Download The orientation bias of Chi sequences is a general tendency of G

Gene 259 (2000) 207–215
www.elsevier.com/locate/gene
The orientation bias of Chi sequences is a general tendency
of G-rich oligomers
Reina Uno, Yoichi Nakayama, Kazuharu Arakawa, Masaru Tomita *
Laboratory for Bioinformatics, Keio University 5322 Endo, Fujisawa, Kanagawa 252-8502, Japan
Received 18 April 2000; received in revised form 7 July 2000; accepted 8 September 2000
Received by T. Gojobori
Abstract
The Chi sequences are specific oligomers that stimulate DNA repair by homologous recombination, and are different sequences
in each organism. Approximately 75% of the copies of the Chi sequence (5∞-GCTGGTGG-3∞) of Escherichia coli reside on the
leading strand, and this orientation bias is often believed to be a consequence of the biological role of Chi sequences as the signal
sequence of RecBCD pathway in DNA replication. However, our computer analysis found that many G-rich oligomers also show
this asymmetric orientation pattern. The shift in the Chi orientation bias appears around the replication origin and terminus, but
these locations are also coincident with the shift points in GC content or GC skew. We conducted the same analysis with the
genome of Bacillus subtilis, and found that in addition to Chi, other G-rich oligomers show similar asymmetric orientation
patterns, whose shift points were coincident with those of the GC skew. However, the genome of Haemophilus influenzae Rd,
whose GC skew is not so pronounced, does not clearly show asymmetric orientation patterns of Chi or other G-rich oligomers.
These results lead us to suggest that the uneven distribution of the Chi orientation between the two strands of the double helix is
mostly due to the uneven distribution of G content (GC skew) and that the replication-related function of Chi sequences is not
the primary factor responsible for the evolutionary pressure causing the orientation bias. © 2000 Elsevier Science B.V. All
rights reserved.
Keywords: Comparative genomics; Computational analysis; DNA replication; GC skew; Homologous recombination
1. Introduction
Chi sequences (5∞-GCTGGTGG-3∞) are cis-acting
DNA elements that enhance recombination promoted
by the RecBCD pathway in E. coli (Smith et al., 1995).
The Chi sequence attenuates the activity of 3∞-to-5∞
exonucleases and activates a weaker 5∞-to-3∞ exonuclease
but does not affect the helicase activity of RecBCD
(Dixon and Kowalczykowski, 1991). It has been proposed that the orientation of the Chi sequences plays
an important role in the reconstruction of arrested
replication forks (Horiuchi and Fujimura, 1995;
Kuzminov, 1995; Cox, 1998). After replication fork
arrest and the introduction from the double-stranded
Abbreviations: Chi , Chi-like sequence of B. subtilis; Chi , Chi
BS
EC
sequence of E. coli; Chi , Chi-like sequence of H. influenzae; ds DNA,
HI
double-stranded DNA; ss DNA, single-stranded DNA.
* Corresponding author. Tel.: +81-466-47-5111;
fax: +81-466-47-5099.
E-mail address: [email protected] (M. Tomita)
(ds) break, RecBCD enters the ds DNA molecule and
degrades it into a single-stranded (ss) DNA with a 3∞
-OH end and oligonucleotides (Seigneur et al., 1998;
Michel, 2000). When the enzyme meets a properly
oriented Chi sequence, its exonuclease activity is suppressed, and the helicase activity creates ss DNA tails,
which are then used by RecA and ss DNA-binding
proteins to form a D-loop with intact sequences having
homology with the ss tails (Marians, 2000). On the
D-loop molecule, a new replication fork is then
reconstructed.
The whole genome sequence project (Blattner et al.,
1997; Itoh et al., 1999) of E. coli revealed that 75% of
all Chi sequences are oriented in the direction of DNA
replication ( Eggleston and West, 1997). These properties
of RecBCD and Chi sequences have led to the widely
accepted notion that Chi sequences are over-represented
on the leading strand to direct the activity of RecBCD
enzymes toward OriC (Blattner et al., 1997; Tracy et al.,
1997b; Cox, 1998). The analogs of Chi sequences in E.
coli (Chi ) that are also G-rich ( El Karoui et al., 1999)
EC
0378-1119/00/$ - see front matter © 2000 Elsevier Science B.V. All rights reserved.
