Document Detail

Accumulation of large non-circular forms of the chromosome in recombination-defective mutants of Escherichia coli.
Jump to Full Text
MedLine Citation:
PMID:  12718760     Owner:  NLM     Status:  MEDLINE    
BACKGROUND: Double-strand breakage of chromosomal DNA is obviously a serious threat to cells because various activities of the chromosome depend on its integrity. However, recent experiments suggest that such breakage may occur frequently during "normal" growth in various organisms - from bacteria through vertebrates, possibly through arrest of a replication fork at some endogenous DNA damage.
RESULTS: In order to learn how the recombination processes contribute to generation and processing of the breakage, large (> 2000 kb) linear forms of Escherichia coli chromosome were detected by pulsed-field gel electrophoresis in various recombination-defective mutants. The mutants were analyzed in a rich medium, in which the wild-type strain showed fewer of these huge broken chromosomes than in a synthetic medium, and the following results were obtained: (i) Several recB and recC null mutants (in an otherwise rec+ background) accumulated these huge linear forms, but several non-null recBCD mutants (recD, recC1001, recC1002, recC1003, recC1004, recC2145, recB2154, and recB2155) did not. (ii) In a recBC sbcA background, in which RecE-mediated recombination is active, recA, recJ, recQ, recE, recT, recF, recO, and recR mutations led to their accumulation. The recJ mutant accumulated many linear forms, but this effect was suppressed by a recQ mutation. (iii) The recA, recJ, recQ, recF and recR mutations led to their accumulation in a recBC sbcBC background. The recJ mutation showed the largest amount of these forms. (iv) No accumulation was detected in mutants affecting resolution of Holliday intermediates, recG, ruvAB and ruvC, in any of these backgrounds.
CONCLUSION: These results are discussed in terms of stepwise processing of chromosomal double-strand breaks.
Naofumi Handa; Ichizo Kobayashi
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2003-04-28
Journal Detail:
Title:  BMC molecular biology     Volume:  4     ISSN:  1471-2199     ISO Abbreviation:  BMC Mol. Biol.     Publication Date:  2003 Apr 
Date Detail:
Created Date:  2003-07-08     Completed Date:  2003-07-25     Revised Date:  2013-04-18    
Medline Journal Info:
Nlm Unique ID:  100966983     Medline TA:  BMC Mol Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  5     Citation Subset:  IM    
Division of Molecular Biology, Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108-8639 Japan.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Chromosome Breakage / genetics
Chromosomes, Bacterial / genetics*
Culture Media / metabolism
Electrophoresis, Gel, Pulsed-Field / methods
Endodeoxyribonucleases / deficiency,  genetics
Escherichia coli / enzymology,  genetics*,  growth & development
Escherichia coli Proteins*
Exodeoxyribonuclease V
Exodeoxyribonucleases / deficiency,  genetics,  physiology
Recombination, Genetic / genetics*
Reg. No./Substance:
0/Culture Media; 0/Escherichia coli Proteins; EC 3.1.-/Endodeoxyribonucleases; EC 3.1.-/Exodeoxyribonucleases; EC I; EC V; EC V, E coli

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

Full Text
Journal Information
Journal ID (nlm-ta): BMC Mol Biol
ISSN: 1471-2199
Publisher: BioMed Central, London
Article Information
Download PDF
Copyright ? 2003 Handa and Kobayashi; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
Received Day: 12 Month: 3 Year: 2003
Accepted Day: 28 Month: 4 Year: 2003
collection publication date: Year: 2003
Electronic publication date: Day: 28 Month: 4 Year: 2003
Volume: 4First Page: 5 Last Page: 5
ID: 156651
Publisher Id: 1471-2199-4-5
PubMed Id: 12718760
DOI: 10.1186/1471-2199-4-5

Accumulation of large non-circular forms of the chromosome in recombination-defective mutants of Escherichia coli
Naofumi Handa12 Email:
Ichizo Kobayashi1 Email:
1Division of Molecular Biology, Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108-8639 Japan
2Present address: Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA 95616 USA


Double-strand (ds) breakage of chromosomal DNA is obviously a serious threat to cells because various activities of the chromosome ? gene expression, replication and partition ? depend on its integrity. However, recent experiments suggest that such chromosomal ds breakage may occur relatively frequently during "normal" growth in several organisms ? in bacteria [1,2], yeast [3] and chicken cells [4].

In Escherichia coli, spontaneous breakage and degradation of the chromosome associated with a replication fork were predicted from early genetic analysis and were detected under various conditions of altered replication (for review, see [5]). DNA ds breaks play a key role in homologous recombination. From a DNA ds break, RecBCD enzyme starts degrading DNA (for review, see [6]). When it encounters a specific sequence called Chi, it promotes its pairing with a homologous DNA. Even in the absence of RecBCD enzyme, sbcA mutation confers other recombination pathway, called RecET pathway. The recE gene product of the Rac prophage converts dsDNA ends into 3' protruding single-stranded form and the recT gene product promotes recombination by annealing them with a homologous DNA in its vicinity (for review, see [7,8]). This recombination may result in one progeny DNA (non-conservative recombination) or two progeny DNAs (conservative double-strand break repair) [9]. In a recBC sbcBC background, a ds end stimulates homologous recombination that results in only one progeny DNA (non-conservative recombination) [10]. Analysis of the stimulation of recombination by replication (for review, see [11]) and analysis of altered chromosomal replication (for review, see [12]) led to the proposal that a chromosomal ds break formed during replication fork arrest triggers homologous recombination, which would reconstitute a replication fork (for review, see [5]).

