Modification of the Properties of Elongating RNA Polymerase by Persistent Association with Nascent Antiterminator RNA

Sen, Ranjan; King, Rodney A.; Weisberg, Robert A.

doi:10.1016/s1097-2765(01)00243-x

Cited by 36 publications

(40 citation statements)

References 16 publications

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“…(30) In contrast, the bacteriophage HK022 system is unique in that it appears that signals in the nascent transcript are sufficient to cause processive antitermination, in the absence of any phage-encoded protein. (31) Direct interference with Rho function Rho-dependent termination requires binding of the Rho hexamer to sites in a nascent transcript and its interaction with a downstream, paused RNA polymerase complex. In the example described below, blockage of Rho's access to a binding site on a transcript by a stalled ribosome prevents Rhodependent transcription termination.…”

Section: N Protein-mediated Antiterminationmentioning

confidence: 99%

Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions

2002

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Regulation of gene expression by premature termination of transcription, or transcription attenuation, is a common regulatory strategy in bacteria. Various mechanisms of regulating transcription termination have been uncovered, each can be placed in either of two broad categories of termination events. Many mechanisms involve choosing between two alternative hairpin structures in an RNA transcript, with the decision dependent on interactions between ribosome and transcript, tRNA and transcript, or protein and transcript. In other examples, modification of the transcription elongation complex is the crucial event. This article will describe and compare several of these regulatory strategies, and will cite specific examples to illustrate the different mechanisms employed.

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Section: N Protein-mediated Antiterminationmentioning

confidence: 99%

Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions

2002

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“…The put RNAs interact directly with the elongating RNAP and convert it into a termination-resistant form (15). The modification is stable and promotes persistent transcription antitermination over long distances (15,27,32). In this study, we have presented the discovery of eight put-like antiterminator RNA sequences that are located in bacteriophages or prophages.…”

Section: Discussionmentioning

confidence: 98%

Newly Discovered Antiterminator RNAs in Bacteriophage

King¹,

Wright²,

Miles³

et al. 2011

Journal of Bacteriology

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Antiterminator RNA directly modifies the transcription elongation complex so that it terminates less efficiently at intrinsic and factor-dependent terminators. These unusual RNAs were first discovered in bacteriophage HK022, where the nascent transcripts of the phage put sites promote full expression of phage genes during lytic infection. The activity of antiterminator RNA depends on specific structural elements that form as the transcript exits RNA polymerase. To further our understanding of the critical sequence features that permit RNA to serve as a transcriptional antiterminator, we have identified eight antiterminator RNA sequences in bacteriophages or prophages. There is strong sequence conservation among most of the put sequences, but sequence divergence is tolerated if critical structural elements are preserved. The most diverged antiterminator RNA is found in bacteriophage HK639. The HK639 putL transcript is an efficient antiterminator, and it has a novel structural feature that is critical for its activity. HK639 also displays a unique pattern of sensitivity to amino acid substitutions in the ␤ subunit zinc binding domain of RNA polymerase, adding to existing evidence that this domain interacts specifically with antiterminator RNA.Persistent transcription antitermination was first discovered in bacteriophage , and it is a common regulatory mechanism found in members of the phage family (reviewed in references 12, 23, and 35). In , full expression of most of the early genes requires the binding of an RNA binding protein encoded by the N gene to specific sites called nut, located in the early nascent transcripts. The N-nut complex modifies RNA polymerase so that pausing and termination at downstream sites is suppressed. Several host-encoded proteins stabilize the N-nut-RNA polymerase complex through protein-protein interactions (25). Bacteriophage HK022 is a member of the family of phages and also uses processive antitermination to transcribe most of its early genes (36). However, the modification of the elongating RNA polymerase is accomplished in a surprisingly different way. No protein, other than RNA polymerase, is required for antitermination (15,21). This factorindependent antitermination mechanism is mediated by the transcripts of two closely related cis-acting phage sites, putL and putR (polymerase utilization, left and right, respectively), that directly modify RNA polymerase so that it reads through downstream terminators with increased efficiency (15, 16). The put transcripts of HK022 are predicted to form similar structures, each consisting of two stem-loops separated by an unpaired base (2, 15). The structures differ from each other in the lengths of the stems and the location, composition, and size of various bulges and loops, but they have nearly identical antitermination activities. The proposed put RNA structure is based on computer modeling, genetic studies, and enzymatic structure-probing experiments on in vitro-synthesized put RNA. Nevertheless, our understanding of the functionally a...