PII: S0 3 7 8 -1 1 1 9 ( 0 0 ) 0 0 43 0 - 3
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R. Uno et al. / Gene 259 (2000) 207–215
are found in B. subtilis (Chi 5∞-AGCGG-3∞), H.
BS
influenzae (Chi 5∞-GNTGGTGG-3’ and 5∞-G[C/G ]TGHI
GAGG-3∞), and Lactococcus lactis (Chi 5∞-GCGCGLL
TG-3∞) (Biswas et al., 1995; Chédin et al., 1998; Sourice
et al., 1998). Every Chi sequence found is known to
have a role in attenuating 5∞-to-3∞ exonuclease activity,
and Chi has already been identified as having recombiLL
nase activity ( El Karoui et al., 1998). In addition,
research has shown that the processing of ds DNA end
by the AddAB enzyme produces a duplex DNA molecule
with a protruding 3∞-terminated ss tail, a universal
intermediate of the recombination process in B. subtilis
(Chédin et al., 2000). While these functions of RecBCD
(in H. influenzae), AddAB (in B. subtilis), and RexAB
(in L. lactis) are conserved, the structures of these
proteins are not (El Karoui et al., 1999).
The GC skew, which represents a bias of G over C
content in one of the duplex DNA strands, is clearly
visible in the leading strands of the chromosomes of E.
coli and B. subtilis but not as evident on that of H.
influenzae (Lobry, 1996; Blattner et al., 1997; Francino
and Ochman, 1997; Mrázek and Karlin, 1998). Regions
on the DNA containing a shift in GC content (hereafter
referred to as the shift point of the GC skew) often
correlate with the locations of the replication origin and
terminus. Several explanations for the cause of GC skew
have been suggested:
1. Asymmetric DNA replication between the leading
and lagging strands could result in strand-dependent
mutation patterns (Lobry, 1996; Francino and
Ochman, 1997; Beletskii and Bhagwat, 1998).
2. The requirement that genes that encode proteins
cause biases in the base composition at codon positions 1 and 2 on the sense strand (McLean et al.,
1998; Mrázek and Karlin, 1998; Romero et al., 2000).
It is proposed that 75% of the Chi sequences are
oriented for the replication mechanism. However, it is
also known that several octamer sequences switch their
preferred orientation at the replication origin of several
genomes (Salzberg et al., 1998). Species in which GC
skew is clearly observed tend to contain many biased
oligomers. In this work, we hypothesized that the Chi
sequence reflects the tendency of the genome exemplified
by the GC skew, so the orientation bias of the Chi
sequence did not result from its function in replication
mechanism. Under this hypothesis, the orientations of
all G-rich oligomers should be similar to that of the Chi
sequence. The genomes of E. coli, B. subtilis, and H.
influenzae were analyzed (Fig. 1) for this purpose.
2. Materials and methods
The complete genome sequences of the three prokaryotes were downloaded from the GenBank database
(ftp://ncbi.nlm.nih.gov/genbank/genomes/). GC skew
was estimated from the formula (C−G)/(C+G) with
non-overlapping windows whose lengths were fixed at
Fig. 1. GC skew (upper) and the distribution of Chi sequences ( lower). Non-overlapping windows of 10 kb were used for this analysis. In each
graph of Chi distribution, vertical lines above the center indicate positions of the Chi sequences on one DNA strand, and lines below the center
indicate positions on the complementary strand. Arrows indicate the replication origin and terminus. Clear shift points of GC skew and of Chi
distribution correspond to the replication origin and terminus in (a) E. coli, (b) B. subtilis and (c) H. influenzae. No clear shift point is observed
in H. influenzae.
R. Uno et al. / Gene 259 (2000) 207–215
209
Fig. 2. Calculation process of orientation fraction. The orientation fraction, that is expressed as the percentage of an oligomer, was calculated as
follows. We counted the number of occurrences of an oligomer on both strands, then counted the number of occurrences in the direction of
replication, and calculated the fraction of these counts. The orientation fractions from tetramer to octamer were calculated.
10 kb. The value of the GC skew is positive when the
number of Cs is more than that of Gs in the same
window, or vice versa. Transition of GC skew values
over the entire genome was then graphed.
The orientation fraction of oligomers was defined as
the number of oligomers oriented towards the origin of
replication divided by the total number of oligomers
(Fig. 2). The data set was arranged according to the
number of Gs in the oligomers, in order to clarify the
effect of the GC skew. The orientation fractions were
calculated and plotted for all oligomers of different lengths
for the genomes of E. coli, B. subtilis and H. influenzae.
