Bacterial Growth and Division
537
without any apparent impairment of cell
growth.
3.2.4
Protein Factors Controlling DNA
Replication
Initiation of replication of DNA is a
function of numerous proteins. The key
regulatory
protein
appears
to
be
the
product of the
dnaA
gene. The dnaA
protein binds to the 9 bp ‘‘dnaA boxes’’
in the oriC region. After binding to the
origin, the protein promotes melting of the
DNA (i.e. separation of the DNA strands
in a local region) and helps in loading
additional proteins such as the dnaB
protein. After this initial opening of the
DNA strands, replication fork movement
is allowed to proceed bidirectionally from
the origin.
Initiation of replication is distinct from
the continued replication of DNA that
has been initiated. Once initiated, DNA
replication can continue even though
the accumulation of cell cytoplasm is
inhibited.
3.2.5
Chromosome Organization and
Bidirectional Replication
The phenomenon of bidirectional replica-
tion has two effects on the organization of
the chromosome. One effect is the varia-
tion in the relative abundance of G residues
versus C residues in one of the strands.
While G
=
C in the double helix, such an
equality need not exist in a given strand or
in a particular region of a strand. As a gen-
eral rule, it is found that in the two halves
of the bidirectionally replicated bacterial
genome, one half of the chromosome (e.g.
that from noon past three down to six on
a clock representation of the genome) has
G
>
C and the other half (noon, past nine,
down to six) has G
<
C. If one calculates
the G
C/G
+
C for a running window
of nucleotides, and accumulates the value
of this ‘‘GC-skew,’’ there is a valley that
corresponds to the origin and a peak that
corresponds to the terminus. As long as
one reads the strand in the 5
0
to 3
0
direc-
tion, the location of the peak and the valley
is independent of the strand being used to
deFne the origin and the terminus.
The bidirectional organization of the
genome also affects the direction of gene
transcription. As a general rule (with
numerous exceptions), the direction of
gene transcription is in the same direction
as the movement of the replication fork.
The rationale for this phenomenon is
that this correspondence of direction of
replication and transcription reduces the
‘‘head-on collision’’ of replication and
transcription. The fact that there are many
exceptions means that the replication
system can accommodate running into
transcriptional units without a problem.
3.2.6
DnaA Protein Is Involved in
Initiation of DNA Replication
The DnaA protein, identiFed by mutants
affecting the initiation of DNA replication
and not the progression of rounds of
replication already in process, appears
to be the ultimate regulatory protein
with regard to the initiation of DNA
synthesis. The initiation process involves
the cooperative binding of approximately
20 DnaA protein molecules to the origin
of replication. This complex then leads to
the open complex in which a region of
AT-rich 13-mer repeats denatures so that
single-stranded DNA is exposed. Other
proteins such as the DnaB helicase are
now introduced into the forks of the melted
DNA where it expands the region of single-
stranded DNA. Other molecules then
join the initiation complex with the Fnal
loading of DNA polymerase III. When this
occurs, the replication of DNA progresses
previous page 537 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online next page 539 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online Home Toggle text on/off