The Role of LRP and H-NS in Transcription Regulation: Involvement of Synergism, Allostery and Macromolecular Crowding

Pul, Ümit; Wurm, Reinhild; Wagner, Rolf

doi:10.1016/j.jmb.2006.11.067

Cited by 46 publications

(42 citation statements)

References 66 publications

(89 reference statements)

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“…The footprinting results for the P1 fragment obtained in this study are in very good agreement with work published previously, in which the interaction of H-NS and LRP with DNA was analysed in greater detail (Pul et al, 2007).…”

Section: Dnase I Footprint Analysissupporting

confidence: 91%

“…The results support the findings of previous binding and DNase I footprint analyses, which demonstrate that LRP can bind at the rrnB P1 promoter between the 235 and 210 regions ( Fig. 3; Pul et al, 2007). In the P2 construct, which lacks a binding site upstream of the promoter core region, inhibition at 2 mM LRP was reduced to 40 % (Fig.…”

Section: Effects Of H-ns and Lrp On The Transcriptional Activity Of Tsupporting

confidence: 91%

“…Only at sufficiently high concentrations (.3 mM), after initial binding to a curved DNA target site, was H-NS able to polymerize into the core promoter region. The retardation analysis of promoter fragments without the bending module thus confirmed our previous results, namely that efficient H-NS binding requires a curved DNA region of the rrn P1 promoter (Pul et al, 2005(Pul et al, , 2007. Moreover, we found that the transcription factor FIS binds to the genuine rrnB P2 core promoter region (data not shown), which implies repression and therefore indicates the potential for differential regulation of the two rRNA promoters (Liebig & Wagner, 1995).…”

Section: Binding Of H-ns and Lrp To Promoter Fragments Without Upstresupporting

confidence: 89%

“…The NAPs FIS, H-NS and LRP have been described previously as acting as transcription factors for rRNA synthesis (Hillebrand et al, 2005;Hirvonen et al, 2001;Pul et al, 2005Pul et al, , 2007. In E. coli all rRNA P1 promoters are preceded by a curved regulatory DNA region responsible for transcription factor binding.…”

Section: Discussionmentioning

confidence: 99%

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Effect of upstream curvature and transcription factors H-NS and LRP on the efficiency of Escherichia coli rRNA promoters P1 and P2 – a phasing analysis

et al. 2008

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To study the influence of DNA curvature and DNA-binding proteins, which interact with curved DNA on bacterial promoters, we constructed two sets of promoter variants in which a synthetic DNA-bending module was fused at defined distances and angular orientations with respect to the transcription start sites. The distance between the synthetic binding site centre and the transcription start site of the different constructs varied by up to 20 bp, corresponding to almost two complete helical B-DNA turns. The rRNA promoters rrnB P1 and rrnB P2 were selected as target promoters. While in its natural context P1 depends on upstream curved DNA and several transcription factors that bind to this region, promoter P2 is not preceded by curved DNA, nor is it believed to be directly regulated by transcription factors. In vitro transcription measurements of both promoters in the absence of transcription factors varied with the phase of the curved upstream DNA element, underlining the importance of DNA conformation to promoter efficiency. Specific binding of H-NS and LRP to the curved DNA element was demonstrated by gel shift and footprint analysis. Binding affinity was not notably altered for the different distance variants. We demonstrated that the two proteins acted as repressors for both promoters. The extent of H-NS-mediated repression for both promoters did not vary strongly with the phasing of the upstream binding module. In contrast, LRP-dependent repression showed a clear dependence on the angular orientation of the constructs. Phasing-dependent repression is very distinct for P2 but only rudimentary for the P1 promoter.

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Section: Dnase I Footprint Analysissupporting

confidence: 91%

Section: Effects Of H-ns and Lrp On The Transcriptional Activity Of Tsupporting

confidence: 91%

Section: Binding Of H-ns and Lrp To Promoter Fragments Without Upstresupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

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Effect of upstream curvature and transcription factors H-NS and LRP on the efficiency of Escherichia coli rRNA promoters P1 and P2 – a phasing analysis

et al. 2008

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“…In addition to RNAP, three transcription factors have been reported to bind site-specifically to the E. coli rRNA promoter region, Fis, Lrp, and H-NS (Ross et al 1990;Hirvonen et al 2001;Dame et al 2002;Pul et al 2007). Each has been reported to influence chromosome structure (Skoko et al 2006;Bouffartigues et al 2007;Hadizadeh et al 2012), making these factors candidates for contributors to rRNA operon colocalization.…”

Section: (C) Oric Rrnc (Rlg11999) (D) Rrnb Oric (Rlg7440) (E) λAtmentioning

confidence: 99%

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

et al. 2016

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The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180°on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA operon pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus.

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Translational Components in Prokaryotes: Genetics and Regulation of Ribosomes

Wagner

2009

Encyclopedia of Life Sciences

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The regulation of the biosynthesis of ribosomes, which constitute the catalytic organelles for the translation reaction, is central for the adaptation of bacteria to different growth conditions. The synthesis of the different ribosomal ribonucleic acid (rRNA) and ribosomal protein (RP) components is controlled and coordinated by a complex network of regulatory mechanisms to adjust the translational capacity to the required cell demands. Regulation of rRNA transcription plays a key role in ribosome formation. Quality control steps are operated during processing and assembly to ensure functionally competent particles and to avoid the accumulation of defective products and waste of energy and resources. Key concepts: Bacterial growth rates depend on the number of ribosomes. Ribosome synthesis is adapted to environmental changes. Biosynthesis of ribosomes involves quality control steps. Ribosome synthesis is determined by the rate of rRNA transcription. Synthesis of many ribosomal proteins is adjusted to the amount of free rRNA by a translational feedback mechanism. Many ribosomal proteins have extra‐ribosomal functions in the cell. A limited number of sequence heterogeneities in the redundantly encoded rRNA genes provide the potential for the formation of specialized ribosomes. The stringent control is one of the major mechanisms for the adaptation of ribosomes in response to nutritional changes.

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The Role of LRP and H-NS in Transcription Regulation: Involvement of Synergism, Allostery and Macromolecular Crowding

Cited by 46 publications

References 66 publications

Effect of upstream curvature and transcription factors H-NS and LRP on the efficiency of Escherichia coli rRNA promoters P1 and P2 – a phasing analysis

Effect of upstream curvature and transcription factors H-NS and LRP on the efficiency of Escherichia coli rRNA promoters P1 and P2 – a phasing analysis

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

Translational Components in Prokaryotes: Genetics and Regulation of Ribosomes

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