Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli

Zhong, Qian; Trostel, Andrei; Lewis, Dale E.A.; Lee, Sang Jun; He, Ximiao; Stringer, Anne M.; Wade, Joseph T.; Schneider, Thomas D.; Durfee, Tim

doi:10.3389/fmolb.2016.00074

Cited by 10 publications

(8 citation statements)

References 59 publications

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“…Similarly, Qian et al . (38) created a TAP-tagged GalR strain to identify GalR binding sites in E. coli and Stringer et al . (39) constructed a TAP-tagged AraC to map AraC binding sites in E. coli .…”

Section: Discussionmentioning

confidence: 99%

DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolor

Šmídová

Ziková

Pospíšil

et al. 2018

Nucleic Acids Research

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HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation of protein-coding genes with HrdB alone and with a complex of HrdB and a transcriptional cofactor RbpA, using gene expression time series, identified 1694 genes that were under their direct control. When using the HrdB–RbpA complex in the model, an increase of the model fidelity was found for 322 genes. Functional analysis revealed that HrdB controls the majority of gene groups essential for the primary metabolism and the vegetative growth. Particularly, almost all ribosomal protein-coding genes were found in the HrdB regulon. Analysis of promoter binding sites revealed binding motif at the −10 region and suggested the possible role of mono- or di-nucleotides upstream of the −10 element.

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Section: Discussionmentioning

confidence: 99%

DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolor

Šmídová

Ziková

Pospíšil

et al. 2018

Nucleic Acids Research

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“…However, some of the apparently “non-functional” or “spurious” binding sites might turn out to play pivotal roles in maintaining adequate transcriptional regulation under the condition of genetic or environmental abnormalities (Spivakov, 2014 ). In addition, an increasing number of examples of transcription factor binding sites are not associated with specific gene regulation in prokaryotes (Grainger et al, 2005 ; Qian et al, 2016 ). Eight genes have recognized dre sites but are not differentially expressed; we speculated that some of them might be involved in the type of specific non-functional interactions, such as gene bofA (BTF1_26160).…”

Section: Discussionmentioning

confidence: 99%

NagRBt Is a Pleiotropic and Dual Transcriptional Regulator in Bacillus thuringiensis

et al. 2018

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NagR, belonging to the GntR/HutC family, is a negative regulator that directly represses the nagP and nagAB genes, which are involved in GlcNAc transport and utilization in Bacillus subtilis. Our previous work confirmed that the chitinase B gene (chiB) of Bacillus thuringiensis strain Bti75 is also negatively controlled by YvoABt, the ortholog of NagR from B. subtilis. In this work, we investigated its regulatory network in Bti75 and found that YvoABt is an N-acetylglucosamine utilization regulator primarily involved in GlcNAc catabolism; therefore YvoABt is renamed as NagRBt. The RNA-seq data revealed that 27 genes were upregulated and 14 genes were downregulated in the ΔnagR mutant compared with the wild-type strain. The regulon (exponential phase) was characterized by RNA-seq, bioinformatics software, electrophoretic mobility shift assays, and quantitative real-time reverse transcription PCR. In the Bti75 genome, 19 genes that were directly regulated and 30 genes that were indirectly regulated by NagRBt were identified. We compiled in silico, in vitro, and in vivo evidence that NagRBt behaves as a repressor and activator to directly or indirectly influence major biological processes involved in amino sugar metabolism, nucleotide metabolism, fatty acid metabolism, phosphotransferase system, and the Embden–Meyerhof–Parnas pathway.

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“…Finally, we cannot rule out the possibility that intragenic PhoB sites in E. coli are functional. For example, they could contribute, en masse, to titration of PhoB, they could facilitate DNA looping that impacts chromosome structure, as has been suggested for some TFs (22)(23)(24)(25)(26)(27), or they could regulate transcription by unknown mechanisms.…”

Section: Most Intragenic Phob Sites Appear To Be Non-functional and A...mentioning

confidence: 99%

Genome-wide mapping of theEscherichia coliPhoB regulon reveals many transcriptionally inert, intragenic binding sites

Fitzgerald

Stringer

Smith

et al. 2023

Preprint

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Genome-scale analyses have revealed many transcription factor binding sites within, rather than upstream of genes, raising questions as to the function of these binding sites. Here, we use complementary approaches to map the regulon of theEscherichia colitranscription factor PhoB, a response regulator that controls transcription of genes involved in phosphate homeostasis. Strikingly, the majority of PhoB binding sites are located within genes, but these intragenic sites are not associated with detectable transcription regulation and are not evolutionarily conserved. Many intragenic PhoB sites are located in regions bound by H-NS, likely due to shared sequence preferences of PhoB and H-NS. However, these PhoB binding sites are not associated with transcription regulation even in the absence of H-NS. We propose that for many transcription factors, including PhoB, binding sites not associated with promoter sequences are transcriptionally inert, and hence are tolerated as genomic "noise".

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Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli

Cited by 10 publications

References 59 publications

DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolor

DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolor

NagRBt Is a Pleiotropic and Dual Transcriptional Regulator in Bacillus thuringiensis

Genome-wide mapping of theEscherichia coliPhoB regulon reveals many transcriptionally inert, intragenic binding sites

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