Game and his colleagues have developed a sensitive means of detecting chromosomal ds breakage using a circular chromosome [3]. Under most conditions of pulsed-field gel electrophoresis, a circular yeast chromosome and circular bacterial chromosomes will not enter the gel, very likely because they are trapped by the branches of the network of agarose [3,13,14]. One double-strand break transforms this circular form into a linear form, which can now move slowly in the gel [3]. We used this procedure to detect double-strand breakage of a circular bacterial chromosome occurring spontaneously or after loss of a restriction-modification gene complex [15,16]. We found increased chromosome breakage in recBC-null and recC1002 mutants of E. coli under both conditions [1]. Michel and her colleagues used pulsed-field gel electrophoresis to detect degraded chromosomal DNAs arising spontaneously in recBC mutants and arising during replication fork arrest [2]. RuvABC proteins, which catalyze migration and cleavage of Holliday junctions, are responsible for the occurrence of the degraded DNAs following replication fork arrests [17].

In this work, we employed the pulsed-field gel electrophoresis procedure to measure large non-circular forms of the chromosome obtained from various recombination-defective mutants in rec+, recBC sbcA, and recBC sbcBC genetic backgrounds.

Effect of growth medium on the accumulation of large chromosomal fragments

Large linear chromosomal fragments were measured by pulsed-field gel electrophoresis. In our analysis, growing E. coli cells are harvested, embedded in an agarose plug, and lysed in situ. The chromosomes in a plug are electrophoresed in varying electric fields. An example of such a gel is shown in Figure 1. The DNA is partitioned in three places in the gel ? the well, the area just below the well (marked by a bar to the right of the gel), and the lower area. Intact circular chromosomes stay in the well [3,14] likely because they are trapped in the branches of agarose resin [13]. Large linear forms generated by a ds break in this circle would escape from agarose trap and form broad bands beneath the well (marked by the bar). This area corresponds to unbranched linear forms DNA of more than 2000 kb when compared with yeast chromosome markers. When the DNAs become smaller by degradation, they will migrate further. These interpretations are based on a previous work with a yeast circular chromosome and on our analysis of E. coli chromosomal breakage after loss of restriction-modification genes [3,15,16]. In this work, we focus on the second DNA species ? the huge linear forms in the area just below the well (Figure 1, marked by the bar).

In the experiment shown in Figure 1, a rec+ strain (in AB1157 background) grown in minimal medium (M9) (Figure 1, lane 2) gave rise to some of these huge linear DNAs in this area. There was less of this DNA species when the cells were grown in a rich medium (LB) (Figure 1, lanes 3). In an isogenic recB21 recC22 strain, the amount was larger than in rec+.

We do not know why the medium makes such a difference. It could reflect properties of the spontaneous DNA damages, the replication fork, the number of replication forks, the number of chromosomes, the organization and structure of the chromosomes, the repair machinery, or the availability of homologous chromosomes for repair. All of these features will influence the chromosome stability not only in rec+, but also in mutants. This medium-dependence is in the opposite direction to what is simply expected from generation of a double-stranded chromosomal end by collapse of a replication fork with another, replication fork moving in the same direction [18], because replication initiation should be more frequent in a rich medium than in a poor medium. Whatever the reason, we chose to use the rich medium in which the rec+ strain produce less linear forms, because the background is clear and may allow sensitive detection of their increase in a survey of various recombination-defective mutants.

rec and ruv mutations

The accumulation of huge linear DNAs was also seen in other recBC null mutants in this AB1157 genetic background (recB21, recC22 and recC73 (Figure 2A)) and in another, V66, genetic background (recC73 (Figure 2B)), as observed earlier [1,2]. A recD mutant showed no accumulation. The other non-null recBCD alleles examined (recC1001, recC1002, recC1003, recC1004, recC2145, recB2154, and recB2155) did not accumulate the huge linears (Figure 2B). We do not know why the same mutant allele, recC73, shows more accumulation in V66 background than in AB1157 background in a reproducible manner (Figures 2A and 2B).

The other mutants tested ? recA, recF, recG, recJ, recN, recO, recQ, recR, ruvAB, and ruvC ? did not accumulate huge linear DNAs. The recF mutation partially suppressed the effect of the recC73 mutation in accumulating the huge linear chromosomes (Figure 2B).

recBC sbcA background

In the recBC sbcA strain, an sbcA mutation on the Rac prophage expresses recET genes, which promotes homologous recombination at a ds end [7]. The accumulation of the huge linears was seen with recA, recE, recT, recJ, recQ, recF, recO and recR strains (Figure 2C). Mutations in genes involved in processing Holliday structures ? recG, ruvAB and ruvC ? did not lead to their accumulation. The accumulation by recJ mutation was suppressed by a recQ mutation (Figure 2C, lanes 7 and 15).

recBC sbcBC background

In the recBC sbcBC strain, RecBCD enzyme is inactive and RecFOR and RecQJ proteins promote recombination together with RecA [19]. In the recBC sbcBC background, recA, recF, recJ, recQ and recR mutants accumulated these huge linears to varying extents (Figure 2D). However, again the ruvC mutation did not lead to accumulation.

