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Chapter 6 : Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes

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Abstract:

This chapter reviews classical results and incorporates a selected set of facts into models of chromosome dynamics. It emphasizes the topology of DNA during replication and transcription because these two processes exert the most dramatic topological influence on DNA. One focus is on structural properties of bacterial chromosomes that allow rapid adaptability. The chapter also discusses chromosome structure considered from a stochastic as opposed to a highly ordered perspective. The introduction of a limited number of single-strand nicks causes nucleoid sedimentation values to decrease in gradual stages. In vitro nucleoid studies stimulated searches for the controlling elements of domain behavior. Three generalizations of the interval have been extended to 2% of the chromosome. First, supercoil domains are more abundant when cells are undergoing DNA replication than when DNA replication is suppressed. Second, the resolution efficiency diminishes as a first-order function of distance along the chromosome. Third, the number of domains detected depends on the time period of the assay. Global structure provided by four topoisomerases and a group of about 10 DNA-binding proteins allows a plasticity that is useful for adaptation to different physiological conditions. These observations indicate that the organizational framework of a bacterial chromosome must be described in statistical terms rather than the highly ordered and predictable models that represent the crystal structures of many folded proteins that do biochemical work on the chromosome.

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6

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Figures

Image of Figure 1
Figure 1

Image of an chromosome. Exponential cells treated with lysozyme and Brij 58 in the presence of 1MNaCl were layered onto a 10 to 30% sucrose gradient and subjected to centrifugation. An aliquot of the fraction with highest DNA content was applied to a glow-discharged carbon-coated grid, stained with uranyl acetate, rotary shadowed, and photographed using a JEOL 1200EXII electron microscope. Micrograph by Christine Hardy, University of California at Berkeley.

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6
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Image of Figure 2
Figure 2

Supercoil behavior in chromosomes. (A) DNA supercoils in eukaryotes are created by wrapping DNA on the surface of the highly conserved histone octamer. Eubacteria introduce supercoils enzymatically with gyrase, which causes DNA to adopt the interwound or plectonemic supercoiled conformation. Proteins like HU and H-NS restrain half of bacterial supercoiling. (B) A 114-bp site includes three subsites, I, II, and III, that each bind a resolvase dimer. Recombination occurs within the I site. A three-node synapse precisely juxtaposes two I sites for catalytic exchange within a protein-DNA recombination complex. Slithering (C) and branching (D) are movements that allow synapse of two sites.

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6
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Image of Figure 3
Figure 3

Resolution analysis in a 100-kb interval using two resolvase enzymes, the WT Res (top curve) with a half-life of more than 1 h or the modified Res-SsrA protein (bottom curve), which is a substrate for the ClpXP protease and has a 5-min half-life in exponential cultures of or .

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6
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Image of Figure 4
Figure 4

Topological problems at the terminus. (A) As replication forks converge, positive supercoiling builds up to slow fork progression. (B) In WT strains, gyrase can remove the topological barrier, but gyrase mutants may fail to complete DNA synthesis due to fork regression (C) or replication-mediated linearization of one chromosome (D and E). An R loop impedes further transcription (F), exposes the displaced strand of DNA to chemical and enzymatic attack (G), and creates a barrier to replication fork progression (H).

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6
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Figure 5

Resolution efficiency in a 14-kb segment of the serovar Typhimurium chromosome changes dramatically depending on the state of expression. (A) Genetic map of a 14-kb deletion interval, which leads to a deleted circle containing a Tet-regulated copy of . (B) Effect of transcription on site-specific resolution. Cultures of bacteria harboring the genetic interval shown in panel A were grown in log phase with continuous presence (open square) or absence (open circle) of 5 µg/ml CLT. At time 0, CLT was added (solid squares) or washed out (solid circles) of the medium, and cells were exposed to a 10-min expression period of a resolvase with a 5-min half-life. Recombination efficiency is plotted against the time of transcription induction or repression (see reference ). (C) Model for transcription-induced domains in bacterial chromosomes. Addition of CLT causes RNA polymerase binding at promoters p and p and transcription of the and genes. Persistent transcription induces formation of a domain in which an unknown protein(s) stabilizes a loop that isolates DNA associated with the transcribing RNA polymerases (ovals) from the rest of the genome. Inclusion of the res site adjacent to the transcription terminator (rrnB) inhibits recombination with the site near the gene to the left.

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6
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Figure 6

Alternative explanations for RNA and membrane involvement in domain behavior. (A) RNA transcription produces novel RNA species that organize specific domains within the bacterial chromosome. Lysis releases a structure, and digestion with RNase unfolds the nucleoid by digesting "organizational" RNA. (B) Cotranscriptional translation of integral membrane proteins transiently handcuffs DNA to the membrane through a link involving RNA polymerase, mRNA, ribosomes, and nascent membrane protein. Lysis causes the membrane-attached complexes to collapse to the center, forming an inverted structure. Digestion by RNase releases DNA from the membrane, allowing nucleoid expansion.

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6
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Figure 7

Hypothetical use of transcription and membrane attachment to reform nucleoids after DNA replication. (A) Chromosomal replication of the parental nucleoid (large gray oval) is initiated in a DNA factory (open square) positioned at mid cell. A replication fork initiated at OriC loops out one continuously synthesized strand leftward (black) and a complementary strand rightward that is discontinuously synthesized as Okazaki fragments (gray). After DNA passes through a SeqA zone (aggregate), expression of genes encoding integral membrane proteins (black bars) or proteins exported to the periplasm and outer membrane (gray triangles) handcuff DNA to the membrane-forming domains. (B) A second replisome extrudes the second replichore rightward and leftward. The template chromosome diminishes as the replisomes approach the terminus. (C) Two new nucleoids remain intermittently and dynamically linked to the membrane.

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6
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Figure 8

Examples of supercoil-assisted protein assembly and disassembly. (A) Six dimers of the Res protein (triangles) form a synapse that contains three negative supercoils. The time required to form this alignment on a supercoiled 4-kb plasmid is about 1 s. (B) Phage Mu transposition requires interactions of three sites in phage DNA. These sites include the left end of the virus (attL), the right end of the virus (attR), and the internal activation sequence (IAS). The plectosome or transposition intermediate contains a tetramer of MuA protein and five plectonemic crossings of DNA. (C) Mu transposition immunity involves interactions between a Mu transpososome and a DNA complex of the target selector, MuB protein. MuB binding to DNA is highly cooperative and requires an ATP. Interactions between MuA and MuB stimulate hydrolysis and a conformation change that displaces MuB from DNA.

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6
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Tables

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Table 1

Thirty years of supercoil domain studies in vitro and in vivo: evidence of short- and long-range interaction in a highly dynamic yet organized bacterial chromosome whose structure is determined by biochemical functionality

Citation: Higgins N, Deng S, Pang Z, Stein R, Champion K, Manna D. 2005. Domain Behavior and Supercoil Dynamics in Bacterial Chromosomes, p 133-154. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch6

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