tRNA as a positive regulator of transcription antitermination in B. subtilis

Grundy, Frank J.; Henkin, Tina M.

doi:10.1016/0092-8674(93)80049-k

Cited by 264 publications

(393 citation statements)

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“…In summary, almost all of the information that we have is consistent with the ilv-leu operon being controlled by a mechanism similar to that proposed by Grundy and Henkin (5). However, it should be noted that many of the features of a translation-dependent mechanism and an uncharged-tRNAdependent mechanism are the same, namely, the involvement of overlapping RNA secondary structures (protector, antiterminator, and terminator), tRNA synthetase, and tRNA.…”

Section: Resultssupporting

confidence: 60%

“…We suggest that the protector prevents formation of the antiterminator, thereby promoting terminator formation. A protector stem-and-loop structure was not postulated by Grundy and Henkin (5) for the tRNA synthetase genes, but our results suggest that it is a critical part of the mechanism for the ilv-leu operon. A search for secondary structures capable of precluding antiterminator formation in the leader regions of tyrS, thrS, valS, trpS, and leuS indicated that such structures may exist in these leaders but not in the pheS leader.…”

Section: Resultsmentioning

confidence: 42%

“…Grundy and Henkin proposed a model in which the leader regions of these operons fold in such a way that three consecutive nucleotides, termed the specifier, are exposed on a bulge region of the secondary structure (5). They presented evidence that the specifier codon of tyrS is essential for regulation of this operon by tyrosine and showed that this requirement is not due to involvement of this triplet in translation.…”

Section: Resultsmentioning

confidence: 99%

“…We also identified a region of the ilv-leu leader required for derepression in response to leucine limitation and show that the attenuation mechanism probably involves formation of three different secondary structures that are analogous to protector, antiterminator, and terminator stem-and-loop structures. As we point out in Discussion, the ilv-leu operon of B. subtilis shows many of the features of operons regulated by translation-dependent attenuation, but the weight of evidence supports the model of Grundy and Henkin (5).…”

mentioning

confidence: 79%

“…Grundy and Henkin recently presented evidence to support their model for translation-independent regulation of the B. subtilis tyrS gene (5). In this model, uncharged tyrosine tRNA acts as a positive regulatory factor and directly interacts with leader mRNA at a cognate triplet located in the bulge region of a specific stem and loop.…”

mentioning

confidence: 93%

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Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

et al. 1993

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The ilv-ku operon ofBacillus subtilis is regulated in part by transcription attenuation. The cis-acting elements required for regulation by leucine lie within a 683-bp fragment of DNA from the region upstream of ilvB, the first gene of the operon. This fragment contains the ilv-ku promoter and 482 bp of the ilv-ku leader region. Spontaneous mutations that lead to increased expression of the operon were shown to lie in an imperfect inverted repeat encoding the terminator stem within the leader region. Mutations within the inverted repeat of the terminator destroyed most of the leucine-mediated repression. The remaining leucine-mediated repression probably resulted from a decrease in transcription initiation. A systematic analysis of other deletions within the ilv-ku leader region identified a 40-bp region required for the derepression that occurred during leucine limitation. This region lies within a potential RNA stem-and-loop structure that is probably required for leucine-dependent control. Deletion analysis also suggested that alternate secondary structures proximal to the terminator are involved in allowing transcription to proceed beyond the terminator. Additional experiments suggested that attenuation of the ilv-ku operon is not dependent on coupling translation to transcription of the leader region. Our data support a model proposed by Grundy and Henkin (F. J. Grundy and T. M. Henkin, Cell 74:475-482, 1993) in which uncharged tRNA acts as a positive regulatory factor to increase gene expression during amino acid limitation.The ilv-leu operon of Bacillus subtilis contains seven genes encoding enzymes for the biosynthesis of isoleucine, valine, and leucine ( Fig. 1). Transcription of this operon is repressed by leucine but not by isoleucine or valine (21). In work published previously we showed that transcription is initiated 482 bp upstream of the start codon for ilvB, the first gene in the operon (4).In vitro transcription studies defined a strong transcription termination site at position +405, immediately downstream from an extended inverted repeat. Ninety percent of transcripts initiated at the promoter in vitro were terminated at this site. Analysis of mRNA levels in vivo suggested that repression by leucine occurs by attenuation of transcription within the 482-bp leader region and that the transcription terminator within the ilv-leu leader region is involved in the mechanism of leucine control (4).The ilv and leu genes in enteric bacteria are regulated mostly by translation-dependent attenuation, which relies on translation of a short open reading frame (ORF) within the leader RNA upstream of the structural genes. In the case of the leu operon, limitation for leucine results in stalling of the ribosome at leucine control codons within the leader. Stalling at these sites prevents formation of a terminator stem and loop by promoting formation of an antiterminator stem, leading to readthrough (10). When leucine is in excess, the ribosome does not stall and formation of the terminator is favored because...

