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Journal of Bacteriology, March 1999, p. 1576-1584, Vol. 181, No. 5
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Direct Selection for Mutators in
Escherichia coli
Jeffrey H.
Miller,*
Anjali
Suthar,
Jennifer
Tai,
Annie
Yeung,
Cindy
Truong, and
Jean Lee
Stewart
Department of Microbiology and Molecular
Genetics and The Molecular Biology Institute, University of
California, Los Angeles, California 90095
Received 28 August 1998/Accepted 8 December 1998
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ABSTRACT |
We have constructed strains that allow a direct selection for
mutators of Escherichia coli on a single plate medium. The
plate selection is based on using two different markers whose reversion is enhanced by a given mutator. Plates containing limiting amounts of
each respective nutrient allow the growth of ghost colonies or
microcolonies that give rise to full-size colonies only if a reversion
event occurs. Because two successive mutational events are required,
mutator cells are favored to generate full-size colonies. Reversion of
a third marker allows direct visualization of the mutator phenotype by
the large number of blue papillae in the full-size colonies. We also
describe plate selections involving three successive nutrient markers
followed by a fourth papillation step. Different frameshift or base
substitution mutations are used to select for mismatch-repair-defective
strains (mutHLS and uvrD). We can detect and
monitor mutator cells arising spontaneously, at frequencies lower than
10
5 in the population. Also, we can measure a mutator
cascade, in which one type of mutator (mutT) generates a
second mutator (mutHLS) that then allows stepwise
frameshift mutations. We discuss the relevance of mutators arising on a
single medium as a result of cells overcoming successive growth
barriers to the development and progression of cancerous tumors, some
of which are mutator cell lines.
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INTRODUCTION |
Several successive genetic
alterations are required for a cancer cell to develop, proliferate, and
be able to metastasize (70). In fact, as many as 6 to 10 mutations may be needed to turn a normal cell into a full-blown
invasive tumor line (2), which is one reason why many
cancers take decades to develop. Loeb (35) has postulated
that an early step in the progression of some cancers may be the
creation of a mutator cell, since the low spontaneous mutation rate
might not account for the incidence of cancer. However, the elevated
mutation rates in mutators would greatly increase the probability of
cells accumulating all of the necessary mutations (27, 35),
especially if repetitive rounds of clonal expansion and somatic
selection occurred (48). In accord with this idea was the
exciting finding that the inherited susceptibility to human
nonpolyposis colon cancer (HNPCC) and ovarian cancer is due to a defect
in one copy of one of the genes involved in the human counterpart to
the bacterial mismatch repair system (3, 18, 30, 49).
Presumably, when a somatic cell loses the other copy, the resulting
cell is completely defective for mismatch repair and has a higher
mutation rate. In fact, tumor lines from HNPCC patients are mutators
with greatly increased repeat-tract or microsatellite instability
(1, 26, 30, 36, 52, 53, 69), a propensity for frequent
additions or deletions at repetitive nucleotide sequences (such as
repetitive mono-, di-, tri-, and tetranucleotide repeats), in analogy
with the repeat-tract instability seen in mismatch-repair-deficient strains of bacteria and yeast (11, 57, 66). These tumor lines also show elevated mutation rates in genes such as
hprt (1, 3, 21). The realization that mutator
cells are cancer prone (1, 30, 50, 51) has led to increased
research in this area, including a search for new types of mutators and
for a better understanding of how mutators proliferate.
Experiments with bacteria aimed at finding mutators (12, 23, 24,
34) or at examining the behavior of wild-type or mixed
populations in chemostats (6, 9, 20, 46, 61, 65) showed that
continuous selection increases the proportion of mutators in cell
populations. In a previous paper, we demonstrated how easily a
population of Escherichia coli cells could become principally or totally mutators in response to several successive selections (39). Here, we ask whether instead of changing
medium in successive selections a single medium that selects directly for mutator colonies could be devised. By asking cells to overcome several barriers to growth on a medium with limiting amounts of each
required nutrient, we developed a plate medium on which only mutator
cells grow. We have employed this medium to examine the occurrence of
mutators under several conditions, and we discuss how this mimics the
situation in mammalian cells that need to overcome several growth
restrictions before becoming proliferating cancer cells. We also show
that one mutator can induce a second mutator that then stimulates
useful genetic changes, as part of a mutator cascade.
