Inhibition of a Transcriptional Pause by RNA Anchoring to RNA Polymerase

Комиссарова, Н. В.; Velikodvorskaya, Tatiana; Sen, Ranjan; King, Rodney A.; Banik-Maiti, Sarbani; Weisberg, Robert A.

doi:10.1016/j.molcel.2008.06.019

Cited by 24 publications

(31 citation statements)

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“…1A and Table S2): (i) the β′ coiled-coil/β gate loop, targeted by RfaH and its paralogs (15); (ii) the β flap/RNA exit channel, targeted by N, Q and gp39 (4, 7, 9-11); and (iii) the β′ N terminus and adjacent regions, involved in antitermination by p7. In addition, p7 seems to partially share its target site with an RNA-based antiterminator, the put hairpin encoded by phage HK022, the function of which was shown to depend on the β′ ZBD (20,43,44). Despite the different binding sites, all classes of factors suppress transcription pausing by bacterial RNAP, which therefore is likely a universal part of all antitermination mechanisms (Table S2).…”

Section: Discussionmentioning

confidence: 99%

Distinct pathways of RNA polymerase regulation by a phage-encoded factor

Esyunina

Klimuk

Severinov

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Transcription antitermination is a common strategy of gene expression regulation, but only a few transcription antitermination factors have been studied in detail. Here, we dissect the transcription antitermination mechanism of Xanthomonas oryzae virus Xp10 protein p7, which binds host RNA polymerase (RNAP) and regulates both transcription initiation and termination. We show that p7 suppresses intrinsic termination by decreasing RNAP pausing and increasing the transcription complex stability, in cooperation with host-encoded factor NusA. Uniquely, the antitermination activity of p7 depends on the ω subunit of the RNAP core and is modulated by ppGpp. In contrast, the inhibition of transcription initiation by p7 does not require ω but depends on other RNAP sites. Our results suggest that p7, a bifunctional transcription factor, uses distinct mechanisms to control different steps of transcription. We propose that regulatory functions of the ω subunit revealed by our analysis may extend to its homologs in eukaryotic RNAPs.RNA polymerase | transcription antitermination | transcription pausing | omega subunit | NusA T ranscription promoters and terminators are the main "punctuation marks" that control the expression of individual genes in the genome. In bacteria, transcription termination is an essential regulatory step that determines the relative levels of expression of promoter-proximal and distal genes within operons. Depending on the factors involved, transcription termination in bacteria can be classified as intrinsic (depends on RNAencoded signals) or factor-dependent (requires additional protein factors such as Rho helicase). Intrinsic terminators consist of a G/C-rich hairpin formed in the nascent RNA followed by a downstream oligo(U) tract. During intrinsic termination, RNA polymerase (RNAP) pauses after synthesizing an oligo(U) sequence, accompanied by hairpin formation, leading to subsequent dissociation of the transcription elongation complex (TEC) (1, 2). Despite the relatively simple overall scenario, the exact mechanisms of pausing and hairpin-induced TEC destabilization remain an issue of debate (1, 3).Transcription antitermination is a widespread phenomenon involved in regulation of bacterial and phage operons (2). Transcription antitermination is often mediated by specialized protein factors that target host RNAP and can suppress termination at multiple sites in the operon. The well-studied examples of phage antiterminators include proteins N and Q of Escherichia coli phage λ and the gp39 protein of Thermus thermophilus phage P23-45. These factors suppress RNAP pausing, thus inhibiting the first step of the termination pathway (4-6). The antitermination activity of N and Q, but not gp39, is enhanced by cell-encoded proteins, including transcription elongation factor NusA, which by itself stimulates termination but reverses its activity to additionally stabilize the TEC in cooperation with N and Q (5, 6). Curiously, the N, Q, gp39, and NusA proteins all target the flexible β flap domain of RNAP (2, 4...

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Section: Discussionmentioning

confidence: 99%

Distinct pathways of RNA polymerase regulation by a phage-encoded factor

Esyunina

Klimuk

Severinov

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…RNA elements in the putL transcript from bacteriophage HK022 have been shown to bind RNAP and to influence its elongation properties. However, in this case, the nascent RNA suppresses, rather than promotes, pausing at a downstream site (37,38). It is notable that in the case of putL, formation of a stem-loop is also required for the nascent RNA to affect pausing.…”

Section: +mentioning

confidence: 95%

Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator

Hollands

Sevostiyanova²,

Groisman

2014

Proc. Natl. Acad. Sci. U.S.A.

