Nucleoid-Associated Proteins: Structural Properties

Pul, Ümit; Wagner, Rolf

doi:10.1007/978-90-481-3473-1_8

Cited by 8 publications

(9 citation statements)

References 119 publications

(151 reference statements)

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“…A number of abundant proteins contribute to in vivo constrained supercoil density (σ C ) (Johnson et al ., 2005; Pul and Wagner, 2010). They include the small nucleoid‐associated proteins IHF, HU, H‐NS and FIS (Browning et al ., 2010; Dorman, 2010), the structural maintenance of chromosome (SMC) complex MukBEF (Petrushenko et al ., 2006) and RNAP (Gamper and Hearst, 1982).…”

Section: Discussionmentioning

confidence: 99%

DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium

Booker

Deng

Higgins

2010

Molecular Microbiology

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SummaryBacteria differ from eukaryotes by having the enzyme DNA gyrase, which catalyses the ATP-dependent negative supercoiling of DNA. Negative supercoils are essential for condensing chromosomes into an interwound (plectonemic) and branched structure known as the nucleoid. Topo-1 removes excess supercoiling in an ATP-independent reaction and works with gyrase to establish a topological equilibrium where supercoils move within 10 kb domains bounded by stochastic barriers along the sequence. However, transcription changes the stochastic pattern by generating supercoil diffusion barriers near the sites of gene expression. Using supercoildependent Tn3 and gd resolution assays, we studied DNA topology upstream, downstream and across highly transcribed operons. Whenever two Res sites flanked efficiently transcribed genes, resolution was inhibited and the loss in recombination efficiency was proportional to transcription level. Ribosomal RNA operons have the highest transcription rates, and resolution assays at the rrnG and rrnH operons showed inhibitory levels 40-100 times those measured in low-transcription zones. Yet, immediately upstream and downstream of RNA polymerase (RNAP) initiation and termination sites, supercoiling characteristics were similar to poorly transcribed zones. We present a model that explains why RNAP blocks plectonemic supercoil movement in the transcribed track and suggests how gyrase and TopA control upstream and downstream transcriptiondriven supercoiling.

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Section: Discussionmentioning

confidence: 99%

DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium

Booker

Deng

Higgins

2010

Molecular Microbiology

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“…Biochemical, biophysical and single-molecule experiments have shown that NAPs package DNA by several different mechanisms. For example, IHF and Fis package DNA by bending the target site, and, as mentioned above, H-NS forms bridges between DNA molecules 77,146,[153][154][155] . Chromatin immunoprecipitation studies have determined the genome-wide binding profiles of some NAPs, which have shown that many NAPs bind to hundreds of target sites [156][157][158] .…”

Section: Box 3: Nucleoid-associated Proteinsmentioning

confidence: 97%

“…This compaction enables large bacterial chromosomes to fit inside cells and is achieved by the combined effects of DNA supercoiling, molecular crowding, and the presence of RNA and nucleoid-associated proteins (NAPs). Initially, it was thought that NAPs would have similar structures to eukaryotic histones, but it is now clear that NAPs are, instead, a diverse group of proteins that recognize DNA target sites using many different structural motifs 77,146 . Escherichia coli has at least 12 different NAPs, including Fis (Factor for Inversion Stimulation), IHF (Integration Host Factor), HU (Histone protein from strain U9), H-NS (Histone-like Nucleoidstructuring protein) and LRP (Leucine Responsive Protein), all of which have been studied extensively 77,79 .…”

Section: Box 3: Nucleoid-associated Proteinsmentioning

confidence: 99%

Local and global regulation of transcription initiation in bacteria

2016

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Gene expression in bacteria relies on promoter recognition by the DNA-dependent RNA polymerase and subsequent transcription initiation. Bacterial cells are able to tune their transcriptional programmes to changing environments, through numerous mechanisms that regulate the activity of RNA polymerase, or change the set of promoters to which the RNA polymerase can bind. In this Review, we outline our current understanding of the different factors that direct the regulation of transcription initiation in bacteria, whether by interacting with promoters, with RNA polymerase or with both, and we discuss the diverse molecular mechanisms that are used by these factors to regulate gene expression.

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“…The leading member is HU protein, a hetero-dimer composed of HupA and HupB protomers in E. coli (Dillon and Dorman 2010 I), and it accounts for 6000 supercoils or roughly 40 % of the constrained DNA supercoils. About 50 % of σ C is presumed to associate with the NAPs IHF, H-NS, STPA, FIS, and DPS (Johnson et al 2005;Pul and Wagner 2010).…”

Section: Constrained Supercoilsmentioning

confidence: 99%

Species-specific supercoil dynamics of the bacterial nucleoid

Higgins

2016

Biophys Rev

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Bacteria organize DNA into self-adherent conglomerates called nucleoids that are replicated, transcribed, and partitioned within the cytoplasm during growth and cell division. Three classes of proteins help condense nucleoids: (1) DNA gyrase generates diffusible negative supercoils that help compact DNA into a dynamic interwound and multiply branched structure; (2) RNA polymerase and abundant small basic nucleoid-associated proteins (NAPs) create constrained supercoils by binding, bending, and forming cooperative protein-DNA complexes; (3) a multi-protein DNA condensin organizes chromosome structure to assist sister chromosome segregation after replication. Most bacteria have four topoisomerases that participate in DNA dynamics during replication and transcription. Gyrase and topoisomerase I (Topo I) are intimately involved in transcription; Topo III and Topo IV play critical roles in decatenating and unknotting DNA during and immediately after replication. RNA polymerase generates positive (+) supercoils downstream and negative (−) supercoils upstream of highly transcribed operons. Supercoil levels vary under fast versus slow growth conditions, but what surprises many investigators is that it also varies significantly between different bacterial species. The MukFEB condensin is dispensable in the high supercoil density (σ) organism Escherichia coli but is essential in Salmonella spp. which has 15 % fewer supercoils. These observations raise two questions: (1) How do different species regulate supercoil density? (2) Why do closely related species evolve different optimal supercoil levels? Control of supercoil density in E. coli and Salmonella is largely determined by differences encoded within the gyrase subunits. Supercoil differences may arise to minimalize toxicity of mobile DNA elements in the genome.

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Nucleoid-Associated Proteins: Structural Properties

Cited by 8 publications

References 119 publications

DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium

DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium

Local and global regulation of transcription initiation in bacteria

Species-specific supercoil dynamics of the bacterial nucleoid

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