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Chapter 13 : The Terminus Region of the Chromosome, or, All's Well That Ends Well

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Abstract:

Research on termination of the replication cycle and the terminus region was prompted by the discovery of bidirectional replication of the chromosome. Studies of the Tus-Ter system and the terminus region had other fruitful consequences, since they led to the recognition of phenomena important in the cell cycle, which are restricted to the terminus region by features of the global organization of the bacterial nucleoid. This chapter describes one's current understanding of the features of the terminus region. The core of this chapter deals with resolution of chromosome dimers by the -XerCD/FtsK system and its regional control. Other aspects, such as the organization in nondivisible zones (NDZ), local hyper recombination, and evolution of terminus sequences, are also presented in this chapter. Stress is placed the role of the terminus in the ultimate operations of the replication cycle and the postreplicative processing of sister chromosomes. The first evidence for bipolarization of the terminus region was provided by the distribution of the Ter pause sites. According to the author, the arrangement of polar pause sites on the chromosome, which forces replication to terminate in the center of the terminus macrodomain near , facilitates temporal harmony between end of replication and triggering of events which, like movements of the TER domains away from the septal plane, involve the chromosome polarization centered on . The function of the terminus region about which the most is known is the resolution of circular dimer chromosomes.

Citation: Louarn J, Cornet F, Kuempel P. 2005. The Terminus Region of the Chromosome, or, All's Well That Ends Well, p 251-274. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch13

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Figures

Image of Figure 1
Figure 1

Main features of the terminus region. (A) Location of dif and Ter sites on the chromosome. The inner circle shows chromosome organization in the strain carrying the large inversion from 29 to 78 min. (B) Enlargement of the terminus region. Above the linear map are indicated some striking features of the sequence. From bottom to top: presence of polar elements, with change of orientation at ( ); the regions rich in potential target sites for nucleoid-associated FIS protein ( ); the region deprived of BIME-2 elements ( ); the regions rich in potential target sites for nucleoid-associated IHF protein ( ). Below the linear map are shown zones of occurrence of phenomena characteristic of the terminus. From bottom to top: the TER macrodomain ( ); the regions refractory to inversion (NDZ) ( ); the HOT segments ( ); the region where maps when active in dimer resolution (DAZ), or which becomes fragile when is inactive (TRZ) ( ); the deletable zone, which carries no essential gene ( ); the poorly transcribed zone ( ); the replication fork trap ( ). Graded ends indicate that domain limits are not precisely known (for TER and NDZ) or that phenomenon intensity decreases gradually on either side (for DAZ and TRZ).

Citation: Louarn J, Cornet F, Kuempel P. 2005. The Terminus Region of the Chromosome, or, All's Well That Ends Well, p 251-274. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch13
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Image of Figure 2
Figure 2

Distribution of polarized sequences. (A) Distribution of RAG (RRNAGGGS) sequences along the K-12 chromosome (N=any base, R=any purine, S=G or C). This map shows the percentage of RAG elements facing in every 100 kb of each replichore, starting from dif. Note the decrease in polarity with distance from dif. The number of RAG sequences per 100 kb is randomly distributed, ranging from 46 to 77, with an average of 1 element per 1.6 kb. (B) Comparison between regions of K-12 (50 kb on each side of ) and serovar Typhi (40 kb on each side of ). The Salmonella enterica serovar Typhi sequence was obtained from the Sanger Institute (http://www.sanger.ac.uk). Maps are aligned at ; the flag indicates the position of TerC. Horizontal heavy lines joined by dotted arrows indicate regions of detected homology between the two genomes. Vertical lines indicate RAG sequences; the orientation is indicated by position above or below the maps. Note the dramatic inversion of RAG polarization at dif in both genomes. Horizontal arrows indicate chi sites (5´GCTGGTGG3´); the arrowhead indicates the 5´ end. Consequently, the arrows indicate the direction that RecBCD must go through a given chi site in order to stimulate recombination. Note the relative scarcity of chi sites near in E. coli, and that the inversion of chi site polarization seems to occur at TerC.

Citation: Louarn J, Cornet F, Kuempel P. 2005. The Terminus Region of the Chromosome, or, All's Well That Ends Well, p 251-274. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch13
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Figure 3

Generation of chromosome dimers and resolution at . (A) Formation of a circular dimer by homologous recombination. A replicating chromosome ( ) suffers breakage of a replication fork ( ). Repair of the fork by recombination, which can include resolution of the Holliday junction such that sister chromatid exchange occurs, followed by some further replication, gives structure 3. Note that only two strands of DNA are now present, and further synthesis adds onto the ends of these two strands. Completion of the replication cycle gives a circular dimer ( ). (B) Dimer resolution at can be detected by formation of physical recombinants ( ). Cells growing exponentially in heavy (C N) rich medium were transferred to light medium and grown for two generations. At this time, total chromosomal DNA must be found as hybrid or light material in equal amount. ( ) Predictions. Recombination between sites after the first replication cycle produces single strands that shift from heavy to light density at the site. These can be detected after the next replication cycle (in light medium), which yields semihybrid-density double-stranded DNA. (2) Experimental data. Chromosomal DNA harvested after two rounds of replication in light medium was digested to produce restriction fragments in which dif was centered in its fragment. Hybrid, semihybrid, and light material were separated by centrifugation in cesium chloride density gradients, and the carrying fragments were identified by hybridization with a radioactive probe. (2a) Typical profile obtained with wild-type bacteria: about 15% of the dif DNA was present as semihybrid material. This was unique to dif. (2b) Typical profile obtained in mutants, or when cell division was blocked by cephalexin treatment or temperature shift of an mutant. No semihybrid material was detected at .

