architektura: Nucleoid

Evidence: 100 • authority: 72

The nucleoid (meaning nucleus-like) is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. The chromosome of a typical prokaryote is circular, and its length is very large compared to the cell dimensions, so it needs to be compacted in order to fit. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. Instead, the nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. Genome length varies widely (generally a few Mbp within a prokaryote phylum), and a cell may contain multiple copies of its genome…

Evidence: 36 • authority: 88

<i>Escherichia coli tyrT</i> gene transcription is sensitive to DNA supercoiling in its native chromosomal context: effect of DNA topoisomerase IV overexpression on <i>tyrT</i> promoter function. Summary We have investigated the in vivo DNA supercoiling sensitivity of the Escherichia coli tRNA tyr 1 gene ( tyrT ) promoter in its normal chromosomal location. Here, the native tyrT promoter is found to be exquisitely sensitive to mutations and to drugs which alter the level of DNA supercoiling. We show that the response of the tyrT promoter to supercoiling is qualitatively similar to that of a known supercoiling‐sensitive tRNA gene promoter, hisR. Specifically, treatments which increase in viv…

Evidence: 36 • authority: 88

In vivo supercoiling of plasmid and chromosomal DNA in an Escherichia coli hns mutant. We have used trimethylpsoralen to measure localized levels of unconstrained DNA supercoiling in vivo. The data provide direct evidence that plasmid and chromosomal DNA supercoiling is altered in vivo in an hns mutant. This increase in supercoiling is independent of transcription or changes in the activity of topoisomerase I. These data have implications for the mechanisms by which the chromatin-associated protein H-NS may influence chromosome organization and gene expression.

Evidence: 36 • authority: 72

Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life. The two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases…

Evidence: 36 • authority: 72

DNA supercoiling refers to the amount of twist in a particular DNA strand, which determines the amount of strain on it. A given strand may be "positively supercoiled" or "negatively supercoiled" (more or less tightly wound). The amount of a strand's supercoiling affects a number of biological processes, such as compacting DNA and regulating access to the genetic code (which strongly affects DNA metabolism and possibly gene expression). Certain enzymes, such as topoisomerases, change the amount of DNA supercoiling to facilitate functions such as DNA replication and transcription. The amount of supercoiling in a given strand is described by a mathematical formula that compares it to a referen…

Evidence: — • authority: 80

The formation of paranemic and plectonemic joints between DNA molecules by the recA and single-stranded DNA-binding proteins of Escherichia coli.

Evidence: — • authority: 92

Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics, and organization.. Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with ∼180 000 copies per cell. Dps binds DNA and oxidizes iron, facilitating survival in harsh environments. Dps-DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganizes the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics, and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that after 96 h of star…

Evidence: — • authority: 92

Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon.. Conjugative plasmids drive bacterial evolution and antibiotic resistance spread, yet their gene expression must be silenced to protect the host. A histone-like protein H-NS represses many mobile and sedentary xenogenes but fails to silence the conjugal transfer vir operon of R6K, a prototype IncX plasmid. Instead, R6K encodes its own H-NS homolog, Sfx, to repress the vir operon. Here, we show that, unlike other plasmid silencers that target promoters, Sfx cooperates with Rho factor to arrest transcription elongation. ChIP-seq reveals that Sfx and H-NS share similar DNA motifs and a preference for negati…

Evidence: — • authority: 92

Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.. DNA-protein interactions underlie genome activity, governing gene expression as well as the physical organisation of DNA. Until recently, DNA-protein complexes were predominantly described at atomic resolution using short DNA fragments, concealing how proteins recognise and manipulate the long, supercoiled DNA present in cells. Now single-molecule imaging and cryo-electron microscopy (cryo-EM) are showing how longer DNA sequences are recognised by proteins and computations are predicting how these elements influence larger-scale genomic structures. Here we discuss how the polymeric nature of DNA…

Evidence: — • authority: 88

Molecular processing of DNA folding anoinalies in <i>Escherichia coli</i>. Abstract For evolution to proceed, there must be a balance between genetic stability and rearrangement. Chromosomal arrangements that prove beneficial to an organism are expected to be maintained while retaining the potential to generate radically new organizations over an evolutionary time-scale. In order to maintain this balance, cells have evolved mechanisms to reduce the frequency of chromosomal rearrangements. An important threat to DNA stability comes from sequences that have the potential for unusual folding. Unusually folded DNAs also pose problems for DNA replication, which may be particularly critical for o…

Evidence: — • authority: 92

Apical localization of RNA polymerases modulates transcription dynamics and supercoiling domains revealed by cryo-ET.. Protein interactions with canonical B-form DNA are well characterized, yet the effect of torsionally constrained DNA on these interactions-ubiquitous in cells-remains underexplored. Using cryo-electron tomography (cryo-ET), we 3D-reconstructed entire negatively supercoiled DNA substrates bound to active RNA polymerase (RNAP), revealing diverse DNA supercoiling conformations and their interplay with transcription. RNAP preferentially localizes at plectoneme apices in a swiveled, pause-prone state. RNAP, along with other DNA-melting proteins such as dCas9, can act as torsiona…

Evidence: — • authority: 92

A DNA-binding protein senses DNA superhelicity to switch between bridging and nucleoprotein filament formation. The torsional state of DNA encodes regulatory information beyond sequence, yet how chromosome-associated proteins read this mechanical signal to switch between distinct functional outputs remains poorly understood. Using real-time single-molecule fluorescence imaging on topologically constrained DNA, we demonstrate that DNA superhelical polarity is the primary determinant of H-NS binding mode with direct consequences for chromosomal domain organization and gene silencing. On positively supercoiled DNA, H-NS assembles into nucleoprotein filaments at AT-rich loci, acting as a topolo…