Shifting RNA polymerase into overdrive

Two Different Wound Signals Evoke Very Rapid, Systemic CMBP Transcript Accumulation in Tomato

Flaming a tomato leaf evokes a variation potential; excising an unwounded leaf evokes an action potential; while excising a wounded leaf 90 sec after flame-wounding evokes an action potential superimposed on the variation potential. Furthermore, flaming one leaf induces rapid (15 min), systemic and biphasic accumulation of CMBP transcript, excising the unwounded leaf causes slower, monophasic transcript accumulation, while excising the wounded leaf after 90 sec has no effect on CMBP transcript accumulation in response to the flame-wound. We propose that both of these electrical signals, the flame-evoked variation potential and the cut-wound evoked action potential are capable of inducing CMBP transcript accumulation, although with somewhat different kinetics. Earlier work by others found the cut-wound had no effect on pin transcript accumulation, thus leaf excision could be used as a tool to determine whether transport of wound hormones out of the leaf could trigger pin gene expression. Here, however, leaf excision could not be used to prevent signal transmission, since excision itself evoked an electrical signal and transcript accumulation. Instead, the results show that two different electrical signals are involved in rapid, systemic CMBP mRNA accumulation and their effects are not additive implying they may share some common aspects.

Transcriptional pausing in vivo: a nascent RNA hairpin restricts lateral movements of RNA polymerase in both forward and reverse directions

Transcriptional pausing by RNA polymerase has been the subject of extensive investigations in vitro, yet little is known about its occurrence and significance in vivo. The transient nature of the pausing events makes them difficult to observe inside the cell, whereas their studies in vitro by classical biochemical methods are usually conducted under non-physiological conditions that increase the pause duration. Here, we have used an Escherichia coli system in which several RNA polymerase molecules transcribing in tandem traverse a pausing sequence while approaching a protein roadblock. The in vivo DNA footprinting and RNA 3' end mapping of the elongation complexes are consistent with a dynamic view of the pausing event, during which RNA polymerase first loses its lateral stability and slides backward, and is subsequently rescued from extended backtracking and stabilized at the pause site by a nascent RNA hairpin. Our results show also that the folding of the hairpin provides an assisting force that promotes forward translocation of a trailing polymerase under a strained configuration by balancing the opposing force created by a steric clash with a leading elongation complex.

Transcriptional fidelity and proofreading in Archaea and implications for the mechanism of TFS-induced RNA cleavage

We have addressed the question whether TFS, a protein that stimulates the intrinsic cleavage activity of the archaeal RNA polymerase, is able to improve the fidelity of transcription in Methanococcus. Using non-specific transcription experiments, we could demonstrate that misincorporation of non-templated nucleotides is reduced in the presence of TFS. A more detailed analysis revealed that elongation complexes containing a misincorporated nucleotide were arrested, but could be reactivated by TFS. RNase as well as exonuclease III footprinting experiments demonstrated that this arrest was not combined with extended backtracking. Analysis of paused elongation complexes demonstrated that TFS is able to induce a cleavage resynthesis cycle in such complexes, which resulted in the accumulation of dinucleotides corresponding to the last two nucleotides of the transcript. Further analysis of cleavage products revealed that, even under conditions that strongly promote misincorporation, still 50% of the released dinucleotides were correctly incorporated. Therefore, we assume that pausing of elongation complexes is an important determinant of TFS-induced RNA cleavage from the 3' end. As the incorporation rate of wrong nucleotides is about 700-fold reduced, it is possible that this delay also provides an appropriate time window for cleavage induction in order to maintain transcriptional fidelity by preventing misincorporation.

Viral DNA polymerase scanning and the gymnastics of Sendai virus RNA synthesis

mRNA synthesis from nonsegmented negative-strand RNA virus (NNV) genomes is unique in tht the genome RNA is embedded in an N protein assembly (the nucleocapsid) and the viral RNA polymerase does not dissociate from the template after release of each mRNA, but rather scans the genome RNA for the next gene-start site. A revised model for NNV RNA synthesis is presented, in which RNA polymerase scanning plays a prominent role. Polymerase scanning of the template is known to occur as the viral transcriptase negotiates gene junctions without falling off the template.