Citation: Louarn J, Cornet F, Kuempel P. 2005. The Terminus Region of the Chromosome, or, All's Well That Ends Well, p 251-274. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch13
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Image of Figure 4
Figure 4

Extents of the activity zone (DAZ) and of the zone where terminal recombination is detected in absence of dimer resolution (TRZ). The DAZ extent has been determined in three ways. (i) Recovery of a Dif phenotype after transposition of transposon (Tn ) into the chromosome of Ddif (1 kb) mutant ( ). The shaded vertical area spanning the normal location of the site shows the region of the seven Δif insertions analyzed in this study. (ii) Measure of increased viability due to an ectopic site (open circles), with reference to the isogenic -deleted strain ( ). The percentage of abortive divisions increased with the distance between the ectopic site and the dif wild-type position, to reach a maximum value of about 15% when this distance is higher than 20 kb and/or is inactive. (iii) Frequency of loss per generation (closed circles) of a kanamycin resistance determinant located between two dif sites inserted at ectopic locations ( ). The percentage of excision reached a value of about 12% per generation when the cassette was inserted at the dif normal location, and rapidly decreased when the cassette was moved in either direction. The extent of the region involved (the TRZ) was estimated from the frequency of bacteria cured of a prophage inserted by homologous recombination at the indicated positions (closed arrowheads). Data are shown only for prophage insertions that maintained the RAG polarity in the two sides of the terminus region, centered at .

Citation: Louarn J, Cornet F, Kuempel P. 2005. The Terminus Region of the Chromosome, or, All's Well That Ends Well, p 251-274. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch13
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Figure 5

Activity of is controlled by polarization of flanking regions. Determinants of the DAZ (see Fig. 4 ) were characterized by analysis of deletions and inversions near ( ), and the location of DAZ in wild-type and rearranged chromosomes is indicated by the boxed region. On the drawings, DOPEs are symbolized by arrows—gray or black, depending on the replichore. The orientation of the arrows indicates the direction in which DNA is proposed to be pulled (or pushed) away from the ingrowing septum (see “The Colocation Model for Dimer Resolution”). Deletions and inversions are described from top to bottom. Deletion type 1: deletions that had both endpoints on the same side of were wild type for dimer resolution (Difþ). Deletion type 2: deletions that had endpoints on opposite sides of dif were mutant for dimer resolution (Dif–). This phenotype was suppressed when was reinserted at the deletion junction. These deletion data indicated that no unique site (besides ) is needed for dif activity, and that a DAZ is always found at the junction between the severed replichores. Inversion type 1: inversions that had endpoints on opposite sides of dif were always wild type for dimer resolution (Dif). Inversion type 2: inversions that had endpoints on the same side of were mutant for dimer resolution (Dif¯), provided that the inverted region was large enough and close enough to dif. When the proximal endpoint mapped at more than 30 kb away from dif, these inversions had no effect on dif activity. Suppression of inversion type 2: the inversion generates a new DAZ at the endpoint distal from the normal location of dif. When is transplaced to this location, dimer resolution activity is regained (Dif).

Citation: Louarn J, Cornet F, Kuempel P. 2005. The Terminus Region of the Chromosome, or, All's Well That Ends Well, p 251-274. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch13
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Image of Figure 6
Figure 6

The colocation model for control of dimer resolution. The gray area represents the part of the cell within which septum-anchored FtsK protein (filled tailed circles) can access the other partners of resolution: chromosomal sites (black and white squares) and XerC and XerD recombinases (open circles). Since Xer recombinases are most probably free in the cytoplasm, the other important topological factor is the mechanism which positions a pair of dif sites within the FtsK activity space. It is proposed that this involves the polarization of dif-flanking regions. DOPEs (represented as in Fig. 5 ) are supposed to be sequences recognized by the partitioning process which tends to pull (or push) all chromosomal DNA away from the septum plane. In the case of dimer chromosomes (A), forces acting in opposite directions will place the DAZ at the ingrowing septum. FtsK plays a crucial role in the positioning step. The next step is formation of the synaptic complex /XerC/XerD/FtsK, and recombination between sites can then proceed. After exchange, the forces involved in partitioning separate the recombinant sites from each other, thus precluding regeneration of a chromosome dimer. When chromosomes are monomers (B), is transplaced outside the DAZ (C), or an inversion moved the DAZ away from (D), dif sites do not enter within the FtsK activity space, and Xer recombination is rare. Adapted from reference .

Citation: Louarn J, Cornet F, Kuempel P. 2005. The Terminus Region of the Chromosome, or, All's Well That Ends Well, p 251-274. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch13
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