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This chapter provides a review of the current structural and kinetic models for transcription elongation and termination. It describes the regulatory molecules that are known to influence the elongation/termination decision by RNA polymerase (RNAP), with the emphasis on the most recent findings and on the mechanism of ‘‘active’’ regulators whose actions are not limited to changes in RNA folding. Interactions between RNAP and the nucleic acid chains, as well as the RNA:DNA pairing in the hybrid, all contribute to the extraordinary stability of the elongating transcription elongation complexes (TECs). RNA release is triggered at sites where the nascent RNA folds into a stable, GC-rich hairpin followed by a stretch of the U-rich RNA. Rho is the main termination protein in Escherichia coli, where it is thought to control ~ 50% of all termination events. Feedback control of the operons that encode ribosomal protein synthesis is commonly accomplished by autogenous regulation by one of the products. Alc protein terminates transcription at several sites on a nonmodified host DNA, but not on the phage DNA that contains hydroxymethyl cytosine residue. The bgl operon in E. coli is regulated in response to the availability of a substrate β-glucoside by BglG induced antitermination. The RNA binding by BglG is regulated by BglF-mediated phosphorylation: in the absence of inducer, BglF phosphorylates BglG and inhibits its RNA binding activity; when β-glucosides are available, BglF dephosphorylates BglG, which now binds to its target and prevents transcription termination.
Schematic model of the TEC. RNAP (gray oval) is bound to the DNA duplex (black circles; T, template strand; NT, nontemplate strand) from ~-20 to ~+15 relative to the position of the 50 end of the encoded RNA (as judged from the protection against cleavage by various probes that it confers to the DNA). The 12 to 13 bp of the DNA duplex are melted in the transcription bubble. The nontemplate DNA strand is exposed on the surface of RNAP ( 48 ), where it becomes available for interactions with the regulatory proteins ( 5 , 77 ).The nascent RNA (white circles) is annealed to the template strand to form 8 to 9 bp of the RNA● DNA hybrid (bound in the HBS) and is extruded from the TECs at ~14 nt from the 30 end. In the active TECs, the 3′ end of the RNA is located in the active site. In the backtracked TECs, the 3′ portion of the RNA (dashed circles) is threaded through the active site into the secondary channel, thus preventing the substrate NTP entry. Three principal interactions are distinguished ( 47 ): the DNA-binding site (DBS), the front zip-lock (FZ), and the rear zip-lock (RZ). Cross-linking analysis of the E. coli RNAP core (α2ββ′ complex) bound to the RNA and DNA to form the TEC (see reference 48 and references therein) identifies the β′ jaw/β lobe module as the DBS, the active site as the FZ, and a combination of β flap, β region D, and β′ rudder as the RZ. Although originally the rudder was postulated to play a key role in RNA displacement, recent evidence indicates that the rudder stabilizes the TEC through direct contacts with RNA, but is not required for either RNA displacement or the maintenance of the transcription bubble ( 50 ).
Branched regulatory pathways in transcript elongation. At least two TEC states that are competent for elongation can be distinguished ( 20 ). The activated pathway (asterisk) may require binding of the NTP in an "allosteric" site ( 25 ) or a conformational change induced by a substitution in RNAP. The unactivated pathway is characterized by a lower rate of NMP addition and represents a collection of intermediate states from which all the off-pathway states (pause, arrest, termination, and editing) are formed. This mechanism incorporates a previously proposed pathway (on a gray background) where certain nucleic acid signals trigger isomerization of TEC into a slow intermediate state ( 4 ). From the slow intermediate (n), the TEC can either slowly escape to the elongation pathway (upon nucleotide addition), or further isomerize into different types of pause, arrest, and termination complexes. Formation of an RNA hairpin would result in class I pausing, whereas backtracking would lead to a class II pause or arrest; termination could occur via either of these pathways. The principal difference between the slow intermediate and the parallel-path mechanisms is that the slow state is assumed to be short-lived in the former, and returns to the activated pathway upon NMP addition (escape) or NTP binding (reverse isomerization), but could persist for many rounds of catalysis in the latter. Isomerization into the termination and arrested states is irreversible and may proceed via formation of a significant kinetic intermediate ( 21 , 24 , 108 ).
Antitermination mechanisms. Isomerization of a rapidly elongating TEC into a terminating complex proceeds through several steps at both Rho-dependent (top) and intrinsic (bottom) sites. Regulatory mechanisms that target one or more steps are known. As pausing precedes termination, RNA release can be inhibited by factors that also inhibit pausing (λ N, λ Q, and put). In contrast, other factors may preferentially inhibit hairpin formation at intrinsic terminators (alternative RNA structures, ssRNA-binding proteins, and possibly p7) or Rho access to the nascent RNA (the stalled ribosome, maybe Psu). Antitermination factors may also actively stabilize the TEC against dissociation (λ N and λ Q). Two alternative models for the mechanism of the nascent RNA release have been proposed. In a forward translocation model, RNAP slides forward (without necessarily changing its conformation), leaving the transcript behind ( 107 ). In an allosteric model, a regulatory signal (e.g., formation of a terminator hairpin) triggers a series of cooperative conformational changes in the TEC that lead to opening of a crab-claw-shaped TEC and the concomitant release of the nucleic acids ( 51 ).
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