Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli

Arakawa, Kazuharu; Uno, Reina; Nakayama, Yoichi; Tomita, Masaru

doi:10.1016/j.gene.2006.12.022

Cited by 15 publications

(15 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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: 96%

“…In vitro analysis would later reveal that Chi was the single-stranded DNA sequence 5Ј-GCTGGTGG-3Ј (33). 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).…”

Section: Crossover Hotspot Instigatormentioning

confidence: 99%

See 1 more Smart Citation

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

Dillingham

Kowalczykowski

2008

Microbiol Mol Biol Rev

507

599

View full text Add to dashboard Cite

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.

show abstract

Section: Crossover Hotspot Instigatormentioning

confidence: 96%

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

View full text Add to dashboard Cite

show abstract

“…Chi sequences are over-represented in the E. coli genome in one orientation relative to the progression of the replication fork (8, 18) and occur about once every 4 kb. The probability that RecBCD will recognize a single Chi element is about 30% in vitro (80, 243); in vivo, multiple Chi sites can additively protect linear DNA from degradation in a RecA-dependent fashion (143).…”

Section: E Coli Exonucleases: Properties Structure and Functionmentioning

confidence: 99%

The DNA Exonucleases of Escherichia coli

Lovett

2011

EcoSal Plus

View full text Add to dashboard Cite

DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB) and III (dnaQ/mutD), Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG) and X (exoX), the RecBCD, RecJ, and RecE exonucleases, SbcCD endo/exonuclease, the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo) and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.

show abstract

“…The tandem repeats that are frequently seen in eukaryotic noncoding regions (Tóth et al 2000) have seldom been reported in bacteria (van Belkum et al 1998), but dispersed repeated sequences are common: transposons and minitransposons (Siguier et al 2006), long palindromic sequences in the range of from 60 to 200 nt (Wilson and Sharp 2006), short palindromic sequences in the range of from 27 to 60 nt and their composites (Bachellier et al 1999;Tobes and Ramos 2005), and very short dispersed repeats (Robinson et al 1995;Smith et al 1999;Mrázek et al 2002;Arakawa et al 2007). Considering the ubiquity of dispersed repeated sequences and their emerging role in genome evolution (Shapiro 2005;Siguier et al 2006), we can hardly be said to comprehend bacterial genomes without first giving an account of what they are, what they do, and how they arise.…”

mentioning

confidence: 99%

Very small mobile repeated elements in cyanobacterial genomes

Elhai

Kato²,

Cousins³

et al. 2008

Genome Res.

View full text Add to dashboard Cite

Mobile DNA elements play a major role in genome plasticity and other evolutionary processes, an insight gained primarily through the study of transposons and retrotransposons (generally ∼1000 nt or longer). These elements spawn smaller parasitic versions (generally >100 nt) that propagate through proteins encoded by the full elements. Highly repeated sequences smaller than 100 nt have been described, but they are either nonmobile or their origins are not known. We have surveyed the genome of the multicellular cyanobacterium, Nostoc punctiforme, and its relatives for small dispersed repeat (SDR) sequences and have identified eight families in the range of from 21 to 27 nucleotides. Three of the families (SDR4, SDR5, and SDR6), despite little sequence similarity, share a common predicted secondary structure, a conclusion supported by patterns of compensatory mutations. The SDR elements are found in a diverse set of contexts, often embedded within tandemly repeated heptameric sequences or within minitransposons. One element (SDR5) is found exclusively within instances of an octamer, HIP1, that is highly over-represented in the genomes of many cyanobacteria. Two elements (SDR1 and SDR4) often are found within copies of themselves, producing complex nested insertions. An analysis of SDR elements within cyanobacterial genomes indicate that they are essentially confined to a coherent subgroup. The evidence indicates that some of the SDR elements, probably working through RNA intermediates, have been mobile in recent evolutionary time, making them perhaps the smallest known mobile elements.[Supplemental material is available online at www.genome.org.] The mechanisms by which new copies of dispersed repeats are generated are well understood in some, but by no means, all cases. Transposon copies arise through DNA intermediates, catalyzed by transposases (Gueguen et al. 2005). Copies of retroposons (and degenerate retroposons, such as Alu sequences) are made through RNA intermediates, catalyzed by reverse transcriptase (Ostertag and Kazazian 2001). Minitransposons (also called MITEs), a category that may include the well-studied ERIC sequences (De Gregario et al. 2005), are thought to rely on transposases encoded outside of the mobile element (Siguier et al. 2006). The 8-nt highly iterated palindromic (HIP1) sequences observed in the genomes of many related cyanobacteria are thought not to be mobile but rather to form through mutation from pre-existing sequences (Robinson et al. 1997), The mechanisms by which small dispersed repeats are generated are otherwise unknown.The genomes of the cyanobacterium Nostoc punctiforme ATCC 29,133 and its relatives are unusual in that about 1.5% (∼7.5% of intergenic sequences) is taken up by tandem repeats at least 20 nt in length (Meeks et al. 2001; J. Elhai, T. Katayama, R. Narikawa, S. Okamoto, C. Friedland, R. Nayak, M. Ikeuchi, and M. Kanehisa, unpubl.). Repeating units of 7 nt (Mazel et al. 1990;Meeks et al. 2001) are by far the most common, with only a few of the possible families ...

show abstract

Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli

Cited by 15 publications

References 39 publications

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

The DNA Exonucleases of Escherichia coli

Very small mobile repeated elements in cyanobacterial genomes

Contact Info

Product

Resources

About