Characterization of a novel RNA polymerase II arrest site which lacks a weak 3' RNA-DNA hybrid

Transcript elongation by RNA polymerase II is blocked at DNA sequences called arrest sites. An exceptionally weak RNA-DNA hybrid is often thought to be necessary at the point of arrest. We have identified an arrest site from the tyrosine hydroxylase (TH) gene which does not fit this pattern. Transcription of many sequence variants of this site shows that the RNA-DNA hybrid over the three bases immediately preceding the major arrest point may be strong (i.e. C:G) without interfering with arrest. However, arrest at the TH site requires the presence of a pyrimidine at the 3' end and arrest increases when the 3'-most segment is pyrimidine rich. We also demonstrated that arrest at the TH site is completely dependent on the presence of a purine-rich element immediately upstream of the RNA-DNA hybrid. Thus, the RNA polymerase II arrest element from the TH gene has several unanticipated characteristics: arrest is independent of a weak RNA-DNA hybrid at the 3' end of the transcript, but it requires both a pyrimidine at the 3' end and a polypurine element upstream of the RNA-DNA hybrid.

Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion

The ability of RNA polymerase (RNAP) to adopt multiple conformations is central to transcriptional regulation. In previous work, we demonstrated that RNAP can exist in an unactivated state that catalyzes synthesis slowly and an activated state that catalyzes synthesis rapidly, with the transition from the unactivated to the activated state being induced by the templated NTP binding to an allosteric site on the RNAP. In this work, we investigate the effects of downstream DNA sequences on the kinetics of single nucleotide incorporation. We demonstrate that changing the identity of the DNA base 1 bp downstream (+2) from the site of incorporation (+1) can regulate the catalytic activity of RNAP. Combining these data with sequence and structural analyses and molecular modeling, we identify the streptolydigin-binding region (Escherichia coli beta residues 543-546), which lies across from the downstream DNA, as the putative allosteric NTP binding site. We present a structural model in which the NTP binds to the streptolydigin loop and upon pairing with the +1 DNA base in the unactivated state or the +2 DNA base in the activated state facilitates translocation via a ratchet motion. This model provides an alternative mechanism for pausing as well as a structural explanation not only for our kinetic data but also for data from elongation studies on yeast RNAP II.

Reaction pathways in transcript elongation

Transcription of DNA into RNA is a central part of gene expression, and is highly regulated in all organisms. In order to approach transcription control systems on a molecular basis we must understand the mechanisms used by the transcription complex to discharge its various functions, which include transcript initiation, elongation, editing, and termination. In this article we describe recent progress in sorting out the multiple reaction pathways that are, at least in principle, available to the transcription complex at each DNA template position, and show how transcription control systems partition active complexes into these pathways. Understanding these regulatory processes requires an elucidation of the molecular details of how sequence- and factor-dependent changes in the conformations, stabilities, and reaction rates of the complexes determine function. Recent progress in unraveling these issues is summarized in this article and emerging principles that govern the regulation of the elongation phase of transcription are discussed.

Active Escherichia coli transcription elongation complexes are functionally homogeneous

The elongation phase of RNA transcription represents a major target for the regulation of gene expression. Two general classes of models have been proposed to define the dynamic properties of transcription complexes in the elongation phase. Stable heterogeneity models posit that the ensemble of active elongation-competent complexes consists of multiple distinct and stable forms that are specified early in the transcription cycle and isomerize to other forms slowly. In contrast, equilibrium or rapid interconversion models require that active elongation complexes interconvert rapidly on the time-scale of single nucleotide addition. Measurements of transcription termination efficiency (TE) can be used to distinguish between these models, because stable heterogeneity models predict that the termination-resistant fraction of an elongation complex population should be enriched after transcription through an upstream terminator, leading to a decreased TE at downstream terminators. In contrast, rapid interconversion models require that the population of active (elongation-competent) complexes equilibrate after transcription through each terminator and, therefore, that the value of TE observed at identical upstream and downstream terminators should be the same. We have constructed transcription templates containing multiple identical terminators and found no significant changes in TE with terminator position along the template. Various other forms of upstream treatment of elongation complex populations also were used to attempt to fractionate the complexes into functionally different forms. None of these treatments changed the apparent TE at downstream terminators. These results are consistent with a rapid interconversion model of transcript elongation. The consequences of these results for the regulation of gene expression are discussed.

The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription

Transcription is highly regulated both by protein factors and by specific RNA or DNA sequence elements. Central to this regulation is the ability of RNA polymerase (RNAP) to adopt multiple conformational states during elongation. This review focuses on the mechanism of transcription elongation and the role of different conformational states in the regulation of elongation and termination. The discussion centers primarily on data from structural and functional studies on Escherichia coli RNAP. To introduce the players, a brief introduction to the general mechanism of elongation, the regulatory proteins, and the conformational states is provided. The role of each of the conformational states in elongation is then discussed in detail. Finally, an integrated mechanism of elongation is presented, bringing together the panoply of experiments.

Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase

Escherichia coli RNA polymerase translocates along the DNA discontinuously during the elongation phase of transcription, spending proportionally more time at some template positions, known as pause and arrest sites, than at others. Current models of elongation suggest that the enzyme backtracks at these locations, but the dynamics are unresolved. Here, we study the role of lateral displacement in pausing and arrest by applying force to individually transcribing molecules. We find that an assisting mechanical force does not alter the translocation rate of the enzyme, but does reduce the efficiency of both pausing and arrest. Moreover, arrested molecules cannot be rescued by force, suggesting that arrest occurs by a bipartite mechanism: the enzyme backtracks along the DNA followed by a conformational change of the ternary complex (RNA polymerase, DNA and transcript), which cannot be reversed mechanically.

Transcription termination: primary intermediates and secondary adducts

In living organisms, stable elongation complexes of RNA polymerase dissociate at specific template positions in a process of transcription termination. It has been suggested that the dissociation is not the immediate cause of termination but is preceded by catalytic inactivation of the elongation complex. In vitro reducing ionic strength can be used to stabilize very unstable and catalytically inactive complex at the point of termination; the previous biochemical characterization of this complex has led to important conclusions regarding termination mechanism. Here we analyze in detail the complexes formed between DNA template, nascent RNA, and Escherichia coli RNA polymerase during transcription through the tR2 terminator of bacteriophage lambda. At low ionic strength, the majority of elongation complexes fall apart upon reaching the terminator. Released RNA and DNA efficiently rebind RNA polymerase (RNAP) and form binary RNAP.RNA and RNAP.DNA complexes, which are indistinguishable from binary complexes obtained by direct mixing of the purified nucleic acids and the enzyme. A small fraction of elongation complexes that reach termination point escapes dissociation because RNA polymerase has backtracked from the terminator to an upstream DNA position. Thus, transcription elongation to a terminator site produces no termination intermediates that withstand dissociation in the time scale appropriate for biochemical studies.

Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA

We find that immediately following transcript initiation, RNA polymerase II pauses at several locations even in the presence of relatively high (200 microM) levels of nucleoside triphosphates. Strong pauses with half-lives of >30 s were observed at +7, +18/19, and about +25 on the template used in these experiments. We show that the strong pause at +7, after the synthesis of 5'-ACUCUCU, leads to repeated cycles of upstream slippage of the RNA-DNA hybrid followed by re-pairing with the DNA and continued RNA synthesis. The resulting transcripts are 2, 4, and 6 bases longer than predicted by the template sequence. Slippage is efficient when transcription is primed with the +1/+2 (ApC) dinucleotide, and it occurs at even higher levels with the +2/+3 primer (CpU). Slippage can occur at high levels with ATP initiation, but priming with CpA (-1/+1) supports very little slippage. This latter result is not simply an effect of transcript length at the point of pausing. Slippage can also occur with a second template on which the polymerase can be paused after synthesizing ACUCU. Slippage is not reduced by an ATP analog that blocks promoter escape, but it is inhibited by substitution of 5Br-U for U in the RNA. Our results reveal an unexpected flexibility of RNA polymerase II ternary complexes during the very early stage of transcription, and they suggest that initiation at different locations within the same promoter gives rise to transcription complexes with different properties.

Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence

We have characterized RNA polymerase II complexes halted from +16 to +49 on two templates which differ in the initial 20 nucleotides (nt) of the transcribed region. On a template with a purine-rich initial transcript, most complexes halted between +20 and +32 become arrested and cannot resume RNA synthesis without the SII elongation factor. These arrested complexes all translocate upstream to the same location, such that about 12 to 13 bases of RNA remain in each of the complexes after SII-mediated transcript cleavage. Much less arrest is observed over this same region with a second template in which the initially transcribed region is pyrimidine rich, but those complexes which do arrest on the second template also translocate upstream to the same location observed with the first template. Complexes stalled at +16 to +18 on either template do not become arrested. Complexes stalled at several locations downstream of +35 become partially arrested, but these more promoter-distal arrested complexes translocate upstream by less than 10 nt; that is, they do not translocate to a common, far-upstream location. Kinetic studies with nonlimiting levels of nucleoside triphosphates reveal strong pausing between +20 and +30 on both templates. These results indicate that promoter clearance by RNA polymerase II is at least a two-step process: a preclearance escape phase extending up to about +18 followed by an unstable clearance phase which extends over the formation of 9 to 17 more bonds. Polymerases halted during the clearance phase translocate upstream to the preclearance location and arrest in at least one sequence context.

Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II

Human RNA polymerase II recognizes a strong transcriptional pause signal in the initially transcribed region of HIV-1. We report the use of a limited-step transcription assay to dissect the mechanism underlying recognition of and escape from this HIV-1 pause. Our results suggest that the primary determinant of transcriptional pausing is a relatively weak RNA:DNA hybrid that triggers backtracking of RNA polymerase II along the RNA and DNA chains and displaces the RNA 3' OH from the active site. In contrast, two alternative RNA secondary structures, TAR and anti-TAR, are not required for pausing and affect it only indirectly, rather than through direct interaction with RNA polymerase II. TAR accelerates escape from the pause, but anti-TAR inhibits formation of TAR prior to pause escape. The behavior of RNA polymerase II at a mutant pause signal supports a two-step, non-equilibrium mechanism in which the rate-determining step is a conformational change in the enzyme, rather than the changes in nucleic-acid base-pairing that accompany backtracking.

Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation

The regulation of transcription elongation and termination appears to be governed by the ability of RNA polymerase elongation complexes to adopt multiple conformational states; however, the factors controlling the distribution between these states remain elusive. We used transient-state kinetics to investigate the incorporation of single nucleotides. We demonstrate that E. coli RNA polymerase contains an allosteric binding site in addition to the catalytic site. Binding of the templated nucleoside triphosphate (NTP), but not nontemplated NTPs, to this site increases the rate of nucleotide incorporation. The data suggest that RNA polymerase can exist in a state that catalyzes synthesis slowly (unactivated) and one that catalyzes synthesis rapidly (activated), with the transition from the slow to the fast state being induced by binding of the templated NTP to the allosteric site.

Transcription elongation complex: structure and function

Our understanding of the mechanisms of transcription has been greatly advanced by recent determination of the X-ray structure of bacterial RNA polymerase. Using crosslinking approaches, extensive mapping of DNA and RNA contacts onto this structure allowed tracking of the path of nucleic acids through the transcription elongation complex. The resulting structural model of the transcription elongation complex is linked to the functional one, which is based on numerous data accumulated during previous studies of RNA synthesis. An integrated structure-function model allows the rational explanation of termination and pausing and provides new insights into the mechanisms of transcription.

Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals

Transcript elongation by RNA polymerase is discontinuous and interrupted by pauses that play key regulatory roles. We show here that two different classes of pause signals punctuate elongation. Class I pauses, discovered in enteric bacteria, depend on interaction of a nascent RNA structure with RNA polymerase to displace the 3' OH away from the catalytic center. Class II pauses, which may predominate in eukaryotes, cause RNA polymerase to slide backwards along DNA and RNA and to occlude the active site with nascent RNA. These pauses differ in their responses to antisense oligonucleotides, pyrophosphate, GreA, and general elongation factors NusA and NusG. In contrast, substitutions in RNA polymerase that increase or decrease the rate of RNA synthesis affect both pause classes similarly. We propose that both pause classes, as well as arrest and termination, arise from a common intermediate that itself binds NTP substrate weakly.

Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement

The type I restriction enzyme EcoR124I cleaves DNA following extensive linear translocation dependent upon ATP hydrolysis. Using protein-directed displacement of a DNA triplex, we have determined the kinetics of one-dimensional motion without the necessity of measuring DNA or ATP hydrolysis. The triplex was pre-formed specifically on linear DNA, 4370 bp from an EcoR124I site, and then incubated with endonuclease. Upon ATP addition, a distinct lag phase was observed before the triplex-forming oligonucleotide was displaced with exponential kinetics. As the distance between type I and triplex sites was shortened, the lag time decreased whilst the displacement reaction remained exponential. This is indicative of processive DNA translocation followed by collision with the triplex and oligonucleotide displacement. A linear relationship between lag duration and inter-site distance gives a translocation velocity of 400+/-32 bp/s at 20 degrees C. Furthermore, the data can only be explained by bi-directional translocation. An endonuclease with only one of the two HsdR subunits responsible for motion could still catalyse translocation. The reaction is less processive, but can 'reset' in either direction whenever the DNA is released.

Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase

Using an optical-trap/flow-control video microscopy technique, we followed transcription by single molecules of Escherichia coli RNA polymerase in real time over long template distances. These studies reveal that RNA polymerase molecules possess different intrinsic transcription rates and different propensities to pause and stop. The data also show that reversible pausing is a kinetic intermediate between normal elongation and the arrested state. The conformational metastability of RNA polymerase revealed by this single-molecule study of transcription has direct implications for the mechanisms of gene regulation in both bacteria and eukaryotes.

HIV-1 Tat: coping with negative elongation factors

The intrinsic processivity of RNA polymerase II complexes arises from a complex interplay between the recently identified positive transcription elongation factor b (P-TEFb) and negative transcription elongation factors, DSIF (5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole [DRB]-sensitivity-inducing factor) and the negative elongation factor complex (NELF). Elements in nascent HIV-1 RNA function in concert with these factors and the HIV-1 Tat protein to ensure that viral transcription is induced strongly in activated T cells. Studies in the past year have elucidated key aspects of the Tat trans-activation mechanism that help to define this important paradigm for RNA-mediated control of transcription elongation.