The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes

  title={The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes},
  author={Martijn S. Luijsterburg and Malcolm F. White and Roel van Driel and Remus T. Dame},
  journal={Critical Reviews in Biochemistry and Molecular Biology},
  pages={393 - 418}
The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be… 
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This work describes the main players in DNA organization and discusses the properties of the bacterial DNA-bridging protein H-NS, which is a key driver of bacterial genome organization and provides a link between 3-D organization and transcription regulation.
High mobility group proteins: the multifaceted regulators of chromatin dynamics
This review focuses on the structure–function relationship of three broad families of High mobility groups (HMGs) of protein, namely HMGA, HMGN and HMG-Box which are major chromatin architectural components of the eukaryotes.
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Role of RNA polymerase and transcription in the organization of the bacterial nucleoid.
This review provides an alternative and/or complementary perspective to the traditional views on bacterial nucleoid compaction and expansion as other recent comprehensive reviews have dealt with the roles of other factors inacterial nucleoid organization.
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Single‐Molecule Unzipping Force Analysis of HU–DNA Complexes
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Single-molecule micromanipulation studies of DNA and architectural proteins.
  • R. T. Dame
  • Biology
    Biochemical Society transactions
  • 2008
Single-molecule micromanipulation approaches that probe the properties of DNA-binding proteins by pulling on individual protein-DNA complexes have proved to be a very powerful alternative in investigating their interaction using biochemical ensemble techniques.
Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome
The histone fold now exists not only in histones but also as a structural motif in eukaryal transcription factors, suggesting that histones may have prevailed during the evolution of the Eukarya.
Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation
An optical tweezers instrument that can independently handle two DNA molecules is developed, which allows the systematic investigation of protein-mediated DNA–DNA interactions and shows that H-NS is dynamically organized between twoDNA molecules in register with their helical pitch.
The role of nucleoid‐associated proteins in the organization and compaction of bacterial chromatin
  • R. T. Dame
  • Biology, Physics
    Molecular microbiology
  • 2005
The bacterial chromosomal DNA is folded into a compact structure called nucleoid, which is determined by a number of factors, which major players are DNA supercoiling, macromolecular crowding and architectural proteins, associated with the nucleoid.
Priming the nucleosome: a role for HMGB proteins?
The high‐mobility‐group B (HMGB) chromosomal proteins are characterized by the HMG box, a DNA‐binding domain that both introduces a tight bend into DNA and binds preferentially to a variety of
Nucleosomes: a solution to a crowded intracellular environment?
The hypothesis is that upon transition from prokaryotic systems to eukaryotes, the nucleosomes were rendered essential in order to negate extensive DNA condensation processes that would have resulted from excluded volume effects, thus enabling conformational flexibility and reversible structural modulations.
DNA topoisomerases: structure, function, and mechanism.
Surprisingly, despite little or no sequence homology, both type IA and type IIA topoisomerases from prokaryotes and the typeIIA enzymes from eukaryotes share structural folds that appear to reflect functional motifs within critical regions of the enzymes.
A common topology for bacterial and eukaryotic transcription initiation?
It is argued that although bacteria and eukaryotes differ in their mode of packaging DNA supercoils, increases in DNA twist are associated with chromatin folding and transcriptional silencing in both and Conversely, decreases in DNA Twist are associatedwith chromatin unfolding and the acquisition of transcriptional competence.
At the heart of the chromosome: SMC proteins in action
  • T. Hirano
  • Biology, Chemistry
    Nature Reviews Molecular Cell Biology
  • 2006
An emerging idea is that SMC proteins use a diverse array of intramolecular and intermolecular protein–protein interactions to actively fold, tether and manipulate DNA strands.