Upstream Binding of Idling RNA Polymerase Modulates Transcription Initiation from a Nearby Promoter

Gerganova, Veneta; Maurer, Sebastian P.; Stoliar, Liubov; Japaridze, Aleksandre; Dietler, Giovanni; Nasser, William; Kutateladze, Tamara; Travers, Andrew; Muskhelishvili, Georgi

doi:10.1074/jbc.m114.628131

Cited by 20 publications

(18 citation statements)

References 82 publications

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“…Unlike the inducible lac promoter, fis promoter activity is exquisitely sensitive to changes of DNA supercoiling, due in part to the GC-rich discriminator sequence between the −10 hexamer and the transcription start site ( 45 ), which mediates the growth phase- and growth rate-dependent control ( 26 , 28 ). This sensitivity to supercoiling might also be related to the observations that the fis promoter region, highly conserved in all pathogenic E. coli and Shigella strains, is characterized by strong intrinsic curvature ( 46 ), is regulated by a higher-order RNA polymerase complex involved in sensing the topological state of DNA ( 41 , 44 ) and appears evolutionarily streamlined to act as a topological switch ( 47 , 48 ). Some or all of these differences could contribute to disparate effects exerted by the insertions of lac and fis promoter constructs on their immediate surroundings.…”

Section: Discussionmentioning

confidence: 92%

“…The repositioned operon contained the promoter upstream sequences comprising all the known binding sites for regulatory proteins involved in fis transcriptional control ( 39 – 41 ). We used the entire operon instead of the fis gene, because the upstream dusB ORF is absolutely required for efficient translation of the fis mRNA, as well as substituted reporter gene message ( 42 – 44 ). We observed that although the displaced operons quantitatively maintained the growth phase-dependent expression pattern and produced the same amount of FIS protein in the cell, the repositioning of the dusB-fis operon exerted pleiotropic effects on the expression of genes distant from the insertion site.…”

Section: Discussionmentioning

confidence: 99%

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Chromosomal position shift of a regulatory gene alters the bacterial phenotype

et al. 2015

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Recent studies strongly suggest that in bacterial cells the order of genes along the chromosomal origin-to-terminus axis is determinative for regulation of the growth phase-dependent gene expression. The prediction from this observation is that positional displacement of pleiotropic genes will affect the genetic regulation and hence, the cellular phenotype. To test this prediction we inserted the origin-proximal dusB-fis operon encoding the global regulator FIS in the vicinity of replication terminus on both arms of the Escherichia coli chromosome. We found that the lower fis gene dosage in the strains with terminus-proximal dusB-fis operons was compensated by increased fis expression such that the intracellular concentration of FIS was homeostatically adjusted. Nevertheless, despite unchanged FIS levels the positional displacement of dusB-fis impaired the competitive growth fitness of cells and altered the state of the overarching network regulating DNA topology, as well as the cellular response to environmental stress, hazardous substances and antibiotics. Our finding that the chromosomal repositioning of a regulatory gene can determine the cellular phenotype unveils an important yet unexplored facet of the genetic control mechanisms and paves the way for novel approaches to manipulate bacterial physiology.

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Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Chromosomal position shift of a regulatory gene alters the bacterial phenotype

et al. 2015

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“…Topology-dependent binding enables DNA-binding proteins to discriminate between different sites in DNA 50 . For instance, HMG–containing and TATA binding proteins bind to untwisted DNA, and bacterial architectural proteins, such as HU and H-NS, as well as eukaryotic histones, bind and stabilize -SC DNA 51 , 52 . Yet others, for example the bacterial FIS protein preferentially binds intermediate supercoiled DNA as compared with the extremes of the topological spectrum 53 ; the reverse is true for the tumor suppressor p53, which binds preferentially both −SC and +SC DNA, whereas it shows lower affinity for relaxed DNA 54 .…”

Section: Discussionmentioning

confidence: 99%

Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

Bettotti¹,

Visone²,

Lunelli³

et al. 2018

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Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated and the supercoiling degree of defined genome regions may change according to physiological and environmental conditions. Elucidation of structural properties of DNA molecules with different topology may thus help to better understand genome functions. Whereas a number of structural studies have been published on highly negatively supercoiled DNA molecules, only preliminary observations of highly positively supercoiled are available, and a description of DNA structural properties over the full range of supercoiling degree is lacking. Atomic Force Microscopy (AFM) is a powerful tool to study DNA structure at single molecule level. We here report a comprehensive analysis by AFM of DNA plasmid molecules with defined supercoiling degree, covering the full spectrum of biologically relevant topologies, under different observation conditions. Our data, supported by statistical and biochemical analyses, revealed striking differences in the behavior of positive and negative plasmid molecules.

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“…Previous studies have demonstrated that promoter-promoter interaction via TCDS is normally short-range 37 , the separation between PR1-1 and PR1-2 is around 132 bp, so the notion that transcription from PR1-1 can influence the activity of adjacent promoter PR1-2 on the same DNA chain though local supercoiling is therefore reasonable. In the fis promoter there are three tandem RNAP binding sites and it has been proposed that idling of RNAP at an upstream promoter acts as an accessory factor to stimulate transcription from the downstream promoter 38 . The observation that the mutation at position 2 of the -10 of PR1-1, prevented transcription from PR1-2, would argue against RNAP idling at PR1-1 being the mechanism by which PR1-2 is activated, since mutations at this site in the -10 region will not prevent RNAP binding and idling at the PR1-1 promoter 39 .…”

Section: Discussionmentioning

confidence: 99%

Three tandem promoters, together with IHF, regulate growth phase dependent expression of the Escherichia coli kps capsule gene cluster

Jia

King

Goldrick

et al. 2017

Sci Rep

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In this study we characterise three tandem promoters (PR1-1, PR1-2 and PR1-3) within the PR1 regulatory region of the Escherichia coli kps capsule gene cluster. Transcription from promoter PR1-2 was dependent on the activity of the upstream promoter PR1-1, which activated PR1-2 via transcription coupled DNA supercoiling. During growth at 37 °C a temporal pattern of transcription from all three promoters was observed with maximum transcriptional activity evident during mid-exponential phase followed by a sharp decrease in activity as the cells enter stationary phase. The growth phase dependent transcription was regulated by Integration Host Factor (IHF), which bound within the PR1 region to repress transcription from PR1-2 and PR1-3. This pattern of transcription was mirrored by growth phase dependent expression of the K1 capsule. Overall these data reveal a complex pattern of transcriptional regulation for an important virulence factor with IHF playing a role in regulating growth phase expression.

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Upstream Binding of Idling RNA Polymerase Modulates Transcription Initiation from a Nearby Promoter

Cited by 20 publications

References 82 publications

Chromosomal position shift of a regulatory gene alters the bacterial phenotype

Chromosomal position shift of a regulatory gene alters the bacterial phenotype

Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

Three tandem promoters, together with IHF, regulate growth phase dependent expression of the Escherichia coli kps capsule gene cluster

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