RNA sequence and secondary structure requiresments for rho-dependent transcription termination

Morgan, W. T. J.; Bear, David G.; Litchman, Bronwen L.; Hippel, Peter H. von

doi:10.1093/nar/13.10.3739

Cited by 101 publications

(73 citation statements)

References 47 publications

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“…Finally, it may be pointed out that the inverted repeat downstream of the stop codons seems to fit better in the p-independent transcription terminator features, since it is mostly formed by G and C nucleotides and is followed by several U and A residues as described by d'Aubenton Caraffa [26]. Besides, it seems not to fulfill most of the requirements proposed for the p-dependent terminators [27]. More information will be required to define the transcription organization of locus glc.…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterization of Escherichia coli Malate Synthase G

Molina

Pellicer

Badı́a

et al. 1994

European Journal of Biochemistry

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Two genes encoding the enzymes malate synthase G and glycolate oxidase, have been linked to locus glc (64.5 min), responsible for glycolate utilization in Escherichia coli. The gene encoding malate synthase G, for which we propose the notation glcB, has been cloned, sequenced and found to correspond to a 2262-nucleotide open-reading frame, which can encode a 723-amino-acid polypeptide, clearly different from the isoenzyme malate synthase A, which has 533 amino acids. Northern-blot experiments indicate that glcB was expressed as an apparently monocistronic transcript, inducible by glycolate. Malate synthase G was purified to near homogeneity. The molecular mass determined by gel filtration yielded a value of 82 kDa for the purified enzyme and the same value as for the crude extract enzyme, indicating a monomeric structure. Despite the lower sequence similarity between malate synthase G and the other reported malate synthases, three out of nine consensus boxes defined in most of these enzymes are conserved in addition to a cysteine residue that has been reported to be important for the catalytic mechanisms.Two isoenzymes of malate synthase have been described for the metabolism of glyoxylate in Escherichia coli. Malate synthase A (MSA), involved in the glyoxylate by-pass reaction, is encoded by the gene aceB belonging to the ace operon located at 91 min on the genetic map [l], and is predominant (60% total activity) in cells metabolizing the glyoxylate formed in the dissimilation of acetate [2]. The other isoenzyme, malate synthase G (MSG), encoded by a gene mapped in the locus glc, accounts for almost the entire malate-synthesizing activity in cells metabolizing the glyoxylate formed during growth on glycolate [2]. Both isoenzymes catalyze the condensation of glyoxylate and acetyl-CoA to yield malate, display very similar kinetic parameters for the substrate (31, and are distinguished on the basis of their chromatographic separation, thermostability and sensitivity to inhibitors such as glycolate and oxalate [3].In glycolate metabolism, this compound is first oxidized to glyoxylate by the action of glycolate oxidase [4, 51. Glyoxylate is subsequently metabolized by two divergent codensation reactions; one reaction is catalyzed by glyoxylate carboligase, which converts two glyoxylate molecules to tartronic semialdehyde and carbon dioxide [6], and the other reaction is catalyzed by MSG. The latter process can be considered a reaction of an oxidative pathway if glyoxylate is metabolized through the dicarboxylic cycle, or a reaction of Correspondence to L. Baldomi,

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Section: Discussionmentioning

confidence: 99%

Molecular Characterization of Escherichia coli Malate Synthase G

Molina

Pellicer

Badı́a

et al. 1994

European Journal of Biochemistry

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“…Rho-dependent termination specificity also has a &s-specificity element, in that rho will only bind to a subset of nascent transcripts that carry a specific 'rho loading site', defined as a stretch of RNA that is effectively free of secondary structure over 70-80 nucleotide residues [54]. This requirement follows from the fact that rho is a single-stranded RNA binding protein with a hexameric RNA site size of 70-80 nucleotide residues.…”

Section: Cis Effects As Regulatory Elements In Transcript Elongation mentioning

confidence: 99%

Specificity mechanisms in the control of transcription

Hippel

Rees

Rippe

et al. 1996

Biophysical Chemistry

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In this overview we analyze and illustrate the principles underlying some of the specificity mechanisms that control the initiation, elongation, and termination phases of transcription. Thermodynamic mechanisms dominate in the first steps of initiation, where promoters at various levels of activation can be considered to be in competition for a limiting supply of core RNA polymerase. In the later stages of initiation, as well as in elongation and termination, the regulatory mechanisms that control specificity are largely kinetic, involving rate competition between branching reaction pathways where the outcome depends on the rates (and equilibria) of reaction and interconversion of different forms of the transcription complex. Elongation complexes are very stable at most positions along the DNA template, meaning that only RNA chain elongation (and editing) can occur at these positions. However, the stability of transcription complexes decreases abruptly when termination sequences are encountered, and here the outcome can be easily switched between elongation and termination (RNA release) by minor changes in the relative rates of these competing processes. Cis effecters, defined as sites at which regulatory proteins bind to upstream activation loci on either the DNA or the nascent RNA, play important roles in the control of both initiation and of the elongation-termination decision. Examples, drawn from studies of phage A N-dependent antitermination and E. coli rho-dependent termination processes, illustrate the flexibility and additivity of regulatory components within control mechanisms in transcription that involve multiple determinants. The generality of such regulatory principles are stressed.

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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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RNA sequence and secondary structure requiresments for rho-dependent transcription termination

Cited by 101 publications

References 47 publications

Molecular Characterization of Escherichia coli Malate Synthase G

Molecular Characterization of Escherichia coli Malate Synthase G

Specificity mechanisms in the control of transcription

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

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