For calculation, we defined the shift points of leading
and lagging strands, in other words, the replicational
origin and terminus, as follows: in OriC (3 923 488 bp)
and in TerC (1 607 942 bp) for E. coli, in OriC (1 bp)
and in TerC (2 017 790 bp) for B. subtilis, and in the
putative origin (602 999 bp) and between the two potential terminating sequences identified by homology
(1 506 292 bp) for H. influenzae (Fleischmann et al.,
1995; Blattner et al., 1997; Kunst et al., 1997).
3. Results
The orientation fractions of hexamers, heptamers and
octamers on the E. coli genome were calculated. The
distributions of plots and their averages shift to a higher
fraction as the G content of oligomers increases ( Fig. 3).
This shift must be caused by the asymmetry in G content
between both strands, and this corresponds to the GC
skew. Although Chi sequences have higher orientation
fractions than the averages, many other octamers have
even higher fractions ( Fig. 3c). The orientation fractions
of the three hexamers CTGGTG, TGGTGG and
GCTGGT, which are composites of the Chi sequence,
were also above the average (Fig. 3a).
As for B. subtilis, the distributions that showed an
obvious G content bias were similar to those of E. coli
( Fig 1b). The GC skew of B. subtilis represents a strand
bias in G content and it has a direct influence on the
orientation bias of G-rich oligomers. The Chi sequences
of B. subtilis also had an orientation bias toward the
leading strand (Fig. 4), and shift points occurred around
the origin and terminus of replication (Chédin et al.,
1998). However, the orientation fractions of the Chi
sequences were almost equal to the average bias of
pentamers containing three Gs. This result indicates that
the orientation bias is not specific to the Chi sequences
and is separable from the proposed biological role of
the Chi in the replication machinery.
The sequences 5∞-GNTGGTGG-3∞ and 5∞-G[G/C ]TGGAGG-3∞ in H. influenzae are reported to have
functions analogous to those of Chi sequence in E. coli.
(Sourice et al., 1998). The results of our analysis of
these sequences are shown in Fig. 1c. Unlike E. coli and
B. subtilis, almost no orientation bias or clear shift
points were observed at the origin and terminus of
replication. Fig. 5 shows that the correlation between
the orientation fraction and the number of Gs in the
oligomers of H. influenzae was also not as significant as
that in E. coli and B. subtilis. The orientation fractions
of the Chi sequences in H. influenzae were below average,
except for one sequence, GGTGGTGG ( Fig. 5d ).
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R. Uno et al. / Gene 259 (2000) 207–215
(a)
(b)
Fig. 3. Orientation fractions of hexamers (a), heptamers (b) and octamers (c) in E. coli. The horizontal axis represents the orientation fraction,
which is the fraction of skewed distribution with respect to DNA replication. We classified oligomers by G content (the number of Gs) and analyzed
each group; the vertical axis represents the G content. In addition, oligomers whose fraction was under 50% were removed from the data because
the fraction of their complementary sequence is always more than 50%. The result suggests that the Chi sequences of E. coli are not selectively
located on the leading strand, but all G-rich oligomers tend to be located on the leading strand.
Although this Chi sequence GGTGGTGG displayed
some orientation bias, its orientation fraction did not
differ significantly from those of other random oligo-
mers. The orientation fractions of all other Chi
sequences were below average, and most of them showed
no correlation with the direction of replication.
R. Uno et al. / Gene 259 (2000) 207–215
211
(c)
Fig. 3. (continued).
Fig. 4. (a–d ) Orientation fraction of 4–7mers in B. subtilis. Like E. coli, B. subtilis clearly shows the correlation between the orientation fraction
and the G content of all oligomers. The orientation fraction of the Chi sequence of B. subtilis in (b) is only about average.
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R. Uno et al. / Gene 259 (2000) 207–215
Fig. 5. (a–c) Orientation fraction of 6–8mers of H. influenzae genome. H. influenzae shows less correlation between the orientation fraction and
the G content. The six Chi sequences are located lower than, or near, the average orientation fraction (c), and some of them show no orientation bias.
4. Discussion
4.1. Orientational bias of Chi sequence depends on the
bias of Guanines
In summary, the GC skew and the orientation bias
of oligomers are strongly correlated, and the orientation
bias of Chi sequences does not significantly differ from
those of other G-rich oligomers (Fig. 6). While the Chi
sequences of E. coli were oriented with a slight bias,
many other oligomers showed a greater orientation bias.