Control experiments

These assays were carried out more than twice for each strain, and the extent of accumulation of the linear forms was reproducible. The DNA in the area just below the origin was also measured by densitometry to confirm the above results (data not shown).

When the chromosomal DNA in the agar plug was digested with a restriction enzyme (XbaI) before the pulsed-field gel electrophoresis, all the strains examined produced comparable amounts of DNA (Figure 3). This amount is much larger than the large linear forms. This indicates that the total amount of undegraded DNA associated with the cells is comparable for all the strains.


We found that large, non-circular forms of the chromosome accumulate in varying amounts in various recombination-defective mutants of Escherichia coli.

Our operational definition of the non-circular forms is their presence in an area just below the well in our pulsed-field gel, as marked by a bar in Figure 1. The molecular species in this area may not be limited to a simple linear form of varying lengths. If a chromosome carries multiple replication forks as usual at 37?C in rich media, more than one double-strand break may be necessary to form a non-circular, branched species, which should be able to move through the gel. Finding out macroscopic forms of these giant molecules would be a technical challenge (see [20], for example). We do not know why DNAs make two broad bands in this area (Figure 1, 4th lane, for example), either. Depending on the electrophoresis condition, one narrow band, a pair of two bands or one very broad band was observed (data not shown).

Abundance of these huge non-circular forms is expected to be affected by several factors, which might work potentially in opposite directions, such as: (i) breakage in the cell; (ii) degradation in the cell; (iii) repair in the cell; (iv) breakage and degradation out of the cell. Each term is, in turn, affected by other factors such as chromosome organization, number of the replication forks, speed of the replication forks, abundance of specific proteins, and so forth. Therefore, our finding of accumulation of more of the non-linear forms in a rich medium than in a poor medium (Figure 1) does not immediately allow us to conclude that starving conditions induce a chromosomal double-strand breakage.

Spontaneous DNA damages, repair and degradation are expected to be the key processes in interpreting our data. Spontaneous DNA damages may interfere with replication fork progression and produce chromosomal double-stranded breaks. This would lead to extensive exonucleolytic degradation. Complete repair at some of these steps would reconstitute a circular chromosome, which will stay in the well. On the other hand, further degradation of the huge, non-circular forms would result in shorter or no fragments, which will run faster in the gel. The presence of huge linear forms, therefore, probably indicates both the absence of complete repair and the absence of further degradation. The absence of the large linears could either mean the presence of complete repair or the presence of extensive degradation activity. Our control experiments demonstrated that restriction digestion of chromosome DNAs before the electrophoresis results in release of comparable amounts of DNA from the wells in all the strains examined (Figure 3). This result, at least, excludes the possibility that the absence of the large, non-circular chromosomes in some strains (Figure 2) reflects the absence of DNAs in the wells during the process or by extensive and general nuclease action. Of course, we cannot exclude the possibility that the broken chromosomes specifically have suffered extensive degradation.

In spite of these potential complexity and essential ambiguity, our measurements provided a unique clue to the action of recombination-associated enzymes in the chromosome metabolism. Indeed, some of our observations in the mutants can be readily related to the established properties of the affected enzyme.

Accumulation of the huge linear DNAs in the recBC null mutants can be interpreted from the known properties of RecBCD enzyme in a straightforward way. These null mutant enzymes cannot degrade DNA from a ds break nor can they repair DNA by recombination [6]. We assume that they cannot repair the broken chromosomes to form intact circular chromosomes and that they cannot degrade them into smaller pieces. The recD mutant does not show nuclease activity but is recombination-proficient and able to repair the broken DNA molecules [6]. This explains why it does not accumulate the huge linear forms. The other non-null recBCD mutants (recC1001, recC1002, recC1003, recC1004, recC2145, recB2154, and recB2155) are all nuclease positive [21,22]. They would be expected to degrade the huge linears. They retain some to nearly complete recombination proficiency [21,22], which may contribute to repair of the large linears into circles. The other recombination-defective mutants, in otherwise rec+ background, did not accumulate the huge linears probably because the DNA was degraded by active RecBCD enzyme or was not produced.

Partial suppression of the accumulation of the huge linears in a recBC null allele by a recF mutation (Figure 2B) leads to several possible explanations. For example, RecF-mediated homologous recombination may transform a circular chromosome, possibly with a spontaneous damage, into some type of non-circular forms. This is expected because RecF-mediated recombination is non-conservative in the sense that it generates only one progeny DNA molecule from two parental DNA molecules [10]. Alternatively, RecF function may somehow help generation of broken chromosomes or maintenance of break to load RecA [23].

In the recBC sbcA and the recBC sbcBC backgrounds, the absence of RecBCD nuclease may prevent faster degradation of the large non-circular DNAs. However, we see only little accumulation of the broken forms. One might expect that the accumulation of the huge linears may correlate with the capacity for recombination repair that reconstitutes a circular form. Indeed, the effects of recA, recJ and several other rec mutations on accumulation of the huge linear chromosomes in these two recBC backgrounds (Figures 2C and 2D) were similar to their negative effects on conjugational recombination [19] with interesting exceptions (see next paragraph). This accords with the concept that a huge linear fragments of the chromosome is involved in recombination following conjugation. However, any of the recombination mutants that lead to accumulation of linear DNA could affect the probability of breaks occurring in the first place.

