analyzed in the original measurements as well as replicate the original measurement conditions (e.g. ionic composition and temperature).

Cross-linking of promoter DNA to T7 RNA polymerase does not prevent formation of a stable elongation complex

T7 RNA polymerase recognizes a small promoter, binds DNA, and begins the process of transcription by synthesizing short RNA products without releasing promoter contacts. To determine whether the promoter contact must be released to make longer RNA products and at what position the promoter must be released, a mutant RNA polymerase was designed that allows cross-linking to a modified promoter via a covalent disulfide bond. The modifications individually have no measurable effect on transcription. Under oxidizing conditions that produce the protein-DNA cross-link, the complex is able to synthesize short RNA products, strongly supporting a model in which promoter contacts are not lost on translocation through at least position +6. However, cross-linked complexes are impaired in promoter escape in that only about one in four can escape to make full-length RNA. The remainder release 12- and 13-mer RNA transcripts, suggesting an increased energetic barrier in the transition from an initial transcribing complex to a fully competent elongation complex. The results are discussed in the context of a model in which promoter release helps drive initial collapse of the upstream edge of the bubble, which, in turn, drives initial displacement of the 5'-end of the RNA.

Bending of adenovirus origin DNA by nuclear factor I as shown by scanning force microscopy is required for optimal DNA replication

Nuclear factor I (NFI) is a transcription factor that binds to the adenovirus type 5 (Ad5) origin of replication and recruits the adenovirus DNA polymerase, thereby stimulating initiation of DNA replication in vitro. Using scanning force microscopy, we demonstrate that NFI induces a 60 degrees bend upon binding to the origin. The A/T-rich region preceding the core recognition sequence of NFI influences the DNA bend angle, since substitution of A/T base pairs by G/C base pairs severely decreases bending. Mutations in the A/T-rich region do not affect binding of NFI to DNA. However, mutations that reduce the protein-induced bend lead to a loss of NFI-stimulated replication, indicating that DNA bending is functionally important. In contrast, basal initiation or DNA binding of the polymerase is not impaired by these origin mutations. We conclude that binding of NFI to the Ad5 origin causes structural changes in DNA that are essential for the stimulatory function of NFI in replication. We propose that NFI-induced origin bending facilitates the assembly of a functional initiation complex.

Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle

A single-molecule transcription assay has been developed that allows, for the first time, the direct observation of promoter binding, initiation, and elongation by a single RNA polymerase (RNAP) molecule in real-time. To promote DNA binding and transcription initiation, a DNA molecule tethered between two optically trapped beads was held near a third immobile surface bead sparsely coated with RNAP. By driving the optical trap holding the upstream bead with a triangular oscillation while measuring the position of both trapped beads, we observed the onset of promoter binding, promoter escape (productive initiation), and processive elongation by individual RNAP molecules. After DNA template release, transcription re-initiation on the same DNA template is possible; thus, multiple enzymatic turnovers by an individual RNAP molecule can be observed. Using bacteriophage T7 RNAP, a commonly used RNAP paradigm, we observed the association and dissociation (k(off)= 2.9 s(-1)) of T7 RNAP and promoter DNA, the transition to the elongation mode (k(for) = 0.36 s(-1)), and the processive synthesis (k(pol) = 43 nt s(-1)) and release of a gene-length RNA transcript ( approximately 1200 nt). The transition from initiation to elongation is much longer than the mean lifetime of the binary T7 RNAP-promoter DNA complex (k(off) > k(for)), identifying a rate-limiting step between promoter DNA binding and promoter escape.

Two distinct curved DNAs upstream of the light-responsive psbA gene in a cyanobacterium

A functional intrinsic DNA curvature, CIT, and potential DNA-binding factors for the basal transcription of psbA2 have been reported in a cyanobacterium, Microcystis aeruginosa K-81 (Asayama et al., Nucleic Acids Res., 30, 4658-4666 (2002)). In this article, we found another novel curved DNA, which was induced by RNA polymerases binding to the promoter region. Circular permutation analyses showed that the curved center of RNA polymerase-induced DNA bending (RIB) lies at approximately the +10 site, referring to the transcription start point as +1, in the RNA polymerase-DNA complex. Regions containing the curved center of RIB and CIT contributed to the basal transcription in vivo and in vitro. These results indicate that the region upstream of K-81 psbA2 has two distinct curved DNAs, CIT (sequence-directed type) and RIB (protein-induced type).