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MATERIALS AND METHODS |
Bacterial strains and plasmids.
The strain CC107 carries an
F'lacpro episome in the P90C (11, 43) strain
background ara
(gpt-lac)5. The
lac region on the F factor carries a lacI
mutation and also a frameshift in the lacZ gene that reverts
by the addition of a GC base pair to a monotonous run of GC base pairs.
This strain is described by Cupples et al. (11). AS18 is a
Met
derivative of CC107 carrying an ICR-191-induced
frameshift mutation in the metE (or possibly
metR) gene. AS18-29 is a Bgl
derivative of
AS18 carrying an additional ICR-191-induced frameshift mutation, this
time in the blgA gene. AS210 is a Leu
derivative of AS18-29, carrying a mutH-induced frameshift
mutation at the leu locus and a Tn10kan insert
near the wild-type mutH gene (zgh-3159
[62]). We constructed specific mutator derivatives of
certain strains by using P1 transduction from strains in which a
mini-Tn10 had integrated into either the mutT,
mutH, mutS, mutL, or uvrD
gene (45).
Genetic methods.
Mapping experiments were carried out with
P1 cotransduction with Tn10 transposons that had integrated
near either the mutH, mutL, mutS, or
uvrD gene, or near various nutritional markers (62). Auxotrophs were detected after ICR-191 mutagenesis by replicating Luria-Bertani (LB) plates spread with 100 to 300 colonies onto minimal medium plates and recognizing those colonies which failed
to grow. Combinations of supplements were used to restore growth, and
then individual supplements were employed. All other strains and
bacterial genetic methods, such as determination of rifampin resistance
(Rifr), are described by Miller (43). We
initially examined colonies for strong mutator activity by gridding
them onto an LB plate and growing them overnight at 32°C before
replicating them onto a second LB plate. The second plate was grown
overnight, and then colonies were replicated onto an LB plate with 100 µg of rifampin per ml. After overnight growth, mutators defective in
mismatch repair showed many Rifr colonies growing out of
the replicated patch, whereas nonmutator strains did not. More
quantitative measurements were then carried out when relevant.
Preparation of cultures.
Unless otherwise stated, all
cultures for the experiments reported here were prepared by inoculating
a portion of a single colony into LB medium (43) or other
medium and growing it overnight. A different single colony was used for
each culture. Therefore, all mutants occurring in different cultures
are of independent origin, since each single colony is derived from a
single isolated cell. Typically, 5-ml cultures were used.
Mutagenesis.
All methods of mutagenesis were exactly as
described in the work of Miller (43). 2-Aminopurine (2AP;
Sigma) was used at concentrations of 700 µg/ml. Cultures were
prepared by subculturing 104 to 105 cells into
4 ml of LB with 2AP, and these were grown for 12 to 16 generations in
LB with 2AP before plating. ICR-191 (Sigma) was used at concentrations
of 10 µg/ml in minimal A medium (43) supplemented with 1 ml of LB broth, 2 ml of 20% glucose, 0.1 ml of 1 M MgSO4,
and 0.5 ml of B1 (thiamine hydrochloride) per 100 ml of medium.
Specialized media.
Mutators were selected on lactose minimal
A medium (43) supplemented with limiting amounts of required
sugars or nutrients. We used 150 µg of glucose per ml as a limiting
carbon source and 0.5 µg of required amino acids, purines, or
pyrimidines per ml. For instance, in conjunction with strain AS18 or
AS18-29 we used minimal A plates containing lactose, B1, and
MgSO4 (33), supplemented with 150 µg of
lactose per ml and 0.5 µg of methionine per ml. When called for,
these plates were also supplemented with 40 µg of X-Glu
(5-bromo-4-chloro-3-indolyl-
-D-glucoside; Research
Organics) per ml. This dye stains colonies with active
-glucosidase
deep blue. We find that colonies of Bgl
strains on plates
containing glucose as a carbon source and X-Glu will yield blue
papillae without the addition of another substrate for
-glucosidase.