The mutations in Holliday-structure-processing enzymes ? RecG, RuvAB, and RuvC ? did not result in accumulation of the huge linears even in the recBC-minus background. The complex intermediate forms accumulating in these mutants may be trapped in the agarose gel (see [24,25]). An alternative interpretation could be that these enzymes may be involved in generation of double-strand breaks as hypothesized by Seigneur et al. [17].

The accumulation by the recJ mutation in the recBC sbcA background is suppressed by a recQ mutation (Figure 2C). Kusano et al. [26] found that both sensitivity to DNA damaging agents and decreased association of crossing-over with double-strand break repair in a recBC sbcA recJ strain are suppressed by mutant recQ alleles. Such suppressing relationship was interpreted to suggest that RecQ acts prior to or concurrently with RecJ. Pulsed-field gel electrophoresis analysis of chromosomes after ultraviolet irradiation has revealed extensive chromosome degradation dependent on uvrA incision enzyme [27]. A report [28] showed that RecQ and RecJ proteins process nascent DNA at replication forks blocked by ultraviolet irradiation prior to the resumption of DNA synthesis (see also [29]).

The accumulation of the non-circular, broken chromosomes correlated with the growth rate or DNA damage response in most of the recBC-minus background [30]. The recB or recC null mutation showed low viability even in the absence of exogenous DNA damage [31,32]. A simple interpretation of these data is that RecA, RecFOR, and RecQJ functions (and RecET functions for the sbcA background) repair chromosome breakage and/or prevent generation of the breakage. The major contradiction observed here is the phenotype in ruv mutants. The ruv mutants in all the background did not show any accumulation of the broken chromosome. This may suggest that the possible role of Ruv protein is making a break into dsDNA [33].


Our sensitive measurements of the large non-circular forms of the chromosome ? which should be able to detect one ds break out of 4 million bp ? provided unique sets of data that would help in further elucidating the mechanisms of chromosome double-strand break repair. A simplest interpretation of our data is that RecBCD enzyme is involved in repair and degradation of broken chromosomes, and that RecA, RecFOR, RecQJ and RecET functions are involved in prevention and/or repair of the breakage. Interaction was observed between a recC mutation and a recF mutation and between a recQ mutation and a recJ mutation. ruvABC mutants and a recG mutant did not accumulate broken chromosomes. Further molecular analysis would bring about interpretation of the present data in detailed molecular terms.


Escherichia coli K-12 strains used are listed in Table 1.


E. coli cells were grown in M9 medium (1 ? M9 salts [34], 0.2% glucose, 0.05 mM CaCl2, 0.5 mM MgSO4, 0.2% casamino acids and 1 microgram/ml vitamin B1) and LB broth (1.0% Bacto-tryptone, 0.5% Yeast extract and 1.0% NaCl) with antibiotics at the following concentrations when necessary: ampicillin (Amp) at 50 microgram/ml together with methicillin at 200 microgram/ml, chloramphenicol (Cml) at 25 microgram/ml, kanamycin (Kan) at 10 microgram/ml and tetracycline (Tet) at 10 microgram/ml.

Preparation of DNA samples in agarose gel

The cells were lysed in agarose gel by a modification of the method of Kusano et al. [35]. Cells were grown in 5 ml of L-broth with or without antibiotics to an OD660 of 0.4 and were harvested. This OD660 of 0.4 corresponds to 5 ? 10E8 to 1 ? 10E9 cells/ml depending on the strain. One milliliter of the culture was transferred to a micro-tube and mixed with 2,4-dinitrophenol (to the final concentration of 0.01%), which blocks energy metabolism. After centrifugation, the pellet was washed twice with a half volume of 10 mM Tris-HCl (pH 7.5), 1 M NaCl and 2,4-dinitrophenol. The cells were suspended in 0.5 ml of the same buffer, mixed with the same volume of 1.0% of InCert agarose (FMC), split into 10 molds, and allowed to solidify at 4?C. One agarose plug, thus obtained, corresponds to 0.04 OD660 of the culture. Six of these agarose plugs were treated at 37?C for 15 hrs with 2.5 ml of a solution containing 6 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.1 M EDTA, Brij-58 (0.5%), sodium deoxycholate (0.2%), sodium lauryl sarcosinate (0.5%), lysozyme (1 mg/ml) and RNase A (20 mg/ml). The plugs were then washed with 0.5 M EDTA (pH 9.5), treated at 50?C for 48 hrs with 2.5 ml of a solution containing 0.5 M EDTA, 1% SDS and 2 mg/ml proteinase K (pH 9.5), and washed with 0.5 M EDTA (pH 9.5).

Pulsed-field gel electrophoresis

The sample plugs were placed in the wells of a running gel (1.0% (w/v) SeaKem GTG agarose (FMC)) and solidified with molten 1.0% agarose. Pulsed-field gel electrophoresis was carried out in a Pharmacia/LKB apparatus under the following conditions: electrophoresis buffer, 1 ? TBE (45 mM Tris-borate/1.25 mM EDTA); 165V; pulse time, 120 sec; run time, 24 hrs; temperature, 10?C. As a size marker, a plug containing yeast (Saccharomyces cerevisiae) chromosomes (Pharmacia) was used. After the run, the gel was stained with ethidium bromide, and photographed under ultraviolet illumination. The DNA in the region of the huge linear chromosomes was quantified using a VILBER LOURMAT apparatus with BIO-PROFIL software.

