The decatenation and segregation of the newly

The decatenation and segregation of the
newly replicated chromosomes to each of the
daughter cells are highly accurate. Even the
highly asymmetric segregation of sporulating
B. subtilis chromosomes leaves less than 0.02%
of anucleate cells (46). While the chromosome
is replicated, cells elongate and a septum forms
at the cell center. There, translocases, such as
FtsK in E. coli and SpoIIIE in B. subtilis , direc-
tionally pump DNA into the daughter cells by
recognizing motifs that point to the dif site. In
E. coli , these motifs are called KOPS (FtsK
orienting polar sequences) and their density
is higher in the leading strand and increases
toward the replication terminus, thereby in-
dicating the direction of DNA translocation
(7, 62). KOPS polarity constrains the chromo-
some dynamics near the terminus of replica-
tion because inversions lead to inversely polar-
ized KOPS and therefore to a disruption of the
220 Rocha
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5'
3'
3'
5'
3'
5'
a
b
Okazaki fragments (L
O
)
Transcript (L
t
)
Collision fork/RNAP
Truncated mRNA (T):
T
lag =
100%
T
lead
= (1-V
RNAP
/V
fork, lead
) × 100 = 91%
RNAP exclusion time (t
x
):
t
x, lag
= L
O
/V
fork, lag
+L
t
/V
fork, lag
+ L
t
/V
RNAP
= 52.7 s
t
x, lead
= L
t
/V
RNAP
- L
t
/V
fork, lead
= 36.5 s
100 × t
x, lag
/t
d
= 4.4%
100 × t
x, lead
/t
d
= 3.0%
Primase
Helicase
Terminator
Promoter
DNA
polymerase
Effect on total expression (%):
Figure 4
Outcome of collisions between the fork and the RNA polymerase (RNAP) when genes are in the lagging ( red ) and leading ( aqua )
strands and collisions do not lead to replication arrests (in which case the impact of collisions is more important). Truncated mRNA
refers to the fraction of aborted transcriptions while the fork passes in the transcribed region and assumes that all co-oriented collisions
lead to transcription abortion (therefore the estimated difference is conservative). RNAP exclusion is the time when the region is
unavailable for transcription. The effect on total expression of genes is the latter value time divided by the optimal doubling time (t
d
).
Computations and results (using parameters in B. subtilis ) are detailed in supplementary material . (Follow the Supplemental
Material link from the Annual Reviews home page at ). The variables V
x
refer to the rate of RNAP or
the replication fork (nt/s).
decatenation process. As a result, some inver-
sions in these regions are lethal, whereas dele-
tions are viable, providing a striking example
where genome organization prevails over gene
content (88).
GENE STRAND BIAS
AND THE ANTAGONISM
BETWEEN REPLICATION
AND GENE EXPRESSION
The replication fork synthesizes one DNA
strand continuously, the leading strand, and the
other semidiscontinuously, the lagging strand
( Figure 4 ). The different replication mode of
the two strands leads to different mutational
patterns. As a result, the leading strand tends
to be richer in G and the lagging strand richer
in C in the vast majority of bacterial genomes
(66), albeit from different mutational causes
(89). This compositional bias allows the iden-