Characteristics of Chi distribution on different bacterial genomes

Karoui, Meriem El; Biaudet, Véronique; Schbath, Sophie; Gruss, Alexandra

doi:10.1016/s0923-2508(99)00132-1

Cited by 83 publications

(77 citation statements)

References 52 publications

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“…Instead, the overrepresentation and skewing of Chi sequences reflect characteristics of GT-rich sequences that coincide with an underlying bias in codon usage and a bias in transcription polarity (29,70,299,303); however, these characteristics statistically correlate most significantly with replication direction (19,100). This implies that the RecBCD enzyme selected Chi largely from the overrepresented recombinogenic GT-rich sequences, which arise from both codon usage and genome base composition, for use as a regulatory switch and recombination hotspot in recombination-dependent replication (19,100,302,304), rather than there being strong prior selective pressure for the Chi sequence to become overrepresented due to its role in recombinational repair. In other words, the RecBCD enzyme adapted largely to the genome and not vice versa.…”

Section: Crossover Hotspot Instigatormentioning

confidence: 99%

“…Analysis of the E. coli genome reveals that Chi is the third most overrepresented octamer: E. coli contains 1,008 Chi sequences (the original sequence of E. coli MG1655 reported 1,009 sequences [38], but the recent database shows only 1,008) (19); Chi sequences are four-to eightfold more frequent than expected by chance and appear on average once every 4.5 kb (38,100,302). Even more significant is their skew: 75% are oriented toward the origin of replication, making Chi the most directionally biased 8-nucleotide sequence in E. coli (100,246). Furthermore, there is a statistically significant association between Chi sequences and GT-rich "islands"; GT-rich DNA is the preferred substrate for RecA homology-dependent pairing (302).…”

Section: Crossover Hotspot Instigatormentioning

confidence: 99%

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RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

Dillingham

Kowalczykowski

2008

Microbiol Mol Biol Rev

507

599

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SUMMARY The RecBCD enzyme of Escherichia coli is a helicase-nuclease that initiates the repair of double-stranded DNA breaks by homologous recombination. It also degrades linear double-stranded DNA, protecting the bacteria from phages and extraneous chromosomal DNA. The RecBCD enzyme is, however, regulated by a cis-acting DNA sequence known as Chi (crossover hotspot instigator) that activates its recombination-promoting functions. Interaction with Chi causes an attenuation of the RecBCD enzyme's vigorous nuclease activity, switches the polarity of the attenuated nuclease activity to the 5′ strand, changes the operation of its motor subunits, and instructs the enzyme to begin loading the RecA protein onto the resultant Chi-containing single-stranded DNA. This enzyme is a prototypical example of a molecular machine: the protein architecture incorporates several autonomous functional domains that interact with each other to produce a complex, sequence-regulated, DNA-processing machine. In this review, we discuss the biochemical mechanism of the RecBCD enzyme with particular emphasis on new developments relating to the enzyme's structure and DNA translocation mechanism.

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Section: Crossover Hotspot Instigatormentioning

confidence: 99%

Section: Crossover Hotspot Instigatormentioning

confidence: 99%

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

Dillingham

Kowalczykowski

2008

Microbiol Mol Biol Rev

507

599

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“…Thus doubts remain as to the biological significance of this overrepresentation in E. coli (Bell et al, 1998;Biaudet et al, 1998;Uno et al, 2000). Furthermore, very different chi sequences have been found in Haemophilus influenzae and B. subtilis, where the leading strand bias is much less pronounced (El Karoui et al, 1999). Such an overlapping of signals and biases complicates the understanding of the biological reasons behind most oligonucleotide avoidance or overrepresentation (Burge et al, 1992;Mrázek & Karlin, 1998;Salzberg et al, 1998).…”

Section: Oligonucleotide Biasmentioning

confidence: 99%

The replication-related organization of bacterial genomes

2004

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The replication of the chromosome is among the most essential functions of the bacterial cell and influences many other cellular mechanisms, from gene expression to cell division. Yet the way it impacts on the bacterial chromosome was not fully acknowledged until the availability of complete genomes allowed one to look upon genomes as more than bags of genes. Chromosomal replication includes a set of asymmetric mechanisms, among which are a division in a lagging and a leading strand and a gradient between early and late replicating regions. These differences are the causes of many of the organizational features observed in bacterial genomes, in terms of both gene distribution and sequence composition along the chromosome. When asymmetries or gradients increase in some genomes, e.g. due to a different composition of the DNA polymerase or to a higher growth rate, so do the corresponding biases. As some of the features of the chromosome structure seem to be under strong selection, understanding such biases is important for the understanding of chromosome organization and adaptation. Inversely, understanding chromosome organization may shed further light on questions relating to replication and cell division. Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution.