The species that showed a clear GC skew (E. coli and
B. subtilis) also showed a clearly biased orientation
pattern, whereas species with an unclear GC skew (H.
influenzae) showed an unclear orientation pattern.
Regardless of whether the hypotheses listed in Section 1
about the source of GC skew are true, the orientation
bias of Chi sequences seems to be mostly due to the
genomic asymmetry in G content, just like any other
G-rich oligomers in E. coli and B. subtilis, and not
primarily due to the proposed function of Chi sequences
related to DNA replication.
However, there still remains a possibility that
RecBCD and its analogs have selected biased oligomers
to exercise their functions. It has already been shown
experimentally that certain sequences of H. influenzae,
whose Chi sequences do not show a clear GC skew,
have the same function as those of Chi in E. coli and
B. subtilis, at least for the attenuation of exonuclease
activity. If we assume that the requirements of the
homologous recombination pathway of E. coli are the
same as those of B. subtilis and H. influenzae, we can
say that the function-based orientation hypothesis
( Horiuchi and Fujimura, 1995) of the Chi sequence
does not suffice to explain the differences in the oligomer
skew among these species.
We have already mentioned a couple of reasons for
the presence of GC skew in Section 1, but another
possibility is that the GC skew was formed because of
the orientation bias of the Chi sequence (Tillier and
Collins, 2000) and the requirements of the RecBCD
pathway. It was reported that RecA as well as Rad51,
which is a homolog of RecA in Saccharomyces cerevisiae,
has a high affinity for GT-rich sequences (Tracy and
Kowalczykowski, 1996; Tracy et al., 1997a), and that
Chi is frequently located in GT-rich ‘recombination
EC
islands’ that are highly recombinogenic (Tracy et al.,
1997b). RecA homologues and the Chi sequences in
other species may have a similar affinity and genomic
tendency. If the GT-rich ‘recombination islands’ sur-
R. Uno et al. / Gene 259 (2000) 207–215
213
Fig. 6. Summary of the orientation fraction of Chi sequences. The vertical line represents the average orientation fractions of all oligomers with
the same number of Gs as in Chi. The distance of each Chi orientation fraction from the average fraction is indicated by triangles.
rounding the Chi sequences are the source of compositional asymmetry of the genome, GC skew of the
‘recombination islands’ must have an effect on the GC
skew of the whole leading strand. However, the GC skew
of the ‘recombination islands’ multiplied by the percentage they encompass in the whole genome, which is 17%
(Tracy et al., 1997b), is only 25.2% of the GC skew of
the whole leading strand. Moreover, only 75% of all
‘recombination islands’ is in the leading strand, and the
remaining 25% have a negative affect on the asymmetry
of the genome. Taking this fact into consideration, the
net effect of the ‘recombination islands’ will be 12.6%,
and our calculation shows that it is insignificant to say
that they are the source of compositional asymmetry.
4.2. Orientation and number are independent
characteristics of the Chi sequence
Our results suggest that the Chi orientation depends
on the bias of guanines. This is controversial in terms
of the hypothesis of the replication-dependent function
of Chi sequence; however, our results do not deny the
importance of the frequency of Chi sequence. Even if
the orientation of Chi sequence is due to the base
composition and not due to the replication mechanism,
Chi is definitely a signal sequence during replication
fork arrest, and so its frequency is essential. It
is suggested that RecBCD has another role in
protecting the cell from invasion by foreign DNA
( Kowalczykowski et al., 1994; Kuzminov, 1995) such
as bacteriophage DNA. Therefore, the orientation and
number are independent characteristics of Chi sequence,
and our results are not in conflict with the replicationindependent role of RecBCD.
4.3. Relationship among replication, transcription, and
recombination
It was reported that Chi sequences correlate more
with the direction of transcription than with that of
replication (Bell et al., 1998; Lao and Forsdyke, 2000).
The direction of replication and transcription coincide
in only 54% of genes in E. coli, and so these directions
do not seem to be in a causal relationship. There are
suggestions about the characteristic context of selected
codon-usage around the Chi sequences (Biaudet et al.,
1998; Colbert et al., 1998). According to these facts, the
orientation bias of the Chi sequence seems to be affected
more by transcription than by replication.