Thus, in the blue papillation method (47) as originally
described for the lac system,
phenyl-
-D-galactoside is added as a carbon source for
papillae stained blue by X-Gal (5-bromo-4-chloro-3-indolyl-
-D-galactopyranoside). Here,
this second carbon source is not necessary. Perhaps as a result of the
lower concentration of the X-Glu in the role of carbon source, sugars
are utilized in the following order by revertants of the Lac
Bgl
strains: glucose > lactose > X-Glu.
Determination of mutator frequency.
The data from Tables 3
and 4 were used to calculate the spontaneous frequency of
mismatch-repair-deficient mutants. Since the majority of cultures had
no mutators, the fraction of cultures with no mutators was used to
calculate the mean, m, for the Poisson distribution
describing the distribution of mutants. In the case of cells at a
density of 105 cells per plate, the zero fraction is
327/355 = 0.921. Since for the Poisson distribution
Po = e
m, 0.921 is
e
m, and m is 0.082, or, in this case,
0.082 × 10
5. Accounting for the 10% plating
efficiency gives a value of m as 0.82 × 10
5. Similar calculations for cells at a density of
104 cells per plate give 0.63 × 10
5,
for a plating efficiency of 100%. We find that the plating efficiency at 104 cells varies somewhat more than that for
105 cells, so we take 0.8 × 10
5 as a
more probable value. This value is for the fraction of mutators (or
mutant frequency) in a culture grown for about 33 generations.
Plating efficiency of mutators.
Strain AS18-29 was plated at
different densities on selective medium, and then dilutions of a
mutH derivative were plated on the same plates and the
percentages of mutator cells forming colonies were determined.
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RESULTS |
Finding mutants with useful selective markers.
We looked for
mutations which could be used in combination with other mutations to
provide useful selections for mutator strains. We initially targeted
mutators lacking the mismatch repair system. These strains have greatly
enhanced rates of transitions and also of frameshifts at runs of single
base pairs or repeating dinucleotides (11, 33, 57).
Therefore, strains such as CC107 (11), which reverts from
Lac
to Lac+ via the addition of a G to a run
of six G's, are useful for selecting for mutators, as we described
previously (39). In order to find additional markers to use
in concert with Lac
strains such as CC107, we mutagenized
CC107 and derivatives of CC107 and looked for auxotrophs and then
characterized the mutants with regard to reversion rates in both
wild-type and mismatch-repair-deficient (mutH or
mutS) strain backgrounds. We also determined the nutritional requirement and mapped the mutation to one of the known loci on the
chromosome in most cases (see Materials and Methods).
Auxotrophs found after treatment with ICR-191 are usually caused by
additions or deletions at monotonous runs of GC base pairs (5). Some of these should create monotonous runs of 6 bp or more and thus show greatly enhanced reversion rates in a
mismatch-repair-deficient strain compared to reversion in a wild-type
strain. Approximately 1% of the survivors of ICR-191 treatment were
auxotrophs, and about 75% of these could be identified with respect to
the nutritional requirement. Mutants that were leaky or which did not
show a significantly increased reversion in a mutH strain
were discarded. Of 70 mutants derived by ICR-191 mutagenesis, 22 merited further study. These mutants are shown in Table
1. Many of these mutants have low reversion rates but show greatly increased rates in a mutH
background. Thus, they represent promising indicators for mutators.
Several of the strains, including AS18, which carries a mutation in the metE (or metR) gene, were selected for additional
experiments.
Detection of mutations in the bgl operon.
As an
additional indicator of mutator strains, we sought mutations in the
bgl operon that revert in response to
mismatch-repair-defective backgrounds. Since the bgl operon
is cryptic in most E. coli K-12 strains (56,
58), we first scored spontaneous mutants of both CC107 and AS18
that could grow on salicin as a sole carbon source for intense blue
color on glucose minimal plates with X-Glu (see Materials and Methods).