The control experiment (XbaI digestion before the run) was done in a CHEF-DR III system (Bio-Rad) under the following conditions: electrophoresis buffer, 0.5 ? TBE; 6 V/cm; angle, 120?; pulse time, 4 ? 50 sec; run time, 20 hrs; temperature, 14?C. After the run, agarose gels were processed as described above.

Authors' contributions

NH carried out all of the experiment and drafted the manuscript. IK supervised the work and edited the manuscript. All authors read and approved the final manuscript.

List of abbreviations

ds, double-strand. E. coli, Escherichia coli. Amp, ampicillin. Cml, chloramphenicol. Kan, kanamycin. Tet, tetracycline.


We are grateful to those listed in Table 1 for generous gift of materials, to Kohji Kusano and John Clark for comments on manuscript, and to Steve Kowalczykowski for discussion. The work was supported by grants (Tenkai, Repair, Genome Science, Genome Biology, Kiban, Genome Homeostasis, National Project on Protein Structural and Functional Analyses) from MEXT of the Japanese government and by a grant from Uehara Memorial Foundation. NH was supported by JSPS Research Fellowship for Young Scientists and JSPS Postdoctoral Fellowships for Research Abroad.

Handa N,Ichige A,Kusano K,Kobayashi I. Cellular responses to postsegregational killing by restriction-modification genes.J Bacteriol 2000;182:2218–2229. [pmid: 10735865] [doi: 10.1128/JB.182.8.2218-2229.2000]
Michel B,Ehrlich SD,Uzest M. DNA double-strand breaks caused by replication arrest.EMBO J 1997;16:430–438. [pmid: 9029161] [doi: 10.1093/emboj/16.2.430]
Game JC,Sitney KC,Cook VE,Mortimer RK. Use of a ring chromosome and pulsed-field gels to study interhomolog recombination, double-strand DNA breaks and sister-chromatid exchange in yeast.Genetics 1989;123:695–713. [pmid: 2693206]
Sonoda E,Sasaki MS,Buerstedde JM,Bezzubova O,Shinohara A,Ogawa H,Takata M,Yamaguchi-Iwai Y,Takeda S. Rad51-deficient vertebrate cells accumulate chromosomal breaks prior to cell death.EMBO J 1998;17:598–608. [pmid: 9430650] [doi: 10.1093/emboj/17.2.598]
Cox MM. A broadening view of recombinational DNA repair in bacteria.Genes Cells 1998;3:65–78. [pmid: 9605402] [doi: 10.1046/j.1365-2443.1998.00175.x]
Kowalczykowski SC,Dixon DA,Eggleston AK,Lauder SD,Rehrauer WM. Biochemistry of homologous recombination in Escherichia coli.Microbiol Rev 1994;58:41–465.
Kolodner R,Hall SD,Luisi-DeLuca C. Homologous pairing proteins encoded by the Escherichia coli recE and recT genes.Mol Microbiol 1994;11:23–30. [pmid: 8145642]
Kusano K K,Takahashi NK,Yoshikura H,Kobayashi I. Involvement of RecE exonuclease and RecT annealing protein in DNA double-strand break repair by homologous recombination.Gene 1994;138:17–25. [pmid: 8125297] [doi: 10.1016/0378-1119(94)90778-1]
Takahashi NK,Sakagami K,Kusano K,Yamamoto K,Yoshikura H,Kobayashi I. Genetic recombination through double-strand break repair: shift from two-progeny mode to one-progeny mode by heterologous inserts.Genetics 1997;146:9–26. [pmid: 9135997]
Takahashi NK NK,Yamamoto K,Kitamura Y,Luo SQ,Yoshikura H,Kobayashi I. Nonconservative recombination in Escherichia coli.Proc Natl Acad Sci U S A 1992;89:5912–5916. [pmid: 1631073]
Kuzminov A. Recombinational repair of DNA damage.. 1996New York, Springer;
Kogoma T. Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription.Microbiol Mol Biol Rev 1997;61:212–238. [pmid: 9184011]
Beverley SM. Characterization of the 'unusual' mobility of large circular DNAs in pulsed field-gradient electrophoresis.Nucleic Acids Res 1988;16:925–939. [pmid: 3344223]
Birren B,Lai E. Pulsed field gel electrophoresis. 1993San Diego, Academic Press;
Naito T,Kusano K,Kobayashi I. Selfish behavior of restriction-modification systems.Science 1995;267:897–899. [pmid: 7846533]
Kusano K,Naito T,Handa N,Kobayashi I. Restriction-modification systems as genomic parasites in competition for specific sequences.Proc Natl Acad Sci U S A 1995;92:11095–11099. [pmid: 7479944]
Seigneur M,Bidnenko V,Ehrlich SD,Michel B. RuvAB acts at arrested replication forks.Cell 1998;95:419–430. [pmid: 9814711]
Bidnenko V,Ehrlich SD,Michel B. Replication fork collapse at replication terminator sequences.EMBO J 2002;21:3898–3907. [pmid: 12110601] [doi: 10.1093/emboj/cdf369]
Lloyd RG,Low KB. F C N (editor-in-chief)Homologous recombination.Escherichia coli and Salmonella: cellular and molecular biology 1996Washington, D.C., ASM Press; :2236–2255.
Cairns J. Cold Spring Harbor Symposium on Quantitative Biology. 1963Cold Spring Harbor, Cold Spring Harbor Laboratory Press;
Schultz DW,Taylor AF,Smith GR. Escherichia coli RecBC pseudorevertants lacking chi recombinational hotspot activity.J Bacteriol 1983;155:664–680. [pmid: 6348024]
Amundsen SK,Neiman AM,Thibodeaux SM,Smith GR. Genetic dissection of the biochemical activities of RecBCD enzyme.Genetics 1990;126:25–40. [pmid: 2172076]
Ivancic-Bace I,Peharec P,Moslavac S,Skrobot N,Salaj-Smic E,Brcic-Kostic K. RecFOR Function Is Required for DNA Repair and Recombination in a RecA Loading-Deficient recB Mutant of Escherichia coli.Genetics 2003;163:485–494. [pmid: 12618388]
