Recombination and chromosome segregation

Abstract

The duplication of DNA and faithful segregation of newly replicated chromosomes at cell division is frequently dependent on recombinational processes. The rebuilding of broken or stalled replication forks is universally dependent on homologous recombination proteins. In bacteria with circular chromosomes, crossing over by homologous recombination can generate dimeric chromosomes, which cannot be segregated to daughter cells unless they are converted to monomers before cell division by the conserved Xer site-specific recombination system. Dimer resolution also requires FtsK, a division septum-located protein, which coordinates chromosome segregation with cell division, and uses the energy of ATP hydrolysis to activate the dimer resolution reaction. FtsK can also translocate DNA, facilitate synapsis of sister chromosomes and minimize entanglement and catenation of newly replicated sister chromosomes. The visualization of the replication/recombination-associated proteins, RecQ and RarA, and specific genes within living Escherichia coli cells, reveals further aspects of the processes that link replication with recombination, chromosome segregation and cell division, and provides new insight into how these may be coordinated.

Cre Recombinase

“…The reaction is carried out between 34-bp recombination sites called loxP, which are in a directly repeated orientation in the physiological substrates. Hence, Cre functions as a simple version of the Xer system, which performs a similar role for the bacterial chromosome (22).…”

Synapsis of loxP Sites by Cre Recombinase

“…In the simplest systems, typified by the bacteriophage P1 Cre recombinase (3) and the Saccharomyces cerevisiae Flp recombinase (4), only the recombinase enzymes and DNA substrates containing 34-bp recombination sequences are required for efficient recombination. In others, such as the bacteriophage -integrase (-int) 3 (5) and the Escherichia coli XerC and XerD recombinases (6), efficient recombination requires more complex recombination sites and the activities of auxiliary proteins that tightly regulate the forward and reverse reactions. A remarkable property of both the simple and complex systems is their ability to efficiently synapse (associate) recombining sites that can be located far from one another on the same chromosome or, for bacteriophage integration, are in separate DNA molecules.…”

Efficiency and specificity of CTXϕ chromosomal integration: dif makes all the difference

“…The precise role of second site was undetermined, although it was required for integration (5). In addition, the XerC cleavage on attP was separated from XerD cleavage by 12-bp, which is wholly unexpected given the 6-8 bp spacing of XerC and XerD binding at two homologous dif sites, which is essential for interaction between the two recombinases that control synapse formation and catalysis (10,11). McLeod and Waldor's data suggested that synapsis of the two duplexes performed by XerCD at the attP and dif1 sites are potentially less stable than recombination between homologous dif sites.…”

“…A recombinase (integrase), which ordinarily catalyzes this integration in other phages, is not present in the CTXϕ genome; instead, it commandeers two host-encoded tyrosine recombinases, XerC and XerD (9). The XerCD proteins are conserved among eubacteria, as they serve to resolve chromosome dimers during cell division (10,11). In Escherichia coli, XerCD proteins bind and catalyze recombination at homologous 28-bp dif sites, composed of two 12-bp binding sites for XerC and XerD separated by a 6-bp spacer or overlap region, which allows for XerC-XerD interactions that ensure stable synapsis (10,11).…”

“…The XerCD proteins are conserved among eubacteria, as they serve to resolve chromosome dimers during cell division (10,11). In Escherichia coli, XerCD proteins bind and catalyze recombination at homologous 28-bp dif sites, composed of two 12-bp binding sites for XerC and XerD separated by a 6-bp spacer or overlap region, which allows for XerC-XerD interactions that ensure stable synapsis (10,11). Because V. cholerae harbors two distinct, nonhomologous circular chromosomes (chromosome I and II) (12,13), two dif sites are present, dif1 in chromosome I and dif2 in chromosome II (9); similar to E. coli, the same FstKdependent mechanism coordinates dimer resolution on each chromosome with cell division (14).…”