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EcoSal Plus

Domain 2: Cell Architecture and Growth

The Nucleoid: an Overview

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  • Author: Akira Ishihama1
  • Editor: Susan T. Lovett2
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Hosei University, Department of Frontier Bioscience, Koganei, Tokyo 184–8584, Japan; 2: Brandeis University, 415 South Street, Waltham, MA 02453
  • Received 10 December 2008 Accepted 03 February 2009 Published 15 October 2009
  • Address correspondence to Akira Ishihama aishiham@hosei.ac.jp.
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  • Abstract:

    This review provides a brief review of the current understanding of the structure-function relationship of the nucleoid developed after the overview by Pettijohn focusing on the physical properties of nucleoids. Isolation of nucleoids requires suppression of DNA expansion by various procedures. The ability to control the expansion of nucleoids in vitro has led to purification of nucleoids for chemical and physical analyses and for high-resolution imaging. Isolated genomes display a number of individually intertwined supercoiled loops emanating from a central core. Metabolic processes of the DNA double helix lead to three types of topological constraints that all cells must resolve to survive: linking number, catenates, and knots. The major species of nucleoid core protein share functional properties with eukaryotic histones forming chromatin; even the structures are different from histones. Eukaryotic histones play dynamic roles in the remodeling of eukaryotic chromatin, thereby controlling the access of RNA polymerase and transcription factors to promoters. The genome is tightly packed into the nucleoid, but, at each cell division, the genome must be faithfully replicated, divided, and segregated. Nucleoid activities such as transcription, replication, recombination, and repair are all affected by the structural properties and the special conformations of nucleoid. While it is apparent that much has been learned about the nucleoid, it is also evident that the fundamental interactions organizing the structure of DNA in the nucleoid still need to be clearly defined.

  • Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6

Key Concept Ranking

Gene Expression and Regulation
0.69465065
Bacterial Cell Shapes
0.6100844
Bacterial Proteins
0.6035456
DNA Synthesis
0.51908416
DNA Polymerase III
0.49616358
0.69465065

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/content/journal/ecosalplus/10.1128/ecosalplus.2.6
2009-10-15
2017-09-24

Abstract:

This review provides a brief review of the current understanding of the structure-function relationship of the nucleoid developed after the overview by Pettijohn focusing on the physical properties of nucleoids. Isolation of nucleoids requires suppression of DNA expansion by various procedures. The ability to control the expansion of nucleoids in vitro has led to purification of nucleoids for chemical and physical analyses and for high-resolution imaging. Isolated genomes display a number of individually intertwined supercoiled loops emanating from a central core. Metabolic processes of the DNA double helix lead to three types of topological constraints that all cells must resolve to survive: linking number, catenates, and knots. The major species of nucleoid core protein share functional properties with eukaryotic histones forming chromatin; even the structures are different from histones. Eukaryotic histones play dynamic roles in the remodeling of eukaryotic chromatin, thereby controlling the access of RNA polymerase and transcription factors to promoters. The genome is tightly packed into the nucleoid, but, at each cell division, the genome must be faithfully replicated, divided, and segregated. Nucleoid activities such as transcription, replication, recombination, and repair are all affected by the structural properties and the special conformations of nucleoid. While it is apparent that much has been learned about the nucleoid, it is also evident that the fundamental interactions organizing the structure of DNA in the nucleoid still need to be clearly defined.

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Figures

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Figure 1

(Left) Membrane-free nucleoid (bar, 1 μm). (Right) Membrane-associated nucleoid.

Micrographs courtesy of R. Kavenoff.

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 2

Domain size measurements were performed from electron micrographs of isolated nucleoids ( 22 ).

Figures courtesy of L. Postow.

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 3

Boccard and colleagues ( 25 , 26 ) proposed the organization and dynamic behaviors of the macrodomains.

Figures courtesy of F. Boccard.

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 4

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 5

(Right panels) . cells growing at different phases were gently lysed and directly observed with an atomic force microscope ( 60 ). (Left panel) A model of fundamental architecture of the . nucleoids predicted from AFM patterns.

AFMs courtesy of K. Takeyasu.

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 6

Intracellular levels of nucleoid proteins were measured at various phases of growth ( 67 , 72 ).

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 7

Some promoters are regulated by multiple transcription factors including nucleoid proteins. References for each regulon: ( 96 ); ( 97 ); ( 98 ); ( 99 ); ( 100 ); ( 101 ); ( 102 ); ( 103 ); ( 104 ); ( 105 ); ( 106 ); P2 ( 107 ); P1 ( 108 , 109 ).

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 8

Molecular structures from Protein Data. (A) HU ( 45 ). (B) HU-DNA complex ( 111 , 112 ). (C) IHF-DNA complex ( 77 ). (D) Fis ( 115 , 116 ). (E) H-NS ( 117 ). (F) Dps ( 118 ).

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 9

Three different states have been identified for αβ HU heterodimer ( 45 ).

Figures courtesy of S. Adhya.

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Figure 10

Electron microscopic observation of stationary-phase cells. Highly produced Dps forms cocrystals with the genome DNA ( 62 , 64 ).

Figures courtesy of A. Minsky.

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Tables

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Table 1

Nucleoid proteins

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Table 2

Proteins involved in DNA replication

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Table 3

Proteins involved in recombination and repair

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Table 4

Transcription apparatus: RNA polymerase proteins

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6
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Table 5

Transcription apparatus: DNA-binding transcription factor

Citation: Ishihama A. 2009. The Nucleoid: an Overview, EcoSal Plus 2009; doi:10.1128/ecosalplus.2.6

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