Ishioka K,Iwasaki H,Shinagawa H. Roles of the recG gene product of Escherichia coli in recombination repair: effects of the delta recG mutation on cell division and chromosome partition.Genes Genet Syst 1997;72:91–99. [pmid: 9265736] [doi: 10.1266/ggs.72.91]
Nakayama K,Kusano K,Irino N,Nakayama H. Thymine starvation-induced structural changes in Escherichia coli DNA. Detection by pulsed field gel electrophoresis and evidence for involvement of homologous recombination.J Mol Biol 1994;243:611–620. [pmid: 7966286]
Kusano K,Sunohara Y,Takahashi N,Yoshikura H,Kobayashi I. DNA double-strand break repair: genetic determinants of flanking crossing-over.Proc Natl Acad Sci U S A 1994;91:1173–1177. [pmid: 8302849]
Thoms B,Wackernagel W. Interaction of RecBCD enzyme with DNA at double-strand breaks produced in UV-irradiated Escherichia coli: requirement for DNA end processing.J Bacteriol 1998;180:5639–5645. [pmid: 9791113]
Courcelle J,Hanawalt PC. RecQ and RecJ process blocked replication forks prior to the resumption of replication in UV-irradiated Escherichia coli.Mol Gen Genet 1999;262:543–551. [pmid: 10589843] [doi: 10.1007/s004380051116]
Courcelle J,Donaldson JR,Chow KH,Courcelle CT. DNA damage-induced replication fork regression and processing in Escherichia coli.Science 2003;299:1064–1067. [pmid: 12543983] [doi: 10.1126/science.1081328]
Smith GR. Homologous recombination in procaryotes.Microbiol Rev 1988;52:1–28. [pmid: 3280962]
Capaldo-Kimball F,Barbour SD. Involvement of recombination genes in growth and viability of Escherichia coli K-12.J Bacteriol 1971;106:204–212. [pmid: 4928007]
Haefner K. Spontaneous lethal sectoring, a further feature of Escherichia coli strains deficient in the function of rec and uvr genes.J Bacteriol 1968;96:652–659. [pmid: 4895049]
Seigneur M,Ehrlich SD,Michel B. RuvABC-dependent double-strand breaks in dnaBts mutants require recA.Mol Microbiol 2000;38:565–574. [pmid: 11069680] [doi: 10.1046/j.1365-2958.2000.02152.x]
Miller JH. A short course in bacterial genetics. 1992Cold Spring Harbor, Cold Spring Harbor Laboratory Press;
Kusano K,Nakayama K,Nakayama H. Plasmid-mediated lethality and plasmid multimer formation in an Escherichia coli recBC sbcBC mutant. Involvement of RecF recombination pathway genes.J Mol Biol 1989;209:623–634. [pmid: 2685325]
Bachmann BJ. F C Neidhardt J L Ingraham KB Low B Magasanik M Schaechter H E UmbargerDerivation and genotypes of some mutant derivatives of Escherichia coli K-12Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology 1987;2Washington, D.C., American Society for Microbiology; :1190–1219.
Csonka LN,Clark AJ. Deletions generated by the transposon Tn10 in the srl recA region of the Escherichia coli K-12 chromosome.Genetics 1979;93:321–343. [pmid: 395024]
Willetts NS,Clark AJ. Characteristics of some multiply recombination-deficient strains of Escherichia coli.J Bacteriol 1969;100:231–239. [pmid: 4898990]
Lloyd RG,Buckman C,Benson FE. Genetic analysis of conjugational recombination in Escherichia coli K12 strains deficient in RecBCD enzyme.J Gen Microbiol 1987;133:2531–2538. [pmid: 3329215]
Takahashi NK,Kusano K,Yokochi T,Kitamura Y,Yoshikura H,Kobayashi I. Genetic analysis of double-strand break repair in Escherichia coli.J Bacteriol 1993;175:5176–5185. [pmid: 8349557]
Lovett ST,Clark AJ. Genetic analysis of the recJ gene of Escherichia coli K-12.J Bacteriol 1984;157:190–196. [pmid: 6317649]
Nakayama K,Irino N,Nakayama H. The recQ gene of Escherichia coli K12: molecular cloning and isolation of insertion mutants.Mol Gen Genet 1985;200:266–271. [pmid: 2993821]
Saito A,Iwasaki H,Ariyoshi M,Morikawa K,Shinagawa H. Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase.Proc Natl Acad Sci U S A 1995;92:7470–7474. [pmid: 7638215]
Gillen JR,Willis DK,Clark AJ. Genetic analysis of the RecE pathway of genetic recombination in Escherichia coli K-12.J Bacteriol 1981;145:521–532. [pmid: 6257642]
Lloyd RG,Buckman C. Genetic analysis of the recG locus of Escherichia coli K-12 and of its role in recombination and DNA repair.J Bacteriol 1991;173:1004–1011. [pmid: 1846849]
Luisi-DeLuca C,Lovett ST,Kolodner RD. Genetic and physical analysis of plasmid recombination in recB recC sbcB and recB recC sbcA Escherichia coli K-12 mutants.Genetics 1989;122:269–278. [pmid: 2670665]
Mahdi AA,Lloyd RG. Identification of the recR locus of Escherichia coli K-12 and analysis of its role in recombination and DNA repair.Mol Gen Genet 1989;216:503–510. [pmid: 2664459]
Kushner SR,Nagaishi H,Templin A,Clark AJ. Genetic recombination in Escherichia coli: the role of exonuclease I.Proc Natl Acad Sci U S A 1971;68:824–827. [pmid: 4927675]
Lloyd RG,Buckman C. Identification and genetic analysis of sbcC mutations in commonly used recBC sbcB strains of Escherichia coli K-12.J Bacteriol 1985;164:836–844. [pmid: 3932331]
Arnold DA,Handa N,Kobayashi I,Kowalczykowski SC. A novel, 11 nucleotide variant of chi, chi*: one of a class of sequences defining the Escherichia coli recombination hotspot chi.J Mol Biol 2000;300:469–479. [pmid: 10884344] [doi: 10.1006/jmbi.2000.3861]
Handa N,Ohashi S,Kusano K,Kobayashi I. Chi-star, a chi-related 11-mer sequence partially active in an E. coli recC1004 strain.Genes Cells 1997;2:525–536. [pmid: 9348042] [doi: 10.1046/j.1365-2443.1997.1410339.x]