Recent studies indicate an interplay among the mechanisms of transcription, replication, and recombination
in E. coli (McGlynn and Lloyd., 2000). According to
this model, replication is blocked when the DNA polymerase meets a stalled RNA polymerase at a lesion in
the DNA. This model provides an insight into the
relationship among the three functions.
As already mentioned, our results show that the
orientation bias in the direction of replication is one of
the general properties of G-rich oligomers. Therefore,
the replication-related function of the Chi sequence is
not the primary factor responsible for the evolutionary
pressure causing the orientation bias.
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R. Uno et al. / Gene 259 (2000) 207–215
An unanswered issue is how homologous recombination works in DNA replication. The fork reconstruction
model (Horiuchi and Fujimura, 1995) is not contested
by our results, and it is possible that the number of Chi
sequences oriented in the direction of replication is more
than enough for fork reconstruction, even in H. influenzae. A Chi sequence can stimulate recombination within
a region located up to 10 kb away, and the three bacteria
analyzed here have enough oriented Chi sequences to
cover the whole genome.
It should be noted that our results do not deny any
functional characteristics of the Chi sequence; we only
showed that the cause of its biased orientation is not
primarily due to its function.
Acknowledgements
We thank Ichizo Kobayashi, Takashi Horiuchi,
Naofumi Handa, Hirotada Mori and Stephen C.
Kowalczykowski for helpful suggestions during this
work. Furthermore, we would like to acknowledge the
technical advice by Hiroaki Sakai, Takanori Washio,
Kenji Yotsutani, Yumi Kawamura, Naota Ishikawa and
Takehito Mogami. This work was supported in part by
the Japan Science and Technology Corporation and a
Grant-in-Aid for Scientific Research on Priority Areas
‘Genome Science’ from The Ministry of Education,
Science, Sports and Culture of Japan.
References
Beletskii, A., Bhagwat, A.S., 1998. Correlation between transcription
and C to T mutations in the non-transcribed DNA strand. Biol.
Chem. 379, 549–551.
Bell, S.J., Chow, Y.C., Ho, J.Y.K., Forsdyke, D.R., 1998. Correlation
of chi orientation with transcription indicates a fundamental relationship between recombination and transcription. Gene 216,
285–292.
Biaudet, V., El Karoui, M., Gruss, A., 1998. Codon usage can explain
GT-rich islands surrounding Chi sites on the Escherichia coli
genome. Mol. Microbiol. 29, 666–669.
Biswas, I., Maguin, E., Ehrlich, S.D., Gruss, A., 1995. A 7-base-pair
sequence protects DNA from exonucleolytic degradation in Lactococcus lactis. Proc. Natl. Acad. Sci. USA 92, 2244–2248.
Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V.,
Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew,
G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A.,
Rose, D.J., Mau, B., Shao, Y., 1997. The complete genome
sequence of Escherichia coli K-12. Science 277, 1453–1474.
Chédin, F., Noirot, P., Biaudet, V., Ehrlich, S.D., 1998. A five-nucleotide sequence protects DNA from exonucleolytic degradation by
AddAB, the RecBCD analogue of Bacillus subtilis. Mol. Microbiol.
29, 1369–1377.
Chédin, F., Ehrlich, S.D., Kowalczykowski, S.C., 2000. The Bacillus
subtilis AddAB helicase/nuclease is regulated by its cognate Chi
sequence in vitro. J. Mol. Biol. 298, 7–20.
Colbert, T., Taylor, A.F., Smith, G.R., 1998. Genomics, Chi sites and
codons: ‘islands of preferred DNA pairing’ are oceans of ORFs.
Trends Genet. 14, 485–488.
Cox, M.M., 1998. A broadening view of recombinational DNA repair
in bacteria. Genes Cells 3, 65–78.
Dixon, D.A., Kowalczykowski, S.C., 1991. Homologous pairing in
vitro stimulated by the recombination hotspot, Chi. Cell 66,
361–371.
Eggleston, A.K., West, S.C., 1997. Recombination initiation: easy as
A, B, C, D… chi? Curr. Biol. 7, R745–R749.
El Karoui, M., Ehrlich, D., Gruss, A., 1998. Identification of the lactococcal exonuclease/recombinase and its modulation by the putative
Chi sequence. Proc. Natl. Acad. Sci. USA 95, 626–631.
El Karoui, M., Biaudet, V., Schbath, S., Gruss, A., 1999. Characteristics of Chi distribution on different bacterial genomes. Res. Microbiol. 150, 579–587.
Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness,
E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A.,
Merrick, J.M., et al., 1995. Whole-genome random sequencing and
assembly of Haemophilus influenzae Rd. Science 269, 496–512.
Francino, M.P., Ochman, H., 1997. Strand asymmetries in DNA evolution. Trends Genet. 13, 240–245.
Horiuchi, T., Fujimura, Y., 1995. Recombinational rescue of the
stalled DNA replication fork: a model based on analysis of an
Escherichia coli strain with a chromosome region difficult to replicate. J. Bacteriol. 177, 783–791.
Itoh, T., Okayama, T., Hashimoto, H., Takeda, J., Davis, R.W., Mori,
H., Gojobori, T., 1999. A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome
sequences between two different substrains. FEBS Lett. 450, 72–76.
Kowalczykowski, S.C., Dixon, D.A., Eggleston, A.K., Lauder, S.D.,
Rehrauer, W.M., 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiology 58, 401–465.
Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G.,
Azevedo, V., Bertero, M.G., Danchin, A., et al., 1997. The complete
genome sequence of the Gram-positive bacterium Bacillus subtilis.
Nature 390, 249–256.
Kuzminov, A., 1995. Collapse and repair of replication forks in Escherichia coli. Mol. Microbiol. 16, 373–384.
Lao, P.J., Forsdyke, D.R., 2000. Crossover hot-spot instigator (Chi)
sequences in Escherichia coli occupy distinct recombination/transcription islands. Gene 243, 47–57.
Lobry, J.R., 1996. Asymmetric substitution patterns in the two DNA
strands of bacteria. Mol. Biol. Evol. 13, 660–665.
McGlynn, P., Lloyd, R.G., 2000. Modulation of RNA polymerase by
(p)ppGpp reveals a RecG-dependent mechanism for replication
fork progression. Cell 101, 35–45.
McLean, M.J., Wolfe, K.H., Devine, K.M., 1998. Base composition
skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47, 691–696.
Marians, K.J., 2000. PriA-directed replication fork restart in Escherichia coli. Trends Biochem. Sci. 25, 185–189.
Michel, B., 2000. Replication fork arrest and DNA recombination.
Trends Biochem. Sci. 25, 173–178.
Mrázek, J., Karlin, S., 1998. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95,
3720–3725.
Romero, H., Zavala, A., Musto, H., 2000. Codon usage in Chlamydia
trachomatis is the result of strand-specific mutational biases and a
complex pattern of selective forces. Nucleic Acids Res. 28,
2084–2090.
Salzberg, S.L., Salzberg, A.J., Kerlavage, A.R., Tomb, J.F., 1998.
Skewed oligomers and origins of replication. Gene 217, 57–67.
Seigneur, M., Bidnenko, V., Ehrlich, S.D., Michel, B., 1998. RuvAB
acts at arrested replication forks. Cell 95, 419–430.
Smith, G.R., Amundsen, S.K., Dabert, P., Taylor, A.F., 1995. The
initiation and control of homologous recombination in Escherichia
coli. Phil. Trans. R. Soc. Lond. B. Biol. Sci. 347, 13–20.
R. Uno et al. / Gene 259 (2000) 207–215
Sourice, S., Biaudet, V., El Karoui, M., Ehrlich, S.D., Gruss, A., 1998.
Identification of the Chi site of Haemophilus influenzae as several
sequences related to the Escherichia coli Chi site. Mol. Microbiol.
27, 1021–1029.
Tillier, E.R., Collins, R.A., 2000. The contributions of replication orientation, gene direction, and signal sequences to base-composition
asymmetries in bacterial genomes. J. Mol. Evol. 50, 249–257.
Tracy, R.B., Kowalczykowski, S.C., 1996. In vitro selection of pre-
215
ferred DNA pairing sequences by the Escherichia coli RecA protein.
Genes Dev. 10, 1890–1903.
Tracy, R.B., Baumohl, J.K., Kowalczykowski, S.C., 1997a. The preference for GT-rich DNA by the yeast Rad51 protein defines a set of
universal pairing sequences. Genes Dev. 11, 3423–3431.
Tracy, R.B., Chédin, F., Kowalczykowski, S.C., 1997b. The recombination hot spot chi is embedded within islands of preferred DNA
pairing sequences in the E. coli genome. Cell 90, 205–206.