Attenuation in the Escherichia coli tryptophan operon: role of RNA secondary structure involving the tryptophan codon region.

Oxender, Dale L.; Zurawski, Gérard; Yanofsky, Charles

doi:10.1073/pnas.76.11.5524

Cited by 134 publications

(86 citation statements)

References 20 publications

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“…gene regulation | translational control | metabolism R NA structures fulfill important roles in the regulation of gene expression including the control of translational initiation, transcriptional termination, and alternative splicing (1)(2)(3)(4)(5). In many cases, an RNA conformational change is crucial to gene regulation since one RNA sequence may adopt alternate structures.…”

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confidence: 99%

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

Perdrizet

Artsimovitch

Furman

et al. 2012

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

100

124

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Riboswitches are cis-acting elements that regulate gene expression by affecting transcriptional termination or translational initiation in response to binding of a metabolite. A typical riboswitch is made of an upstream aptamer domain and a downstream expression platform. Both domains participate in the folding and structural rearrangement in the absence or presence of its cognate metabolite. RNA polymerase pausing is a fundamental property of transcription that can influence RNA folding. Here we show that pausing plays an important role in the folding and conformational rearrangement of the Escherichia coli btuB riboswitch during transcription by the E. coli RNA polymerase. This riboswitch consists of an approximately 200 nucleotide, coenzyme B12 binding aptamer domain and an approximately 40 nucleotide expression platform that controls the ribosome access for translational initiation. We found that transcriptional pauses at strategic locations facilitate folding and structural rearrangement of the full-length riboswitch, but have minimal effect on the folding of the isolated aptamer domain. Pausing at these regulatory sites blocks the formation of alternate structures and plays a chaperoning role that couples folding of the aptamer domain and the expression platform. Pausing at strategic locations may be a general mechanism for coordinated folding and conformational rearrangements of riboswitch structures that underlie their response to environmental cues.gene regulation | translational control | metabolism R NA structures fulfill important roles in the regulation of gene expression including the control of translational initiation, transcriptional termination, and alternative splicing (1-5). In many cases, an RNA conformational change is crucial to gene regulation since one RNA sequence may adopt alternate structures. Regulation of gene expression is achieved when an input domain senses varying cellular conditions, resulting in shifting the balance between two or more structural states.A prime example of gene regulation by RNA conformational changes in bacteria is riboswitch control. Riboswitches are cisacting elements that regulate gene expression in response to the concentration of an intracellular metabolite. The coenzyme B12 riboswitch is located in the 5′ untranslated region of the btuB gene which encodes an outer membrane transporter for B12 (6) (Fig. 1A). The btuB riboswitch consists of two domains: an upstream coenzyme B12 binding aptamer and a downstream expression platform. When the cellular concentration of coenzyme B12 is high, this metabolite binds to the aptamer, reconfiguring the expression platform to form a structure in which the ribosome binding site (RBS) is base paired and inaccessible. When the concentration of coenzyme B12 is low, the mRNA forms an alternate structure which allows for translation (6, 7).RNA folding and conformational switching occurs during transcription in vivo. Folding during transcription is particularly important for riboswitch regulation (8). Although bacterial RNA ...

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mentioning

confidence: 99%

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

Perdrizet

Artsimovitch

Furman

et al. 2012

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

100

124

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“…30 In essence, the choice between terminator and anti-terminator structures bridges the communication between the translation of the leader peptide and the transcription of operon genes in exchanging the message for the abundance of trp. 10,33 Dual regulatory systems for the operon expression When trp is abundant, the cell uses a repressive system to promote the synthesis of other amino acids in starvation; here, the trpR repressor operates on the transcription initiation whereas the attenuation operates on the progressing transcription. 10 The repression system targets the intracellular trp concentration which depends on the influx trp, the newly synthesised trp, and finally the consumption of trp for protein synthesis.…”

Section: Trp Operon Leadermentioning

confidence: 99%

“…Lee and Yanofsky (1977) concluded that the termination efficiency at the attenuator is correlated with the stability of an embedded secondary structure which is conserved between E. coli and Salmonnella typhimurium; the proposed structures agree with results of a partial RNase T1 digestion that exhibit digestion resistance in the distal portion of this transcript, i.e., where the structural features are located. 32 Thereafter, Oxender et al (1979) conducted structural probing with RNase T1 partial digestion followed by isolation of the comigrating pairing regions in a non-denaturing gel electrophoresis; the base-pairing regions were subsequently identified via denaturing gel electrophoresis and fingerprinting, based on which the two hairpins comprising the terminator structure were drawn. 33 Later on, the secondary structure of DNA template was ruled out as a contributor for this termination signal so the RNA structural features are the one causing the termination.…”