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“…The diversity in DSB repair enzymes may be related to genome plasticity: genome rearrangements are common events that may occur via intrachromosomal transposition, gene duplications and inversions, or entry of exogenous DNA. In L. lactis, there is a 4:1 orientation bias of Chi distribution with respect to the direction of DNA replication (exo/hel recognizes Chi in one orientation) (14,21,23,29,47). Inversion of a large DNA segment could considerably reduce the number of Chi sites available to stimulate repair if a replication fork break occurs in that region (36).…”

Section: Rexbmentioning

confidence: 99%

“…The exo/hel-Chi couples show remarkably little conservation from one bacterium to another. Furthermore, Chi sites are not the same in different species, and their genome distribution properties differ for each organism (7,8,10,21,45). This suggests that the Chi features of high frequency and overrepresentation on the genome had to arise independently in each case (7,21).…”

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confidence: 99%

In Vivo Evidence for Two Active Nuclease Motifs in the Double-Strand Break Repair Enzyme RexAB of Lactococcus lactis

et al. 2001

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In bacteria, double-strand DNA break (DSB) repair involves an exonuclease/helicase (exo/hel) and a short regulatory DNA sequence (Chi) that attenuates exonuclease activity and stimulates DNA repair. Despite their key role in cell survival, these DSB repair components show surprisingly little conservation. The best-studied exo/hel, RecBCD of Escherichia coli, is composed of three subunits. In contrast, RexAB of Lactococcus lactis and exo/hel enzymes of other low-guanine-plus-cytosine branch gram-positive bacteria contain two subunits. We report that RexAB functions via a novel mechanism compared to that of the RecBCD model. Two potential nuclease motifs are present in RexAB compared with a single nuclease in RecBCD. Site-specific mutagenesis of the RexA nuclease motif abolished all nuclease activity. In contrast, the RexB nuclease motif mutants displayed strongly reduced nuclease activity but maintained Chi recognition and had a Chi-stimulated hyperrecombination phenotype. The distinct phenotypes resulting from RexA or RexB nuclease inactivation lead us to suggest that each of the identified active nuclease sites in RexAB is involved in the degradation of one DNA strand. In RecBCD, the single RecB nuclease degrades both DNA strands and is presumably positioned by RecD. The presence of two nucleases would suggest that this RecD function is dispensable in RexAB.In bacteria, double-stranded DNA breaks (DSB) are frequent events that may be provoked, for example, by pauses in the replication fork (36, 43). Such genomic disruptions are lethal in the absence of DNA repair. In Escherichia coli DSB repair requires the activity of a large enzyme complex, known as RecBCD, that has ATP-dependent helicase and exonuclease activities (see reference 32 for a review). The enzyme degrades both strands, starting from the DNA break until it reaches an octanucleotide sequence, known as Chi, that attenuates degradation and stimulates recombination (44,46). The enzyme exhibits helicase activity and residual exonuclease activity with an altered polarity after Chi (4, 16); the remaining activity provides a single-stranded DNA substrate for recombination enzymes to mediate repair.Organization of the three-subunit exonuclease/helicase (exo/hel) RecBCD. Structure-functional studies of RecBCD have revealed some of the roles of each subunit. RecB seems to possess two key activities of the enzyme. The N-terminal 929 amino acids (out of 1,180 total) have confirmed ATPase and helicase activities (13,54

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Characteristics of Chi distribution on different bacterial genomes

Cited by 83 publications

References 52 publications

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

The replication-related organization of bacterial genomes

In Vivo Evidence for Two Active Nuclease Motifs in the Double-Strand Break Repair Enzyme RexAB of Lactococcus lactis

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