Topological measurement of an A-tract bend angle: comparison of the bent and straightened states

It is well established that an A-tract imparts curvature to the DNA double helix. Constructs of such A-tracts have been used as bend standards in a large number of both structural and functional studies, and A-tracts can confer significant activation in transcription. An accurate value for the bend angle induced by an A-tract is centrally important to all such studies, but the estimates reported for the bend angle of an A-tract differ by greater than threefold. To address this problem, we have used the rotational variant method to measure the angle of DNA curvature conferred by a tract of six adenine bases (A6 tract). The original version of the method measured a protein-induced bend angle independent of external standards. It compared the effect of bent and straight forms of the sequence on the topology of a DNA plasmid in which the sequence is cloned as a series of tandem repeats. To adapt the approach to the measurement of an intrinsic bend, high temperature was used to generate the straightened reference state, with the required topological relaxation being performed by a hyperthermophile topoisomerase. Appropriate plasmids containing tandem repeats of A-tracts were constructed and topologically analyzed in this manner. The bend value measured at 4 degrees C was 26(+/-2), and decreased linearly to 17(+/-2) at 37 degrees C. The relationship to other estimates and the application of these values are discussed.

The energetics of consensus promoter opening by T7 RNA polymerase

The consensus 23 base-pair T7 DNA promoter is classically divided into two domains, an upstream binding domain (-17 to -5), and a downstream initiation domain (-4 to +6) relative to the transcription start site at +1. During transcription initiation, T7 RNA polymerase (T7 RNAP) melts specifically the -4 to +2/+3 (TATAGG/G) region of the duplex DNA promoter to form a pre-initiation open complex. No external energy source is used and the energy for open complex formation is derived from the free energy of specific interactions with the binding domain, particularly the specificity region (-13 to -6). Using 2-aminopurine fluorescence-based equilibrium and kinetic measurements, we have measured the binding affinities of various topologically modified DNA promoters (40 bp in length) that represent initial, final, and transition-state analogs of the promoter DNA in the T7 RNAP-DNA complex, to determine the energy of specific binding interactions, and the energy required for forming an initiation bubble. The results indicate that 16-16.5 kcal mol(-1) of free energy is made available upon T7 RNAP binding (through specificity loop) to the promoter binding domain. To melt the TATAGG/G sequence 7-8 kcal mol(-1) of free energy is utilized; this compares with approximately 6 kcal mol(-1) predicted from nearest neighbor analysis. The remaining 8.5-9.5 kcal mol(-1) of net free energy is retained for stabilization of the specific pre-initiation binary complex. Of the 7-8 kcal mol(-1) energy that is used to generate the pre-initiation DNA bubble in the open complex, we estimate that one half (3.5-4 kcal mol(-1)) is utilized for nucleation/deformation process (through bending, untwisting, etc.) in the melting region (-4 to -1 TATA) of the initiation domain (-4 to +6), and appears to be independent of the nucleation site within this region. The other half is utilized in unpairing the +1 to +2/+3 GG/G sequence for initiation. The interactions of T7 RNAP with a 20-bp non-specific DNA on the other hand are very weak (DeltaG<-5k cal mol(-1)), which is not sufficient to melt and stabilize an open complex of a non-specific DNA.

Structural transitions mediating transcription initiation by T7 RNA polymerase

During transcription initiation, RNA polymerases appear to retain promoter interactions while transcribing short RNAs that are frequently released from the complex. Upon transition to elongation, the polymerase releases promoter and forms a stable elongation complex. Little is known about the changes in polymerase conformation or polymerase:DNA interactions that occur during this process. To characterize the transitions that occur in the T7 RNA polymerase transcription complex during initiation, we prepared enzymes with Fe-BABE conjugated at 11 different positions. Addition of H(2)O(2) to transcription complexes prepared with these enzymes led to nucleic acid strand scission near the conjugate. Changes in the cleavage sites revealed a series of conformational changes and rearrangements of protein:nucleic acid contacts that mediate progression through the initiation reaction.

