Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions

Henkin, Tina M.; Yanofsky, Charles

doi:10.1002/bies.10125

Cited by 233 publications

(214 citation statements)

References 37 publications

(36 reference statements)

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“…If no suitable primers were found, we extended the amplified region to 300 bp into each ORF. For AAB promoters known to contain leader peptides 28 , the promoter region included the leader peptide coding region. We designed each of the two primers with either XhoI or BamHI restriction sites.…”

Section: Methodsmentioning

confidence: 99%

Just-in-time transcription program in metabolic pathways

et al. 2004

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A primary goal of systems biology is to understand the design principles of the transcription networks that govern the timing of gene expression 1-5 . Here we measured promoter activity for ∼100 genes in parallel from living cells at a resolution of minutes and accuracy of 10%, based on GFP and Lux reporter libraries 3 . Focusing on the amino-acid biosynthesis systems of Escherichia coli 4 , we identified a previously unknown temporal expression program and expression hierarchy that matches the enzyme order in unbranched pathways. We identified two design principles: the closer the enzyme is to the beginning of the pathway, the shorter the response time of the activation of its promoter and the higher its maximal promoter activity. Mathematical analysis suggests that this 'just-in-time' (ref. 5) transcription program is optimal under constraints of rapidly reaching a production goal with minimal total enzyme production 6,7 . Our findings suggest that metabolic regulation networks are designed to generate precision promoter timing and activity programs that can be understood using the engineering principles of production pipelines.Amino-acid biosynthesis (AAB) in E. coli is carried out by well-characterized enzymatic pathways 4,6-11 . The genes encoding these enzymes are governed by a transcriptional regulatory network 12,13 , which is an excellent model system for studying the design principles of metabolic regulation. To study the dynamics of transcription of AAB genes at high temporal resolution and accuracy, we constructed a library of 52 reporter strains that represent ∼50% of known AAB genes. We designed each reporter strain by cloning one of the promoter regions of E. coli K-12 MG1655 upstream of a Lux or a fast-folding GFP reporter gene (Fig. 1a). We measured promoter activity with a high temporal resolution by measuring fluorescence, luminescence and absorbance from 96 cultures in parallel in a multiwell fluorimeter 3,14 .

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Section: Methodsmentioning

confidence: 99%

Just-in-time transcription program in metabolic pathways

et al. 2004

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“…Expression of the at operon is controlled by tandem transcription and translation regulatory mechanisms based on sensing the level of charged͞uncharged tRNA Trp (17). Transcription of the structural genes of the at operon is regulated via the T-box transcription antitermination mechanism, where elevated levels of uncharged tRNA Trp induce transcription of rtpA (18), leading to AT production and increased trp operon expression and tryptophan biosynthesis (19). Translational control of at operon expression is provided by the ability of a translating ribosome to move along the mRNA region encoding a tryptophan-rich leader peptide.…”

mentioning

confidence: 99%

Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction

Shevtsov

Chen

Gollnick

et al. 2005

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

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In Bacillus subtilis the anti-TRAP protein (AT) is produced in response to the accumulation of uncharged tRNA Trp . AT regulates expression of genes involved in tryptophan biosynthesis and transport by binding to the tryptophan-activated trp RNA-binding attenuation protein (TRAP) and preventing its interaction with several mRNAs. Here, we report the x-ray structure of AT at 2.8 Å resolution, showing that the protein subunits assemble into tight trimers. Four such trimers are further associated into a 12-subunit particle in which individual trimers are related by twofold and threefold symmetry axes. Twelve DnaJ-like, cysteine-rich zincbinding domains form spikes on the surface of the dodecamer. Available data suggest several possible ways for AT to interact with the 11-subunit TRAP. Interaction between the two symmetrymismatching molecules could be assisted by the flexible nature of AT zinc-binding domains.DnaJ ͉ trp RNA-binding attenuation protein ͉ tryptophan biosynthesis ͉ protein-protein interactions

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“…Until recently it was accepted (Goldberger, 1974;Serfling, 1989) that this mechanism involved proteins specified by a given structural gene of the operon acting as a regulatory macromolecule. But during the last decade it has been demonstrated that RNA molecules can also serve as transcriptional enhancers and repressors (Henkin & Yanofsky, 2002). Riboswitches in the paradigms of genetic regulation in eukaryotes and prokaryotes are presently being subjected to intense investigation (Hesselberth & Ellington, 2002;Le Hir et al, 2003;Nudler & Mironov, 2004).…”

Section: Discussionmentioning

confidence: 99%

Autogenous modulation of the Bacillus subtilis sacB–levB–yveA levansucrase operon by the levB transcript

et al. 2004

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Silencing of levB, the second structural gene of the tricistronic levansucrase operon encoding the endolevanase LevB, decreases the level of levansucrase expression in Bacillus subtilis. Conversely, independent expression of levB greatly stimulates operon expression. This autogenous effect is mediated by the levB transcript, which carries an internal sequence (5′-AAAGCAGGCAA-3′) involved in the enhancing effect. In vitro, the levB transcript displays an affinity for the N-terminal fragment of SacY (K D 0·2 μM), the regulatory protein that prevents transcription termination of the levansucrase operon. This positive-feedback loop leads to an increase in the operon expression when B. subtilis is growing in the presence of high sucrose concentrations. Under these conditions, extracellular levan synthesized by the fructosyl polymerase activity of levansucrase can be degraded mainly into levanbiose by the action of LevB. Levanbiose is neither taken up nor metabolized by the bacteria. This work modifies the present view of the status of levansucrase in B. subtilis physiology.

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Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions

Cited by 233 publications

References 37 publications

Just-in-time transcription program in metabolic pathways

Just-in-time transcription program in metabolic pathways

Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction

Autogenous modulation of the Bacillus subtilis sacB–levB–yveA levansucrase operon by the levB transcript

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