Chapter 28 : Chromosome Dimer Resolution

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This chapter presents the processes that can lead to the dimerization of replicons and discusses the mechanisms that ensure their resolution. It also discusses how chromosome dimer resolution is integrated into other aspects of DNA processing during the bacterial cell cycle. The chromosomes and linear plasmids of are linear with hairpin ends. Bidirectional replication is initiated internally and, when complete, generates a circular dimer of the original linear replicon. In this circular dimer, the hairpin sites of the parental DNA are converted into palindromic “telomere” sites, which are used for chromosome dimer resolution. Xer site-specific recombination, which is responsible for chromosome dimer resolution, ensured their stable inheritance within . In and in bacteriophage N15 of , resolution of chromosome dimers is due to the action of a single enzyme, ResT or TelN, respectively. During tyrosine recombinase-mediated site-specific recombination, two tyrosine recombinase molecules bind cooperatively to ~30-bp specific core recombination sites in the DNA. The XerC and XerD site-specific recombinases function in chromosome dimer resolution by adding a single crossover at , a specific 28-bp core site located in the region of termination of replication of the chromosome. In vivo and in vitro studies show that in the absence of FtsK, Holliday junctions (HJs) are created and resolved back to the original substrate in cycles of XerC-mediated strand exchanges. The realization that Xer recombination uses different strategies to ensure resolution selectivity during plasmid and chromosome dimer resolution demonstrates the sophistication that has developed during bacterial evolution.

Citation: Barre F, Sherratt D. 2005. Chromosome Dimer Resolution, p 513-524. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch28
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Figure 1

Chromosome dimer formation. The DNA backbone and the base pairing between two DNA strands in a duplex DNA molecule are schematically represented by “ladders.” Parental strands are represented as thin lines, and replicated daughter strands are represented as thick lines to help in the visualization of strand exchanges. The leading strand is shown as a continuous line, whereas the lagging strand is shown first as a dashed line representing the Okazaki fragments, which later become continuous strands. Arrows depict directions of replication. (A) 's replication strategy for linear replicons with covalently closed hairpin ends. The so-called “telomeres” are shown in light gray. Initiation of bidirectional replication occurs internally within the chromosome. Completion of replication produces a dimeric chromosome with two palindromic inverted repeats of the “telomere” sites. (B) Bidirectional replication of circular replicons. Replication will produce two catenated sister chromosomes in the absence of crossing over. An odd number of crossovers between the sister chromosomes generates a dimeric replicon. The region opposite the origin of replication, where chromosome dimer resolution occurs, is shown in light gray. (C) Rolling circle replication of circular replicons. Replication is initiated at a nick and is unidirectional. After one round of replication, the replication fork can continue to displace one of the sister chromosomes, leading to the formation of a multimeric linear concatemer of sister chromosomes that can be processed back into circular monomers or circular multimers by recombination.

Citation: Barre F, Sherratt D. 2005. Chromosome Dimer Resolution, p 513-524. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch28
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Figure 2

Chromosome dimer resolution. (A) Dimer resolution of and bacteriophage N15. DNA is shown as in Fig. 1 . Two ResT (or two TelN) enzymes bind to each of the two “telomere” sequences present as an inverted repeat in the dimeric replicon. Although no structural data are available, they are depicted as interacting with each other by an extension protruding from one molecule, which fits into a socket of the other molecule. (B) The mechanism of dimer resolution by tyrosine sitespecific recombinases. DNA is shown as in Fig. 1 . The C-terminal domain and the N-terminal domain of the recombinase monomers are represented by a large ellipse and small ellipses shaded with a gradient. These two domains form a C-shaped clamp that encircles half of the recombination site. The extreme C-terminal extension from each monomer is depicted by a small shaded circle. In Cre, this C-terminal extension fits into a socket in the C-terminal domain of a neighbor recombinase. DNA strand exchanges are performed successively by one pair of diagonally opposite recombinases in the complex and then the other. A complete cleavage-rejoining reaction by one of the recombinases proceeds in four steps identical to the ones performed by type IB topoisomerases: the initial protein-DNA complex is converted into a stable covalent enzyme-DNA adduct involving a 3′ phosphotyrosine linkage at the active site, before completion of the reaction by rejoining of the DNA. The phosphodiester linkage of the DNA substrate backbone which is attacked in this reaction lies 3 bp (, and ) or 4 bp () away from the center of the recombination site toward the bound recombinase. (C) Xer recombination at and . The and recombination sites are indicated by a thicker line on one of their DNA strands. The core recombination site is shown in gray. XerC binds to the half-site proximal to the accessory sequences. Three negative supercoils are entrapped by the accessory proteins and sequences. Synapsis of the core recombination sites is in antiparallel, with the C-terminal domain of all four recombinases facing the accessory sequences and proteins complex. The nucleoprotein complex structure is not planar but slightly bent, with the four arms of the DNA strands coming from the side of the C-terminal domains of the recombinases when they enter the nucleoprotein complex.

