Activation of transcription initiation from a stable RNA promoter by a Fis protein‐mediated DNA structural transmission mechanism

Opel, Michael L.; Aeling, Kimberly A.; Holmes, W M; Johnson, Reid C.; Benham, Craig J.; Hatfield, G. Wesley

doi:10.1111/j.1365-2958.2004.04147.x

Cited by 46 publications

(37 citation statements)

References 43 publications

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“…The actual mechanism, however, may involve presentation of specific recognition elements along with a combinatorial effect of diverse factors ranging from DNA topology to cellular interacting partners. The association of the target sites over a broad region (100 bp flanking G4 motifs) is consistent with the observation that transcription factor binding induces transmission of superhelical destabilization to distal promoter sites (Sheridan et al 1999;Opel et al 2004). …”

Section: Discussionsupporting

confidence: 57%

Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation

Rawal¹,

Kummarasetti²,

Ravindran³

et al. 2006

Genome Res.

311

335

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The role of nonlinear DNA in replication, recombination, and transcription has become evident in recent years. Although several studies have predicted and characterized regulatory elements at the sequence level, very few have investigated DNA structure as regulatory motifs. Here, using G-quadruplex or G4 DNA motifs as a model, we have researched the role of DNA structure in transcription on a genome-wide scale. Analyses of >61,000 open reading frames (ORFs) across 18 prokaryotes show enrichment of G4 motifs in regulatory regions and indicate its predominance within promoters of genes pertaining to transcription, secondary metabolite biosynthesis, and signal transduction. Based on this, we predict that G4 DNA may present regulatory signals. This is supported by conserved G4 motifs in promoters of orthologous genes across phylogenetically distant organisms. We hypothesized a regulatory role of G4 DNA during supercoiling stress, when duplex destabilization may result in G4 formation. This is in line with our observations from target site analysis for 55 DNA-binding proteins in Escherichia coli, which reveals significant (P < 0.001) association of G4 motifs with target sites of global regulators FIS and Lrp and the sigma factor RpoD ( 70 ). These factors together control >1000 genes in the early growth phase and are believed to be induced by supercoiled DNA. We also predict G4 motif-induced supercoiling sensitivity for >30 operons in E. coli, and our findings implicate G4 DNA in DNA-topology-mediated global gene regulation in E. coli.

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Section: Discussionsupporting

confidence: 57%

Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation

Rawal¹,

Kummarasetti²,

Ravindran³

et al. 2006

Genome Res.

311

335

View full text Add to dashboard Cite

show abstract

“…We favor a model in which P-PrrA binds with higher affinity to RSP3361 gene PrrA site 2 when in a supercoiled topological conformation than when in a linear form. Similar topologically dependent, preferential DNA binding of transcriptional factors has been previously reported for FIS (64) and IHF (75) in E. coli. While DNA supercoiling levels might affect P-PrrA binding to PrrA site 2, an analysis of the RSP3361 gene regulatory region identified an 8-nt sequence, partly overlapping the 3Ј end of the Ϫ10 region of the presumed promoter and immediate downstream sequence, with a high tendency to become single stranded by absorbing supercoiling energy, as described previously (17,34).…”

Section: Vol 191 2009supporting

confidence: 50%

Regulation of Gene Expression by PrrA in Rhodobacter sphaeroides 2.4.1: Role of Polyamines and DNA Topology

Eraso

Kaplan

2009

J Bacteriol

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In the present study, we show in vitro binding of PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, to the PrrA site 2, within the RSP3361 locus. Specific binding, as shown by competition experiments, requires the phosphorylation of PrrA. The binding affinity of PrrA for site 2 was found to increase 4-to 10-fold when spermidine was added to the binding reaction. The presence of extracellular concentrations of spermidine in growing cultures of R. sphaeroides gave rise to a twofold increase in the expression of the photosynthesis genes pucB and pufB, as well as the RSP3361 gene, under aerobic growth conditions, as shown by the use of lacZ transcriptional fusions, and led to the production of light-harvesting spectral complexes. In addition, we show that negative supercoiling positively regulates the expression of the RSP3361 gene, as well as pucB. We show the importance of supercoiling through an evaluation of the regulation of gene expression in situ by supercoiling, in the case of the former gene, as well as using the DNA gyrase inhibitor novobiocin. We propose that polyamines and DNA supercoiling act synergistically to regulate expression of the RSP3361 gene, partly by affecting the affinity of PrrA binding to the PrrA site 2 within the RSP3361 gene.

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“…2B). The promoter-proximal site I, which accounts for most of the activation in vivo, is required for RNAP recruitment to the region; sites II and III increase transcription only marginally (20 to 30%) (161,179). The FIS protein bends the DNA and untwists the Ϫ10 region, enhancing open complex formation (10).…”

Section: Regulation Of Expression Of Rrn Operonsmentioning

confidence: 99%

Ribosome Biogenesis and the Translation Process inEscherichia coli

Kaczanowska

Rydén-Aulin

2007

Microbiol Mol Biol Rev

359

379

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SUMMARY Translation, the decoding of mRNA into protein, is the third and final element of the central dogma. The ribosome, a nucleoprotein particle, is responsible and essential for this process. The bacterial ribosome consists of three rRNA molecules and approximately 55 proteins, components that are put together in an intricate and tightly regulated way. When finally matured, the quality of the particle, as well as the amount of active ribosomes, must be checked. The focus of this review is ribosome biogenesis in Escherichia coli and its cross-talk with the ongoing protein synthesis. We discuss how the ribosomal components are produced and how their synthesis is regulated according to growth rate and the nutritional contents of the medium. We also present the many accessory factors important for the correct assembly process, the list of which has grown substantially during the last few years, even though the precise mechanisms and roles of most of the proteins are not understood.

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Activation of transcription initiation from a stable RNA promoter by a Fis protein‐mediated DNA structural transmission mechanism

Cited by 46 publications

References 43 publications

Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation

Genome-wide prediction of G4 DNA as regulatory motifs: Role inEscherichia coliglobal regulation

Regulation of Gene Expression by PrrA in Rhodobacter sphaeroides 2.4.1: Role of Polyamines and DNA Topology

Ribosome Biogenesis and the Translation Process inEscherichia coli

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