[Figure ID: F1]
Figure 1 

Detection of large non-circular forms of the chromosome by pulsed-field gel electrophoresis. AB1157 (= rec+) and JC5519 (= recBC) cells were grown either in M9, a minimal medium, or in LB, a rich broth (Materials and Methods). The cells were harvested, embedded in agarose, lysed in situ, and analyzed by pulsed-field gel electrophoresis. Giant circular chromosomes stay in the well. Huge non-circular forms generated by ds breakage will band just below the well (bar in the right). Lane "M" contains Saccharomyces cerevisiae chromosomes as linear size markers.

[Figure ID: F2]
Figure 2 

Accumulation of large non-circular forms of the chromosome in recombination-defective mutants. A: In an otherwise rec+ background. The mutation alleles are as follows: ?recA306::Tn10, recB21 recC22, recB268::Tn10, recC266::Tn10, recC73, recD1901::Tn10, recF143, recG258::mini-Tn10 Kan, recJ284::Tn10, recN1502::Tn5, rec01504::Tn5, recQ1803::Tn3, recR252::mini-Tn10Kan, ?ruvAB100::Cm, ?ruvC100::Cm, ruvC53 eda::Tn10. B: Various recBCD alleles in V66 background. C: In a recBC sbcA background. The mutation alleles are the same as in A except for recE159, recQ1801, recT101::Tn10, and ?ruvAB::Tc. D: In a recBC sbcBC background. The mutation alleles are the same as in A except for recN262 tyrA16::Tn10.

[Figure ID: F3]
Figure 3 

Pulsed-field gel electrophoresis of the chromosomes after restriction enzyme digestion. The cells were lysed in an agarose plug and were treated with XbaI before pulsed-field gel electrophoresis. M indicates yeast chromosome marker.

