The role of nucleoid‐associated proteins in the organization and compaction of bacterial chromatin

@article{Dame2005TheRO,
  title={The role of nucleoid‐associated proteins in the organization and compaction of bacterial chromatin},
  author={Remus T. Dame},
  journal={Molecular Microbiology},
  year={2005},
  volume={56}
}
  • R. T. Dame
  • Published 2005
  • Biology, Medicine
  • Molecular Microbiology
The bacterial chromosomal DNA is folded into a compact structure called nucleoid. The shape and size of this ‘body’ is determined by a number of factors. Major players are DNA supercoiling, macromolecular crowding and architectural proteins, associated with the nucleoid, which are the topic of this MicroReview. Although many of these proteins were identified more than 25 years ago, the molecular mechanisms involved in the organization and compaction of DNA have only started to become clear in… Expand

Topics from this paper

The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective.
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This review provides an overview of the major nucleoid-associated proteins from a structural perspective and discusses their possible roles in dynamically shaping the bacterial nucleoid. Expand
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Nucleoid-associated proteins in Crenarchaea.
TLDR
The knowledge currently available on architectural proteins in Crenarchaea is summarized and the crenarchaeal nucleoid shows similarities with that of Bacteria. Expand
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Important advances in the understanding of three-dimensional genome organization due to the application of Chromosome Conformation Capture and super-resolution microscopy techniques are discussed. Expand
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Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
TLDR
The results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap, so some targets are associated with combinations of bound FIS, H-NS and IHF. Expand
Structure and dynamics of the crenarchaeal nucleoid.
TLDR
The molecular properties of cren archaeal chromatin proteins are described and the possible role of these architectural proteins in organizing the crenarchaeal Chromatin and in gene regulation is discussed. Expand
Organization and segregation of bacterial chromosomes
TLDR
It is argued that the key feature of compaction is the orderly folding of DNA along adjacent segments and that this organization provides easy and efficient access for protein–DNA transactions and has a central role in driving segregation. Expand
The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes
TLDR
It is concluded that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes. Expand
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References

SHOWING 1-10 OF 117 REFERENCES
On the role of H-NS in the organization of bacterial chromatin: from bulk to single molecules and back.
TLDR
The groups of Stavans and Oppenheim have recently embarked on an ambitious project which aims to quantify the compactive effects of the various members of this group of proteins using magnetic tweezers, which could lead to a better understanding of how these proteins work together in the formation of a compact nucleoid. Expand
Structure and partitioning of bacterial DNA: determined by a balance of compaction and expansion forces?
TLDR
Two hypotheses are discussed: (i) the structure of the Escherichia coli nucleoid is determined by DNA binding proteins and DNA supercoiling, representing a compaction force on the one hand, and by the coupled transcription/translation/translocation of plasma membrane and cell wall proteins, representing an expansion force. Expand
An architectural role of the Escherichia coli chromatin protein FIS in organising DNA.
TLDR
It is proposed, in addition to the previously inferred stabilisation of tightly bent DNA microloops in the upstream regions of certain promoters, that FIS may perform the distinct architectural function of organising branched plectonemes in the E.coli nucleoid. Expand
About the organisation of condensed and decondensed non-eukaryotic DNA and the concept of vegetative DNA (a critical review).
TLDR
Experiments are reviewed that allow one to assign naturally occurring DNA-containing plasmas to either of two classes by virtue of their sensitivity to aggregation upon dehydration in organic solvents, and results strongly suggest that the two classes of DNA plAsmas are distinguishable by a low (1:10) or high ( 1:1) protein-to-DNA ratio. Expand
H-NS mediated compaction of DNA visualised by atomic force microscopy.
TLDR
A model for global condensation of the chromosomal DNA by H-NS is proposed and large globular structures were identified that incorporated a considerable amount of DNA. Expand
Dual architectural roles of HU: formation of flexible hinges and rigid filaments.
TLDR
This study used magnetic tweezers and atomic force microscopy to quantify HU-induced DNA bending and condensation and revealed that HU can have two opposing mechanical effects depending on the protein concentration. Expand
Osmotic compaction of supercoiled DNA into a bacterial nucleoid.
  • T. Odijk
  • Chemistry, Medicine
  • Biophysical chemistry
  • 1998
TLDR
A theory is presented of the phase separation of supercoiled DNA into a nucleoid in a bacterial cell and the state of superhelical DNA in the nucleoid could be liquid crystalline and rippled. Expand
Macromolecular crowding and the mandatory condensation of DNA in bacteria
TLDR
It is suggested that direct and indirect macromolecular crowding forces from the surrounding cytoplasm are critical factors for nucleoid condensation, and that within a bacterial cell these crowdingforces are always present at such high levels that the DNA is maintained in a condensed state. Expand
The role of co‐transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation
TLDR
It is proposed that the random diffusion of DNA supercoil segments is transiently constrained by the process of co‐ transcriptional translation and translocation (transertion) of membrane proteins. Expand
IHF and HU: flexible architects of bent DNA.
TLDR
In prokaryotes, IHF and HU are key architectural proteins present at high concentrations, and the adaptation of advanced biophysical and biochemical techniques have led to an improved understanding of how these proteins interact with DNA. Expand
...
1
2
3
4
5
...