Section: Trp Operon Leadermentioning

confidence: 99%

“…32 Thereafter, Oxender et al (1979) conducted structural probing with RNase T1 partial digestion followed by isolation of the comigrating pairing regions in a non-denaturing gel electrophoresis; the base-pairing regions were subsequently identified via denaturing gel electrophoresis and fingerprinting, based on which the two hairpins comprising the terminator structure were drawn. 33 Later on, the secondary structure of DNA template was ruled out as a contributor for this termination signal so the RNA structural features are the one causing the termination. 9,38,39 Indeed, the functional importance of the second hairpin for the transcriptional termination is illustrated by the reduced transcription termination frequency observed in experiments destabilising the central GCC pairing of this hairpin, such as by in vivo mutational analysis or in vitro substitution of G-C bond by I-C bond.…”

Section: Trp Operon Leadermentioning

confidence: 99%

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Four RNA families with functional transient structures

Zhu

Meyer

2015

RNA Biology

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P rotein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since RFAM annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing RFAM families or introduce a new RNA family to RFAM. For each of the four RNA families, we compile a multiplesequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5 0 flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5 0 UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All transient and dominant structures are mapped to our new alignments introduced here.

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“…The expression of operons for the biosynthesis of amino acids like trp (10), his (1,2,7,8,11), pheA (12), leu (13), thr (14), and ilv (15,16) is regulated by transcription termination at the attenuator barrier. Active synthesis and translation of a small mRNA called leader RNA is an essential part of this regulatory mechanism (2,11,17,18).…”

mentioning

confidence: 99%

In vivo and in vitro detection of the leader RNA of the histidine operon of Escherichia coli K-12.

Frunzio¹,

Bruni²,

Blasi³

1981

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

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The DNA ofthe attenuator region ofthe histidine operon of Escherichia coli has been transcribed in a purified in vitro system and found to synthesize two major RNA transcripts. The first one, 180 nucleotides long, has been identified as the histidine-specific leader RNA. It contains the coding sequence for the leader peptide [Di Nocera, P. P., Blasi, F., Di Lauro, R., Frunzio, R. & Bruni, C. B. (1978) Proc. Natl. Acad. Sci. USA 75,[4276][4277][4278][4279][4280] and is terminated at the attenuator site. Termination of transcription at this site is extremely efficient in the in vitro system. The leader RNA also has been detected in vivo in a minicell producer strain transformed with plasmids harboring the regulatory region of the histidine operon of E. coli. A second RNA molecule is synthesized in the in vitro system. It has a divergent direction of transcription with respect to the histidine leader RNA, but its role, if any, in the regulation of the histidine operon remains to be ascertained. The existence ofthe histidine leader RNA lends support to the regulatory mechanism which postulates that regulation of the histidine operon is dependent on the alternative secondary structures that the leader RNA may assume, depending on whether or not the histidine-rich leader peptide is translated.Expression ofthe his operon in bacteria is regulated at the level of transcription (1-3). The levels of his mRNA increase in regulatory mutants and de end on the structure and the levels of charged histidyl-tRNA 's (4, 5). Regulation is exerted at a region of DNA upstream of the structural genes at two different sites: a promoter site (6) and a transcriptional barrier called the attenuator (1,7,8). Histidine-specific regulation seems to occur mostly at the attenuator site (6).Transcription termination, first discovered in A phage (9), is a major regulatory mechanism in prokaryotes. The expression of operons for the biosynthesis of amino acids like trp (10), his (1, 2, 7, 8, 11), pheA (12), leu (13), thr (14), and ilv (15, 16) is regulated by transcription termination at the attenuator barrier. Active synthesis and translation of a small mRNA called leader RNA is an essential part of this regulatory mechanism (2,11,17,18).Although his was the first system in which an attenuator was described (1), no direct proof of a leader RNA has been reported. The transcription termination mechanism is supported by the nucleotide sequence ofa region of DNA upstream ofthe first structural gene hisG (7,8) and of a deletion mutant defective in transcription termination (11).In this paper we present direct evidence for the synthesis of a leader RNA of the his operon of Escherichia coli both in vivo and in vitro. Moreover, a transcription map ofthe his promoter region is presented, which also shows an additional transcription initiation signal about 200 base pairs (bp) upstream of the his promoter. This initiation site is very efficient in vitro and transcribes in an orientation opposite to that of the his operon.MATERIALS AND METHODS DNAs ...

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Attenuation in the Escherichia coli tryptophan operon: role of RNA secondary structure involving the tryptophan codon region.

Cited by 134 publications

References 20 publications

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

Four RNA families with functional transient structures

In vivo and in vitro detection of the leader RNA of the histidine operon of Escherichia coli K-12.

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