[TableWrap ID: T1] Table 1 

Bacterial strains used here

Strain Other name Genotype Source/Reference
AB1157 BIK788 thr-1 leu-6 thi-1 lacY1 galK2 ara-14 xyl-5 mtl-1 proA2 his-4 argE3 str-31 tsx-33 supE44 rec+ [36]
TES1 BIK733 As AB1157, but ?recA306::Tn10 K. Yamamoto/[37]
JC5519 BIK751 As AB1157, but recB21 recC22 T. Kato/[38]
N2101 BIK2876 recB268::Tn10 R. Lloyd/[39]
N2103 BIK2877 recC266::Tn10 R. Lloyd/[39]
BIK3961 As AB1157, but recB268::Tn10 P1 (BIK2876) to AB1157
BIK3963 As AB1157, but recC266::Tn10 P1 (BIK2877) to AB1157
BIK806 As AB1157, but recD1901::Tn10 [40]
JC9239 BIK783 As AB1157, but recF143 A. J. Clark
BIK1538 As AB1157, but recG258::mini-Tn10 Kan P1 (BIK1400) to AB1157
JC12123 BIK 787 recJ284::Tn10 his-4 A. Clark/[41]
BIK2563 As AB1157, but recJ284::Tn10 P1 (BIK787) to AB1157
BIK2565 As AB1157, but recN1502::Tn5 P1 (BIK1044) to AB1157
KEN24 BIK1179 As AB1157, but recO1504::Tn5 K. Yamamoto/[40]
KD2216 BIK1048 recQ1803::Tn3 ilv-145 metE46 his-4 trpC3 pro thi thyA::Tn5 thyR mtl-1 malA1 ara-9 galK2 lac-114 rpsL ton F- H. Nakayama/[42]
BIK2680 As AB1157, but recQ1803::Tn3 P1 (BIK1048) to AB1157
BIK2577 As AB1157, but recR252::mini-Tn10 Kan P1 (BIK1399) to AB1157
HRS1004 BIK1331 ?ruvAB::Tc T. Shiba & H. Shinagawa
HRS2302 BIK1620 As AB1157, but ?ruvAB100::Cm H. Shinagawa/[24]
HRS1100 BIK1618 As AB1157, but ?ruvC100::Cm H. Shinagawa/[43]
KEN72 BIK1051 As AB1157, but ruvC53 eda::Tn10 K. Yamamoto
JC8679 BIK813 As AB1157, but recB21 recC22 sbcA23 A. J. Clark/[44]
BIK1415 As JC8679, but ?recA306::Tn10 [26]
JC8691 BIK784 As JC8679, but recE159 A. J. Clark/[44]
JC9610 BIK786 As JC8679, but recF143 A. J. Clark/[44]
N2796 BIK1400 As JC8679, but recG258::mini-Tn10 Kan R. Lloyd/[45]
BIK814 As JC8679, but recJ284::Tn10 Kusano et al. (1994b)
BIK1044 As JC8679, but recN1502::Tn5 Takahashi et al. (1993)
BIK1192 As JC8679, but recO::Tn5 [26]
RDK1693 BIK1401 As JC8679, but recQ1801 S. Lovett/[46]
BIK1427 As JC8679, but recQ1801 recJ284::Tn10 [26]
BIK1224 As JC8679, but recQ1803::Tn3 [26]
AM265 BIK1399 As JC8679, but recR252::mini-Tn10 Kan R. Lloyd/[47]
BIK3884 As JC8679, but recT101::Tn10 N. Kobayashi-Takahashi
BIK1478 As JC8679, but ?ruvAB::Tc P1 (BIK1331) to JC8679
BIK1050 As JC8679, but ruvC53 eda::Tn10 [26]
JC7623 BIK752 As AB1157, but recB21 recC22 sbcB15 sbcC201 T. Kato/[48,49]
BIK2176 As JC7623, but ?recA306::Tn10 P1 (BIK733) to JC7623
JC8111 BIK749 As JC7623, but recF143 A. J. Clark
BIK1772 As JC7623, but recJ284::Tn10 P1 (BIK814) to JC7623
BIK1212 As JC7623, but recN262 tyrA16::Tn10 [10]
BIK1774 As JC7623, but recQ1803::Tn3 P1 (BIK1224) to JC7623
BIK1776 As JC7623, but recR252::mini-Tn10 Kan P1 (BIK1399) to JC7623
KEN87 BIK1181 As JC7623, but ruvC53 eda::Tn10 K. Yamamoto
V66 BIK796 recF143 his-4 met rpsL31 gal xyl(?) ara(?) argA21 F-?- A. Taylor/[21]
V68 BIK2411 As V66, but recC73 G. Smith/[50]
V73 BIK1275 As V66, but recC73 recC1001 G. Smith/[21,50]
V69 BIK1272 As V66, but recC73 recC1002 G. Smith/[21]
V71 BIK1273 As V66, but recC73 recC1003 G. Smith/[21,50]
V72 BIK1274 As V66, but recC73 recC1004 G. Smith/[21,50]
V1296 BIK1910 As V66, but recC2145 G. Smith/[22]
V1360 BIK1911 As V66, but recB2154 G. Smith/[22]
V1363 BIK1912 As V66, but recB2155 G. Smith/[22]
BIK1288 As V66, but recF+zic::Tn10 [51]
BIK3713 As BIK1288 (tetS) tetS selection from BIK1288
NK5992 BIK800 IN (rrnD-rrnE)1 ?-F-argA81::Tn10 N. Kleckner via A. Taylor
BIK3732 As BIK2411, but argA81::Tn10 P1 (BIK800) to BIK2411
BIK3738 As BIK3713, but recC73 argA81::Tn10 P1 (BIK3732) to BIK3713
BIK4034 As AB1157, but recC73 argA81::Tn10 P1 (BIK3732) to AB1157
A211 BIK1276 IN (rrnD-rrnE)1 ?-F-lacZs20YconstgyrB+recF+zic::Tn10 A. Miura
BIK1286 As BIK1275, but recF+zic::Tn10 P1 (BIK1276) to BIK1275
BIK1290 As BIK1272, but recF+zic::Tn10 P1 (BIK1276) to BIK1272
BIK1282 As BIK1273, but recF+zic::Tn10 [51]
BIK1284 As BIK1274, but recF+zic::Tn10 [51]
BIK2445 As BIK1910, but recF+zic::Tn10 [51]
BIK2446 As BIK1911, but recF+zic::Tn10 [51]
BIK2447 As BIK1912, but recF+zic::Tn10 [51]

Article Categories:
  • Research Article

Previous Document:  Diagnosis of recent and relapsed cases of human brucellosis by PCR assay.
Next Document:  Real-time quantitative reverse transcriptase-polymerase chain reaction as a method for determining l...