Kinetic and thermodynamic basis of promoter strength: multiple steps of transcription initiation by T7 RNA polymerase are modulated by the promoter sequence

Transcription initiation by T7 RNA polymerase (T7 RNAP) is regulated by the specific promoter DNA sequence that is classically divided into two major domains, the binding domain (-17 to -5) and the initiation domain (-4 to +6). The occurrence of non-consensus bases within these domains is responsible for the diversity of promoter strength, the basis of which was investigated by studying T7 promoters with changes in the promoter specificity region (-13 to -6) of the binding domain and/or the melting region (-4 to -1) of the initiation domain. The transient state kinetics and thermodynamic studies revealed that multiple steps in the pathway of transcription initiation are modulated by the promoter DNA sequence. Three base changes in the promoter specificity region at -11, -12, and -13, found in the natural phi 3.8 promoter, reduced the overall affinity of the T7 RNAP for the promoter DNA by 2-3-fold and decreased the rate of pppGpG synthesis, the first RNA product. Promoter opening is thermodynamically driven in T7 RNAP, and a single base change in the melting region (TATA to TAAA) decreased the extent of open complex generated at equilibrium. This base change in the melting region also increased the K(d) of (+1) GTP and the dissociation rate of pppGpG. Thus, transcription initiation at various T7 promoters is differentially regulated by initiating GTP concentration. The specificity and melting regions of T7 promoter DNA act both independently and synergistically to affect distinct steps of transcription initiation. Although each step in the initiation pathway is affected to a small degree by promoter sequence variations, the cumulative effect dictates the overall promoter strength.

Differential modulation of DNA conformation by estrogen receptors alpha and beta

The human estrogen receptor (ER) induces transcription of estrogen-responsive genes upon binding to estrogen and the estrogen response element (ERE). To determine whether receptor-induced changes in DNA structure are related to transactivation, we compared the abilities of ER alpha and ER beta to activate transcription and induce distortion and bending in DNA. ER alpha induced higher levels of transcription than ER beta in the presence of 17 beta-estradiol. In circular permutation experiments ER alpha induced greater distortion in DNA fragments containing the consensus ERE sequence than ER beta. Phasing analysis indicated that ER alpha induced a bend directed toward the major groove of the DNA helix but that ER beta failed to induce a directed DNA bend. Likewise, the ER alpha DNA binding domain (DBD) and hinge region induced a bend directed toward the major groove of the DNA helix, but the ER beta DBD and hinge region failed to bend ERE-containing DNA fragments. Using receptor chimeras we demonstrated that the ER alpha DBD C-terminal extension is required for directed DNA bending. Transient transfection assays revealed that appropriately oriented DNA bending enhances receptor-mediated transactivation. The different abilities of ER alpha and ER beta to induce change in DNA structure could foster or inhibit the interaction of regulatory proteins with the receptor and other transcription factors and help to explain how estrogen-responsive genes are differentially regulated by these two receptors.

The intercalating beta-hairpin of T7 RNA polymerase plays a role in promoter DNA melting and in stabilizing the melted DNA for efficient RNA synthesis

Phage T7 RNA polymerase contains within its single polypeptide all the elements for specific recognition and melting of its promoter DNA. Crystallographic studies indicate that a beta-hairpin (230-245) with an intercalating valine residue plays a role in promoter opening. We mutated V237 to several amino acids, deleted five amino acid residues at the tip of the hairpin, and mutated E242 and D240 at the base of the hairpin to define the roles of the tip and base of the hairpin in DNA strand separation. The affinity of the hairpin mutants for the promoter DNA was not significantly affected. Stopped-flow kinetic studies showed that the bimolecular rate of DNA binding and the observed rate of pre-initiation open complex formation that corresponds to the sum of DNA opening and closing steps were within 20 to 40 % of the wild-type polymerase. Yet, most mutants showed a smaller amount of the pre-initiation open complex at equilibrium, indicating that the individual rates of promoter opening and closing steps were altered in the mutants. The base mutants, E242A and D240A, showed both a lower rate of promoter opening and a higher rate of promoter closing, suggesting their role in stabilization of the open complex. The V237D and the deletion mutant showed mainly a lower rate of promoter opening, suggesting that the tip of the hairpin may nucleate DNA opening. The defect in pre-initiation open complex formation affected downstream steps such as the rate of the first phosphodiester bond formation step, but did not affect significantly the apparent K(d) of initiating GTPs. We propose that D240 and E242 anchor the hairpin to the DNA and position the tip of the hairpin to allow V237 to intercalate and distort the DNA during open complex formation. The interactions of E242 and D240 with the upstream junction of the melted dsDNA promoter also align the template strand within the active site for efficient RNA synthesis.