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Up to half of all transcription termination events in bacteria rely on the RNA-dependent helicase Rho. However, the nucleic acid sequences that promote Rho-dependent termination remain poorly characterized. Defining the molecular determinants that confer Rho-dependent termination is especially important for understanding how such terminators can be regulated in response to specific signals. Here, we identify an extraordinarily long-lived pause at the site where Rho terminates transcription in the 5′-leader region of the Mg 2+ transporter gene mgtA in Salmonella enterica. We dissect the sequence elements required for prolonged pausing in the mgtA leader and establish that the remarkable longevity of this pause is required for a riboswitch to stimulate Rho-dependent termination in the mgtA leader region in response to Mg 2+ availability. Unlike Rho-dependent terminators described previously, where termination occurs at multiple pause sites, there is a single site of transcription termination directed by Rho in the mgtA leader. Our data suggest that Rho-dependent termination events that are subject to regulation may require elements distinct from those operating at constitutive Rhodependent terminators.magnesium | RNA polymerase T ranscription termination is critical for accurate expression and regulation of genes. Bacteria use two types of transcription terminators: intrinsic terminators, which dissociate transcription complexes in the absence of auxiliary proteins, and factor-dependent terminators, which require the action of the RNA-dependent helicase Rho (1). Rho is responsible for 20-50% of termination events in Escherichia coli (2, 3) and performs an array of important functions in bacteria. In addition to terminating transcription at the ends of operons (4), Rho directs transcription termination within coding regions when translation slows or stalls thereby establishing transcriptional polarity (5), silences horizontally acquired DNA (3, 6), protects the chromosome from R-loops and double-strand breaks (7-9), and suppresses pervasive antisense transcription (10).Aside from these genome-wide "housekeeping" functions, Rho has also been recruited to regulate the expression of specific genes in response to signals (11). Long-established examples include a Rho-dependent terminator that controls expression of the E. coli tnaA gene in response to tryptophan availability and terminators that regulate rho mRNA levels in response to the concentration of Rho protein (12-15). The recent identification of two riboswitches and a small regulatory RNA (sRNA) that control gene expression by modulating Rhodependent termination (11,16,17) has now refocused attention on Rho as a regulatory factor. However, it is unclear whether regulated Rho-dependent terminators differ from those performing housekeeping functions.Rho-dependent terminators consist of two elements: a Rho utilization (rut) site in the nascent RNA and a downstream sequence that induces pausing of RNA polymerase (RNAP). The ATPase activity of Rho is stimulated upon...

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“…The functional importance of protein-based RNA biogenesis exposed the transcription machinery to extensive selection, elaboration, and adaptation [17], producing for instance an RNA exit channel that allows RNAP to alter catalytic rate and processivity in response to interactions with different nascent RNA structures [18, 19]. …”

Section: Co-evolution Of Rna Polymerase and Nascent Rna Produced Funcmentioning

confidence: 99%

“…One prominent example is the Lambdoid bacteriophage HK022 putL RNA, which consists of two conserved hairpins linked by an unpaired guanosine. The 65-nt putL nascent RNA exerts a local anti-pausing effect via suppression of RNAP backtracking, and more significantly, modifies the RNAP to render it resistant to multiple intrinsic and factor-dependent terminators over long distances, thus increasing expression of downstream viral genes [19]. Another RNAP-anchored antiterminator RNA, the first found in Gram-positive bacteria, is the recently described EAR RNA structure (~120 nt); EAR enhances the expression of downstream exopolysaccharide genes and thus drives biofilm formation in Bacillus subtilis [63].…”

Section: Nascent Rna Modulates the Activity Of Rnapmentioning

confidence: 99%

A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure

Zhang

Landick

2016

Trends in Biochemical Sciences

119

124

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The vectorial (5′-to-3′ at varying velocity) synthesis of RNA by cellular RNA polymerases creates a rugged kinetic landscape, demarcated by frequent, sometimes long-lived pauses. In addition to myriad gene-regulatory roles, these pauses temporally and spatially program the co-transcriptional, hierarchical folding of biologically active RNAs. Conversely, these RNA structures, which form inside or near the RNA exit channel, interact with the polymerase and adjacent protein factors to influence RNA synthesis by modulating pausing, termination, antitermination, and slippage. Here we review the evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNA polymerase and nascent RNA structure. We categorize and attempt to rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies.

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Inhibition of a Transcriptional Pause by RNA Anchoring to RNA Polymerase

Cited by 24 publications

References 50 publications

Distinct pathways of RNA polymerase regulation by a phage-encoded factor

Distinct pathways of RNA polymerase regulation by a phage-encoded factor

Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator

A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure

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