Citation: Barre F, Sherratt D. 2005. Chromosome Dimer Resolution, p 513-524. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch28
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Figure 3

FtsK and the control of chromosome dimer resolution. (A) Scheme of the FtsK protein, showing the different domains that have been identified and the roles that they have been assigned. The N-terminal domain is shown by a shaded box, and the four transmembrane regions it contains are represented as black lines. A thicker line indicates the long transmembrane helix found at the end of the N-terminal domain. The extreme N terminus points toward the cytoplasm as well as the C-terminal domain of the protein. A dark box at the junction between the N-terminal domain and the linker region of the protein indicates the 50 amino acid residues potentially implicated in multimerization of the FtsK protein. The ATP binding site is shown as a darker box inside the C-terminal domain. (B) FtsK-dependent and independent pathways of Xer recombination at . In the absence of FtsK, the Xer synaptic complex adopts a conformation suitable for XerC-mediated strand exchanges, depicted by a kink at the XerD binding site. FtsK can use the energy of ATP to switch the Xer synaptic complex to a conformation suitable for XerD-strand exchanges, depicted by a kink at the XerC binding site. The intensity of the arrows reflects the probability of recombinational events. XerC and XerD cleavage sites are shown by white and black triangles, respectively. (C) The DNA translocase activity of FtsK can influence the topological outcome of the Xer recombination. Xer recombination between two directly repeated sites (black triangles) on a linear duplex creates one linear and one circular duplex with single sites. The circular product traps negative supercoils (–) preferentially. This is linked to the DNA translocation activity of FtsK, which creates positive supercoils in front of the advancing protein and negative supercoils in its wake. We propose that FtsK translocates along the DNA toward the synaptic complex to contact the recombinases and activate crossover formation by introducing positive writhe and twist onto the complex. Thus, positive supercoils are created between FtsK and the Xer complex, and negative supercoils are created on the other side of FtsK. On the substrate shown, FtsK should load most frequently between the repeated sites. To explain the preferential global negative supercoiling of the circular substrate, we propose two models: (i) the FtsK protein encircles only one duplex DNA; the Xer synaptic complex and/or an additional contact of DNA with the outside of FtsK prevent(s) negative supercoils from diffusing at the ends of the substrate, but allow(s) positive supercoils to diffuse away; (ii) the FtsK protein encircles two duplexes, thus preventing the negative supercoils from diffusing away; the Xer synaptic complex does not prevent the positive supercoils from diffusing away. (D) FtsK plays a safeguard role in DNA segregation when cellular events such as chromosome dimer formation have delayed separation and migration of the two sister chromosomes into the two daughter cells. The two replicated terminus regions remain associated asymmetrically in one of the daughter cells. We propose that FtsK forms an oriented pore through which the two duplex strands of a chromosome can pass. Its directional translocation activity would pump DNA when necessary, while its interaction with Xer- (triangles) can lead to chromosome dimer resolution. FtsK is represented by ovoids, the linker is represented by a zigzag, and the N-terminal part of the protein is represented by rectangles.

Citation: Barre F, Sherratt D. 2005. Chromosome Dimer Resolution, p 513-524. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch28
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