Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters
It is suggested that considering promoter elements according to their involvement in early ( polymerase binding) or later (polymerase isomerization) steps in transcription initiation rather than simply from their match to conventional promoter consensus sequences is a more instructive form of promoter classification.
The BvgAS Regulon of Bordetella pertussis
The first RNA-seq analysis of the BvgAS regulon in B. pertussis is reported, revealing that more than 550 genes are regulated by BVGAS and showing for the first time that genes for multiple and varied metabolic pathways are significantly upregulated in the B.pertussis Bvg(−) mode.
Domain 1.1 of the sigma(70) subunit of Escherichia coli RNA polymerase modulates the formation of stable polymerase/promoter complexes.
- S. Vuthoori, C. W. Bowers, A. McCracken, A. Dombroski, D. Hinton
- BiologyJournal of Molecular Biology
- 8 June 2001
It is suggested that domain 1.1 influences initiation by constraining polymerase to assess a promoter primarily by the fitness of its -10 and -35 regions to the canonical sequences.
Transcription regulation at the core: similarities among bacterial, archaeal, and eukaryotic RNA polymerases.
Details of core promoter recognition in bacteria are examined that reveal the transcriptional similarities throughout biology, from specificity factor exchange to the employment of activators that bind close to or overlap core promoter sequences, directing the transcriptionAL machinery to a new start site.
Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage.
In vitro assays indicate that SegA, like I-Tev I, is a Mg(2+)-dependent DNA endonuclease that has preferred sites for cutting, however, there is no evidence that segA (or the other seg genes) resides within introns.
Transcriptional takeover by sigma appropriation: remodelling of the sigma70 subunit of Escherichia coli RNA polymerase by the bacteriophage T4 activator MotA and co-activator AsiA.
This review discusses how these interactions accomplish the switch to T4 middle promoters by inhibiting the typical contacts of the C-terminal region of sigma(70), region 4, with the host -35 DNA element and with other subunits of polymerase.
The promoter spacer influences transcription initiation via σ70 region 1.1 of Escherichia coli RNA polymerase
- India G. Hook-Barnard, D. Hinton
- BiologyProceedings of the National Academy of Sciences
- 20 January 2009
It is shown that the AT-rich Pminor spacer sequence, rather than promoter recognition elements or downstream DNA, determines the effect of region 1.1 on promoter activity, and it is speculated that the spacer can influence the trajectory or flexibility of DNA as it enters the RNAP channel and that region1.1 acts as a “gatekeeper” to monitor channel entry.
Analysis of regions within the bacteriophage T4 AsiA protein involved in its binding to the sigma70 subunit of E. coli RNA polymerase and its role as a transcriptional inhibitor and co-activator.
The Bordetella pertussis model of exquisite gene control by the global transcription factor BvgA.
Two virulence genes, fim2 and fim3, which encode serologically distinct fimbrial subunits, are regulated using a previously unrecognized RNA polymerase/activator architecture, demonstrating one aspect whereby B. pertussis, which is highly clonal and lacks the extensive genetic diversity observed in many other bacterial pathogens, has been highly successful as an obligate human pathogen.
Novel architectural features of Bordetella pertussis fimbrial subunit promoters and their activation by the global virulence regulator BvgA
- Qing Chen, K. B. Decker, P. Boucher, D. Hinton, S. Stibitz
- BiologyMolecular Microbiology
- 1 September 2010
A prominent feature of the promoters of Bordetella pertussis fimbrial subunit genes fim2, fim3 and fimX is the presence of a ‘C‐stretch’, a monotonic run of C residues, and it is found that the three optimized promoters align perfectly.