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“…In the second model, put RNA impedes or delays binding of Nun to nut RNA. We have shown that nascent put RNA binds to elongating polymerase and that this complex persists as polymerase translocates (35). If the nascent put transcript binds close to the product RNA exit channel in RNAP, it might delay the binding of Nun to the nascent nut transcript until the elongation complex is too distant for efficient transfer of Nun to RNAP.…”

Section: Discussionmentioning

confidence: 99%

“…Nascent put RNA binds to the transcription elongation complex and remains associated with it through subsequent translocation. Stable binding is required for antitermination (35).The distinction between intrinsic and factor-dependent antitermination is highlighted by the following observations. First, E. coli mutants that are defective in put-mediated antitermination supported N-mediated, Q-mediated, and ribosomal operon antitermination (10).…”

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confidence: 87%

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Suppression of Factor-Dependent TranscriptionTermination by AntiterminatorRNA

King

Weisberg

2003

J Bacteriol

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Nascent transcripts of the phage HK022 put sites modify the transcription elongation complex so that it terminates less efficiently at intrinsic transcription terminators and accelerates through pause sites. We show here that the modification also suppresses termination in vivo at two factor-dependent terminators, one that depends on the bacterial Rho protein and a second that depends on the HK022-encoded Nun protein. Suppression was efficient when the termination factors were present at physiological levels, but an increase in the intracellular concentration of Nun increased termination both in the presence and absence of put. put-mediated antitermination thus shows no apparent terminator specificity, suggesting that put inhibits a step that is common to termination at the different types of terminator.After initiating RNA synthesis, RNA polymerase (RNAP) continues to elongate the transcript until it reaches a termination site. At such sites, the enzyme has a high probability of dissociating from the transcript and the template (reviewed in references 26 and 32). Bacteria have two basic types of transcription termination signals, which differ in their requirements for halting elongation. Intrinsic terminators can stop transcription through the action of the nascent transcript. Formation of an RNA stem-loop immediately upstream of a U-rich stretch in nascent RNA disrupts RNA-DNA base pairs within the transcription elongation complex, and this destabilizes the complex (15,20,47). By contrast, factor-dependent terminators recruit a termination factor to the nascent transcript. Two termination factors have been well characterized: the bacterial Rho protein and the bacteriophage-encoded Nun protein. After binding to nascent transcripts, they both act on the nearby elongation complex. Rho has an ATP-driven RNA-DNA helicase activity, which is thought to destabilize the elongation complex (7,30). Nun is transferred from its RNA binding site to the elongation complex, where it is thought to anchor RNAP to the DNA template within a few hundred nucleotides downstream of the binding site (16,39,43). Dissociation of Nun-arrested polymerase from the template and the transcript has not been observed in vitro and appears to require an additional factor or factors. Recent evidence suggests that the Escherichia coli Mfd protein can stimulate the dissociation of Nun-arrested complexes (42).E. coli and its bacteriophages alter the efficiency of transcription termination in order to control the expression of genes located downstream of terminators (reviewed in reference 44). For example, the phage antitermination proteins N and Q modify RNAP so that it reads through intrinsic and rho-dependent terminators. Both N and Q recognize specific phage sequences (nut and qut, respectively) before they modify polymerase, and this limits antitermination to RNAP molecules that are transcribing phage DNA. Elongating RNAP that has been modified by interaction with either protein retains the modification as it translocates, as shown by its abilit...

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Modification of the Properties of Elongating RNA Polymerase by Persistent Association with Nascent Antiterminator RNA

Cited by 36 publications

References 16 publications

Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions

Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions

Newly Discovered Antiterminator RNAs in Bacteriophage

Suppression of Factor-Dependent TranscriptionTermination by AntiterminatorRNA

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