A consensus motif common to all rho-dependent prokaryotic transcription terminators

Allfano, Pietro; Rivellini, F.; Limauro, Danila; Bruni, Carmelo B.; Carlomagno, Maria Stella

doi:10.1016/0092-8674(91)90239-u

Cited by 133 publications

(116 citation statements)

References 61 publications

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“…This region, called the CG bubble (23), is present in every cistron junction in the gal operon, with the exception of the galK-galM junction, as well as the end of the galM gene (1). The CG bubble also appears in all of the known Rho-dependent transcription termination sites at the trp t′, tyrT, bacteriophage f1 IV, lambda tR1, tnaC, hisG2148 mutant, and ilV468 mutant genes analyzed (24) (Fig.…”

Section: Discussionmentioning

confidence: 99%

Two-level inhibition of galK expression by Spot 42: Degradation of mRNA mK2 and enhanced transcription termination before the galK gene

Wang

Jeon

et al. 2015

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

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The Escherichia coli gal operon has the structure Pgal-galE-galTgalK-galM. During early log growth, a gradient in gene expression, named type 2 polarity, is established, as follows: galE > galT > galK > galM. However, during late-log growth, type 1 polarity is established in which galK is greater than galT, as follows: galE > galK > galT > galM. We found that type 2 polarity occurs as a result of the downregulation of galK, which is caused by two different molecular mechanisms: Spot 42-mediated degradation of the galK-specific mRNA, mK2, and Spot 42-mediated Rho-dependent transcription termination at the end of galT. Because the concentration of Spot 42 drops during the transition period of the polarity type switch, these results demonstrate that type 1 polarity is the result of alleviation of Spot 42-mediated galK down-regulation. Because the Spot 42-binding site overlaps with a putative Rho-binding site, a molecular mechanism is proposed to explain how Spot 42, possibly with Hfq, enhances Rhomediated transcription termination at the end of galT.D uring the exponential growth phase of Escherichia coli cells, transcription termination at the end of each cistron of the gal operon operates with less than 100% efficiency; a certain proportion of the transcription initiated from the two promoters of the gal operon terminates at the end of each constituent gene, galE, galT, galK, and galM, of the operon (1). The termination efficiencies measured at the end of each cistron are 16%, 29%, 65%, and 71%, respectively (1). Transcription termination at the end of each cistron generates four mRNA species: mE1, mT1, mK1, and mM1 (Fig.

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Section: Discussionmentioning

confidence: 99%

Two-level inhibition of galK expression by Spot 42: Degradation of mRNA mK2 and enhanced transcription termination before the galK gene

Wang

Jeon

et al. 2015

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

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“…Similarly, no proteins have been shown to interact with RNA sequences at sites of premature termination. Such proteins could function in a manner analogous to the prokaryotic termination factor rho, which binds to an unstructured C-rich region of RNA (Platt, 1986;Alifano et al, 1991;Hart and Roberts, 1991;Richardson, 1991;Rivellini, et al, 1991), or the mammalian protein La, which binds uridylate residues in the RNA at sites of termination by eukaryotic RNA polymerase III (Gottlieb and Steitz, 1989a,b). There is contradictory evidence concerning the actual number of sites of transcriptional attenuation that may be found within any given eukaryotic gene.…”

Section: Regulation Of Transcriptional Elongation Within Eukaryotic Cmentioning

confidence: 99%

Regulation of eukaryotic gene expression by transcriptional attenuation.

Wright

1993

MBoC

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“…[17][18][19], followed by a distal termination zone, dispersed over a wide range, beginning about 60 -90 nts downstream of the rut site (reviewed in Ref. 20).…”

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Transcription Termination Factor Rho Prefers Catalytically Active Elongation Complexes for Releasing RNA

Dutta

Chalissery²,

Sen

2008

Journal of Biological Chemistry

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RNA polymerase pauses at different DNA sequences during transcription elongation, and this pausing is associated with distinct conformational state(s) of the elongation complex (EC). Transcription termination by the termination factor Rho, an RNA-dependent molecular motor, requires pausing of the EC in the termination zone of Rho-dependent terminators. We hypothesized that the conformational state(s) of the EC associated with this pausing would influence the action of Rho. Analyses of the pausing behavior of the EC at the termination points of two well known Rho-dependent terminators revealed that Rho prefers actively transcribing complexes for termination. RNA release kinetics from stalled ECs showed that the rate of RNA release by Rho was reduced if the EC was irreversibly backtracked, if its RNA exit channel was modified by an RNA hairpin, or the bridge helix/trigger loop movement in its active site was perturbed. These defects were overcome significantly by enhancing the rate of ATP hydrolysis either by increasing the concentration of ATP or by using a Rho mutant with higher ATPase activity. We propose that the force generated from ATP hydrolysis of Rho is the key factor in dislodging the EC through its molecular motor action, and this process is facilitated when the EC is in a catalytically competent state, undergoing rapid "Brownian ratchet" motion.The highly processive and stable EC 3 (1-3) dissociates from template DNA only in response to transcription termination signals. There are two types of termination signals in Escherichia coli. The intrinsic terminators are characterized by a GC-rich inverted repeat followed by an oligo(dT) stretch that destabilizes the EC and the factor-dependent terminators, which depend on an essential protein, called Rho, for termination (4, 5).Rho is a homo-hexameric RNA/DNA helicase or translocase capable of dissociating the elongating RNA polymerase from the template DNA by utilizing its RNA-dependent ATPase activity (6 -8). It recognizes the Rho utilization (rut) site on the exiting mRNA through its N-terminal primary RNA binding domain (9). Binding of RNA to the primary binding site of Rho guides the 3Ј-side of the RNA into the central hole of the hexamer, which constitutes the secondary RNA binding domain. Q-loop and R-loop are the two major RNA binding determinants of Rho at this site. Interaction of the RNA with these two loops activates ATP hydrolysis in the nearby P-loop region (10 -16).The Rho-dependent termination region consists of a proximal 70 -80-nt stretch of Cys-rich, unstructured RNA for binding of Rho (the rut site; see Refs. 17-19), followed by a distal termination zone, dispersed over a wide range, beginning about 60 -90 nts downstream of the rut site (reviewed in Ref. 20). Analyses of Rho-dependent terminators revealed that the position of the rut site determines the location of the downstream termination zone (21-24). Unlike Rho-independent terminators, the termination zone of the well characterized Rho-dependent terminators, such as tR1 and trp tЈ, do...

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A consensus motif common to all rho-dependent prokaryotic transcription terminators

Cited by 133 publications

References 61 publications

Two-level inhibition of galK expression by Spot 42: Degradation of mRNA mK2 and enhanced transcription termination before the galK gene

Two-level inhibition of galK expression by Spot 42: Degradation of mRNA mK2 and enhanced transcription termination before the galK gene

Regulation of eukaryotic gene expression by transcriptional attenuation.

Transcription Termination Factor Rho Prefers Catalytically Active Elongation Complexes for Releasing RNA

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