A Synthetic Oligo Library and Sequencing Approach Reveals an Insulation Mechanism Encoded within Bacterial σ 54 Promoters

Levy, Lior; Anavy, Leon; Solomon, Oz; Cohen, Roni; Brunwasser-Meirom, Michal; Ohayon, Shilo; Atar, Orna; Goldberg, Sarah; Yakhini, Zohar; Amit, Roee

doi:10.1016/j.celrep.2017.09.063

Cited by 23 publications

(13 citation statements)

References 42 publications

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“…This would represent a very efficient system for insulating expression from an operon to prevent spurious gene expression, which might be particularly useful to preserve expression of "mobile" operons that are laterally transferred and inserted in different replicons. A similar phenomenon of insulation was previously reported at the E. coli glnK N promoter and thoroughly characterized (Levy et al, 2017).…”

Section: Discussionsupporting

confidence: 81%

Identification of a complete dibenzothiophene biodesulfurization operon and its regulator by functional metagenomics

Martín-Cabello

Terrón-González

Ferrer

et al. 2019

Environmental Microbiology

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Dibenzothiophene biodesulfurization is an important process for removing sulfur from fossil fuels. Functional metagenomics identified a complete operon for biodesulfurization (dszEABC) with a different gene arrangement and containing a gene coding for the FMNdependent reductase that is missing in all other dsz operons. Regulation of the operon is fully characterized in vivo and in vitro and shown to be Ndependent, unlike other operons of cultured bacteria. The N-dependent promoter, the activator gene and the reductase-coding gene have been apparently recruited from a different pathway. An insulation phenomenon that could be relevant in nature to prevent spurious expression of "mobile" operons when laterally transferred to different replicons is also reported here and its mechanism elucidated: an insulator sequence in the promoter region binds to the ribosome binding site of the first gene dszE, thus preventing its translation, combined with translational coupling of the downstream dszABC genes.

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Section: Discussionsupporting

confidence: 81%

Identification of a complete dibenzothiophene biodesulfurization operon and its regulator by functional metagenomics

Martín-Cabello

Terrón-González

Ferrer

et al. 2019

Environmental Microbiology

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“…bEBPs are special hexameric ATPases that use ATP hydrolysis to remodel theRNAP–σ 54 complex [ 103 ]. In addition, it was shown that bEBP binding sites can isolate or filter readthrough transcription from upstream genes [ 13 , 104 ]. This property makes these sequences similar to eukaryotic insulators.…”

Section: Enhancer-like Mechanisms In Eubacteriamentioning

confidence: 99%

Evolution of Regulated Transcription

Bylino

Ibragimov

Shidlovskii

2020

Cells

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The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.

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“…Chromatin immunoprecipitation (ChIP) based methods such as ChIP-chip and ChIP-seq make it possible to determine the genome-wide binding locations of individual transcription factors of interest. Massively parallel reporter assays (MPRAs) have made it possible to read out transcription factor binding position and occupancy in vivo with base-pair resolution, and provide a means for analyzing additional features such as “insulator” sequences [6–8]. In vitro methods based on protein-binding microarrays [9], SELEX [10–12], MITOMI [13–15], and binding assays performed in high-throughput sequencing flow cells [16, 17] have made it possible to measure transcription factor affinity to a broad array of possible binding sites and can also account for features such as flanking sequences [15, 18, 19].…”

Section: Introductionmentioning

confidence: 99%

Mapping DNA sequence to transcription factor binding energy in vivo

et al. 2019

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Despite the central importance of transcriptional regulation in biology, it has proven difficult to determine the regulatory mechanisms of individual genes, let alone entire gene networks. It is particularly difficult to decipher the biophysical mechanisms of transcriptional regulation in living cells and determine the energetic properties of binding sites for transcription factors and RNA polymerase. In this work, we present a strategy for dissecting transcriptional regulatory sequences using in vivo methods (massively parallel reporter assays) to formulate quantitative models that map a transcription factor binding site’s DNA sequence to transcription factor-DNA binding energy. We use these models to predict the binding energies of transcription factor binding sites to within 1 k B T of their measured values. We further explore how such a sequence-energy mapping relates to the mechanisms of trancriptional regulation in various promoter contexts. Specifically, we show that our models can be used to design specific induction responses, analyze the effects of amino acid mutations on DNA sequence preference, and determine how regulatory context affects a transcription factor’s sequence specificity.

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A Synthetic Oligo Library and Sequencing Approach Reveals an Insulation Mechanism Encoded within Bacterial σ 54 Promoters

Cited by 23 publications

References 42 publications

Identification of a complete dibenzothiophene biodesulfurization operon and its regulator by functional metagenomics

Identification of a complete dibenzothiophene biodesulfurization operon and its regulator by functional metagenomics

Evolution of Regulated Transcription

Mapping DNA sequence to transcription factor binding energy in vivo

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