Structural features of an influenza virus promoter and their implications for viral RNA synthesis

The influenza A virus, a severe pandemic pathogen, has a segmented RNA genome consisting of eight single-stranded RNA molecules. The 5' and 3' ends of each RNA segment recognized by the influenza A virus RNA-dependent RNA polymerase direct both transcription and replication of the virus's RNA genome. Promoter binding by the viral RNA polymerase and formation of an active open complex are prerequisites for viral replication and proliferation. Here we describe the solution structure of this promoter as solved by multidimensional, heteronuclear magnetic resonance spectroscopy. Our studies show that the viral promoter has a significant dynamic nature and reveal an unusual displacement of an adenosine that forms a novel (A-A) x U motif and a C-A mismatch stacked in a helix. The characterized structural features of the promoter imply that the specificity of polymerase binding results from an internal RNA loop. In addition, an unexpected bending (46 +/- 10 degrees ) near the initiation site suggests the existence of a promoter recognition mechanism similar to that of DNA-dependent RNA polymerase and a possible regulatory function for the terminal structure during open complex formation.

The T7 RNA polymerase intercalating hairpin is important for promoter opening during initiation but not for RNA displacement or transcription bubble stability during elongation

The recently described crystal structures of a T7RNAP-promoter complex and an initial transcription complex reveal a beta-hairpin which inserts between the template and nontemplate strands of the promoter [Cheetham, G. M., et al. (1999) Nature 399, 80; Cheetham, G. M., et al. (1999) Science 286, 2305]. A stacking interaction between the exposed DNA bases and a valine at the tip of this hairpin may be especially important for stabilizing the opened promoter during initiation. It has been suggested that this hairpin may also be important for holding the transcription bubble open during transcript elongation, and a proposed model for how the RNA exits the transcription complex implies that this hairpin may also help displace the RNA from the template strand. To test these hypotheses, we have characterized both point and deletion mutants of this element. We find that these mutants exhibit reduced activity on linear, double-stranded templates but not on supercoiled or partially single-stranded templates. Probing of promoter-polymerase complexes, initial transcription complexes, and elongation complexes with KMnO(4) and a single-strand specific endonuclease reveals that the mutants have greatly reduced promoter unwinding activity during initiation. However, the structure and stability of the transcription bubble during elongation are not altered in the mutant enzymes, and RNA displacement activity is also normal. Thus, the T7RNAP intercalating hairpin is important, though not essential, for stabilizing the opened promoter during initiation, but is not important for RNA displacement or for transcription bubble structure or stability during elongation.