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Section: Resultssupporting

confidence: 60%

Section: Resultsmentioning

confidence: 42%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 79%

mentioning

confidence: 93%

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Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

et al. 1993

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Antitermination Control of Gene Expression

Gollnick

Babitzke

2002

Encyclopedia of Molecular Biology

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Tails of Three Knotty Switches: HowPreQ₁Riboswitch Structures Control Protein Translation

Belashov

Dutta

Salim

et al. 2015

Encyclopedia of Life Sciences

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Riboswitches are structured RNA molecules that regulate genes by sensing cellular levels of metabolites such as preQ 1 (7‐aminomethyl‐7‐deazaguanine). This economical platform is found predominantly in the 5′‐leader sequences of bacterial mRNAs, attracting attention as a potential antibiotic target. Members of the preQ 1 riboswitch family provide exemplary insights into translational regulation because their high‐resolution structures have been determined, providing a framework to interpret complementary single‐molecule, computational and biochemical analyses. Although class I and II preQ 1 riboswitches possess divergent pseudoknot architectures, both appear to function by burying the Shine‐Dalgarno sequence (SDS) within a core aptamer domain upon preQ 1 binding. By contrast, the class III preQ 1 riboswitch binds its ligand in an aptamer distant from the SDS. PreQ 1 binding increases the population of riboswitches that transiently sequester the SDS, representing an alternative regulatory paradigm. Progress on preQ 1 riboswitches is described, along with expectations for interfacing a riboswitch with the ribosome for translation initiation. Key Concepts Riboswitches are structured non‐protein‐coding RNAs that bind small molecules, tRNA or ions to control gene expression without the need for proteins. Riboswitches bind protein enzyme co‐factors suggesting that they are remnants of an ancient RNA world. Three classes of riboswitches bind the metabolite prequeuosine 1 (preQ 1 ), a pyrrolopyrimidine made exclusively in bacteria as a precursor to the hypermodified base queuosine, which is used widely in the biosphere to confer translational fidelity. PreQ 1 riboswitches adopt pseudoknot folds in which ligand binding stabilises coaxial helical stacking. High‐resolution structures of class I, II and III preQ 1 riboswitches reveal their overall three‐dimensional folds, along with chemical details that explain their high‐affinity ligand binding. Structural observations suggest that riboswitches co‐opt traditional RNA tertiary interactions, such as major‐groove base‐triples and A‐minor motifs, for specialised biological functions. Class I and II preQ 1 riboswitches integrate Shine‐Dalgarno sequences (SDS) into their aptamer cores, producing gene off states in response to preQ 1 binding. Class III preQ 1 riboswitches fold with spatially disparate aptamer and expression platform sequences that do not commingle in response to ligand binding. Single‐molecule fluorescence resonance energy transfer (smFRET) provides insight into ligand‐dependent conformational changes of preQ 1 riboswitches that control gene expression. Modelling suggests that the class II preQ 1 riboswitch must unfold only its anti‐SDS⋅SDS helix to interact with the 16S ribosomal RNA.

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tRNA as a positive regulator of transcription antitermination in B. subtilis

Cited by 264 publications

References 28 publications

Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

Antitermination Control of Gene Expression

Tails of Three Knotty Switches: HowPreQ₁Riboswitch Structures Control Protein Translation

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tRNA as a positive regulator of transcription antitermination in B. subtilis

Cited by 264 publications

References 28 publications

Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

Antitermination Control of Gene Expression

Tails of Three Knotty Switches: HowPreQ1Riboswitch Structures Control Protein Translation

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Tails of Three Knotty Switches: HowPreQ₁Riboswitch Structures Control Protein Translation