Mechanism of Transcriptional Activation by FIS: Role of Core Promoter Structure and DNA Topology

Auner, H. L.; Buckle, Malcolm; Deufel, Annette; Kutateladze, Tamara; Lazarus, Linda; Mavathur, Ramesh; Muskhelishvili, Georgi; Pemberton, Iain K.; Schneider, Robert; Travers, Andrew

doi:10.1016/s0022-2836(03)00727-7

Cited by 65 publications

(77 citation statements)

References 57 publications

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“…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

357

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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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

357

379

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“…Under such circumstances, easily deformable DNA sequences may act as sinks withdrawing such excessive supercoils, which would otherwise impede the translocation of enzymatic machineries [Travers and Muskhelishvili, 2014]. Previous work proposed that cumulative effects of DNA translocating enzymatic machineries, DNA topoisomerases and NAPs determine the genomic distributions of the effective superhelicity that specifies the preferred local geometry and activity of the chromosomal gene promoters [Auner et al, 2003;Opel et al, 2001;Rochman et al, 2002; Order from the Order Muskhelishvili, 2005b], whereas the entire repertoire of such local structures in turn determines the protein binding pattern [see e.g. Cameron and Dorman, 2012] and, ultimately, the expression of the linear genetic code.…”

Section: Regulation Of Dna Supercoil Dynamics and Transcriptionmentioning

confidence: 99%

Order from the Order: How a Spatiotemporal Genetic Program Is Encoded in a 2-D Genetic Map of the Bacterial Chromosome

Muskhelishvili

Travers²

2014

Microb Physiol

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In this article, we sketch out a holistic methodology used for exploring how the genetic program is encoded in a 2-D genetic map of a bacterial chromosome. We argue that the major problem resides in the conceptual integration of the two logically distinct types of information encoded in the chiral double-helical DNA polymer. This integration is accomplished by mapping the genetic function on the genomic sequence organisation and therefore is potentially applicable to any chromosome. The vast generalisation achieved by this approach necessarily ignores exquisite details, yet it is fundamental in providing comprehensive methodology for exploring the role of the DNA sequence organisation in harnessing genetic information and sustaining biological order.

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“…Histone-like proteins also act as pleiotropic regulatory molecules. Their regulatory functions differ from prototypical transcription factors in that they tend to globally regulate gene expression by binding to and altering the topology of gene promoter regions, which subsequently influences transcript synthesis (3,25,58). Histone-like proteins also posttranscriptionally modulate gene expression by binding directly to mRNA molecules and influencing transcript stability and translation (4,13,22).…”

mentioning

confidence: 99%

Characterizing the Effect of theStaphylococcus aureusVirulence Factor Regulator, SarA, on Log-Phase mRNA Half-Lives

et al. 2006

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Bacterial pathogens regulate virulence factor expression at both the level of transcription initiation and mRNA processing/turnover. Within Staphylococcus aureus, virulence factor transcript synthesis is regulated by a number of two-component regulatory systems, the DNA binding protein SarA, and the SarA family of homologues. However, little is known about the factors that modulate mRNA stability or influence transcript degradation within the organism. As our entree to characterizing these processes, S. aureus GeneChips were used to simultaneously determine the mRNA half-lives of all transcripts produced during log-phase growth. It was found that the majority of log-phase transcripts (90%) have a short half-life (<5 min), whereas others are more stable, suggesting that cis-and/or trans-acting factors influence S. aureus mRNA stability. In support of this, it was found that two virulence factor transcripts, cna and spa, were stabilized in a sarA-dependent manner. These results were validated by complementation and real-time PCR and suggest that SarA may regulate target gene expression in a previously unrecognized manner by posttranscriptionally modulating mRNA turnover. Additionally, it was found that S. aureus produces a set of stable RNA molecules with no predicted open reading frame. Based on the importance of the S. aureus agr RNA molecule, RNAIII, and small stable RNA molecules within other pathogens, it is possible that these RNA molecules influence biological processes within the organism.

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Mechanism of Transcriptional Activation by FIS: Role of Core Promoter Structure and DNA Topology

Cited by 65 publications

References 57 publications

Ribosome Biogenesis and the Translation Process inEscherichia coli

Ribosome Biogenesis and the Translation Process inEscherichia coli

Order from the Order: How a Spatiotemporal Genetic Program Is Encoded in a 2-D Genetic Map of the Bacterial Chromosome

Characterizing the Effect of theStaphylococcus aureusVirulence Factor Regulator, SarA, on Log-Phase mRNA Half-Lives

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