Solution structure of an A-tract DNA bend

The solution structure of a DNA dodecamer d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) containing an A-tract has been determined by NMR spectroscopy with residual dipolar couplings. The structure shows an overall helix axis bend of 19 degrees in a geometry consistent with solution and gel electrophoresis experiments. Fourteen degrees of the bending occurs in the GC regions flanking the A-tract. The remaining 5 degrees is spread evenly over its six AT base-pairs. The A-tract is characterized by decreasing minor groove width from the 5' to the 3' direction along the A strand. This is a result of propeller twist in the AT pairs and the increasing negative inclination of the adenine bases at the 3' side of the run of adenine bases. The four central thymine bases all have negative inclination throughout the A-tract with an average value of -6.1 degrees. Although this negative inclination makes the geometry of the A-tract different from all X-ray structures, the proton on N6 of adenine and the O4 of thymine one step down the helix are within distance to form bifurcated hydrogen bonds. The 5' bend of 4 degrees occurs at the junction between the GC flank and the A-tract through a combination of tilt and roll. The larger 3' bend, 10 degrees, occurs in two base steps: the first composed of tilt, -4.1 degrees, and the second a combination of tilt, -4.2 degrees, and roll, 6.0 degrees. This second step is a direct consequence of the change in inclination between an adjacent cytosine base, which has an inclination of -12 degrees, and the next base, a guanine, which has 3 degrees inclination. This bend is a combination of tilt and roll. The large change in inclination allows the formation of a hydrogen bond between the protons of N4 of the 3' cytosine and the O6 of the next 3' base, a guanine, stabilizing the roll component in the bend. These structural features differ from existing models for A-tract bends.For comparison, we also determined the structure of the control sequence, d(GGCAAGAAACGG)/d(CCGTTTCTTGCC), with an AT to GC transition in the center of the A-tract. This structure has no negative inclination in most of the bases within the A-tract, resulting in a bend of only 9 degrees. When ligated in phase, the control sequence has nearly normal mobility in gel electrophoresis experiments.

Two site contact of elongating transcripts to phage T7 RNA polymerase at C-terminal regions

A series of active elongation complexes of the phage T7 RNA polymerase were obtained through stepwise walking of the polymerase along an immobilized DNA template. Transcripts were radiolabeled at the 16th to 18th residues, and a photocross-linkable 4-thio-UMP was separately incorporated at the 22nd, 24th, 32nd, and 38th residues. Such complexes (up to 51 nucleotides) produced by the incorporation of one nucleotide at a time were isolated and individually subjected to long wave UV cross-linking. Only when the cross-linker was positioned at the 3'-end (-1) of the elongating RNA and 8 nucleotides upstream (-9), was the RNA substantially cross-linked to the polymerase, regardless of how far it was from the 5'-end of the transcripts. Linkage of the 3'-end residue was mapped to the Thr(636)-Met(666) region, which contains nucleotide-binding sites. The -9 residue was cross-linked to the Ala(724)-Met(750) region rather than to the N-terminal region. These two contacts were maintained throughout the elongation complexes and reveal a route of nascent RNA through the T7 RNA polymerase in elongation complexes.

Architecture of nucleotide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition

Nucleotide excision repair (NER) is a major DNA repair mechanism that recognizes a broad range of DNA damages. In Escherichia coli, damage recognition in NER is accomplished by the UvrA and UvrB proteins. We have analysed the structural properties of the different protein-DNA complexes formed by UvrA, UvrB and (damaged) DNA using atomic force microscopy. Analysis of the UvrA(2)B complex in search of damage revealed the DNA to be wrapped around the UvrB protein, comprising a region of about seven helical turns. In the UvrB-DNA pre-incision complex the DNA is wrapped in a similar way and this DNA configuration is dependent on ATP binding. Based on these results, a role for DNA wrapping in damage recognition is proposed. Evidence is presented that DNA wrapping in the pre-incision complex also stimulates the rate of incision by UvrC.

Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity

An eight nucleotide RNA:DNA hybrid at the 3' end of the transcript is required for the stability of the elongation complex (EC) of RNA polymerase II. A non-template DNA strand is not needed for the stability of the EC, which contains this minimal hybrid. Here, we apply a recently developed method for promoter-independent assembly of functional EC of RNA polymerase II from synthetic RNA and DNA oligonucleotides to study the minimal composition of the nucleic acid array required for stability of the complex with RNA longer than eight nucleotides. We found that upon RNA extension beyond 14-16 nt in the course of transcription, non-template DNA becomes essential for maintaining a stable EC. Our data suggest that the overextended RNA:DNA hybrid formed in the absence the non-template DNA acts as a negative regulator of EC stability. The dissociation of the EC correlates with the backsliding of the polymerase along the overextended hybrid. The dual role of the hybrid provides a mechanism for the control of a correct nucleic acid architecture in the EC and of RNA polymerase II processivity.