We selected one Bgl+ mutant from each strain, mutagenized
them with ICR-191, and screened for white colonies on X-Glu plates.
These were then tested for enhanced reversion in a mutH
strain in a variation of the blue papillation assay (47),
adapted for X-Glu (see Materials and Methods). One Bgl
mutant was selected for further use. The mutant derived from CC107 was
termed CC107-17, and the mutant derived from AS18 was named AS18-29. In
each case, the frequency of revertants to Bgl+ goes from
approximately 10 per 108 cells in a wild-type strain to
approximately 5,000 per 108 cells in a mutH
strain. These strains form numerous blue papillae in a
mismatch-repair-deficient background on X-Glu plates and thus serve as
indicators for mutHLS and uvrD strains.
Sequential selection on a single medium detects mutators.
We
initially used strain AS18-29, which carries frameshift mutations in
both lacZ and metE, to detect mutators. We
experimented with different media to select colonies of strain AS18-29
that overcome both the Lac
and the Met
defects. We applied the principles depicted in Fig.
1 and 2. Lactose medium with limiting amounts of glucose and methionine should
allow cells to grow to a small population size of approximately 105 cells before exhausting the limiting carbon source
(glucose). To grow further would require metabolizing the lactose, and
this would require a mutation from Lac
to
Lac+. Then, the Lac+ cell could grow until it
exhausted the methionine and again reach 105 cells. Now, a
second mutation to Met+ would be required to allow further
colony growth. In cases where a mutator population of 105
cells would have a Lac+ or a Met+ revertant, we
would expect each mutator cell to give rise to a full colony under the
right conditions, whereas only a fraction (about 10
5 to
10
4) of the nonmutator cells would form colonies (Fig.
1). We therefore examined the plating efficiency of a mutH
derivative of AS18-29 on medium with different limiting amounts of
glucose and methionine and found the best results with 150 µg of
glucose per ml and 0.5 µg of methionine per ml (see Materials and
Methods). On these plates, the mutH strain formed colonies
with a 50 to 100% plating efficiency, while the wild-type derivative
formed no colonies at all. We determined mutator colonies by either
testing for enhanced frequency of Rifr colonies or
including X-Glu in the medium to indicate frequent mutation to
Bgl+ by the appearance of many blue papillae. (In the
absence of X-Glu, colonies are usually picked after 3 days, whereas in
the presence of X-Glu an extra day is needed for optimal papillae
formation.)

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FIG. 1.
Selection for mutator colonies. Lac
Met cells are plated on lactose medium with limiting
amounts of glucose and methionine. Cells form a microcolony before
exhausting the glucose. Revertants to Lac+ can grow
further. Only 1% of the nonmutator microcolonies (left) will have a
Lac+ cell, whereas 100% of the mutator microcolonies
(right) will have a Lac+ cell. Further growth of the
Lac+ cells yields microcolonies that exhaust the
methionine. Again, 1% of the nonmutator Lac+ microcolonies
(left) will have a Met+ cell, whereas 100% of the mutator
Lac+ microcolonies (right) will. The very rare nonmutator
Lac+ Met+ colonies have no Bgl+
papillae (left), but the Lac+ Met+ mutator
colonies show microsatellite instability and give Bgl+
papillae (right; black dots). WT, wild type.
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FIG. 2.
A representation of mutator colonies growing to full
size after the selection described in the legend to Fig. 1. Many small
microcolonies (open dots) are seen in the background, but only two
full-grown colonies appear, and these have many Bgl+
papillae (dark dots).
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To determine whether the selective medium could detect mutators from a
mixed population, we grew AS18-29 overnight in 2AP
and first measured
the mutators by direct visualization on minimal
glucose plates
supplemented with methionine and X-Glu, as well
as on the selective
plates. The glucose-X-Glu plates with methionine
allow the growth of
all colonies, with mutators displaying a large
number of blue papillae.
This can be seen in Fig.
3A, which shows
that of several hundred colonies, one prominent mutator is evident.
In
these experiments, mutators deficient in mismatch repair are
found in
between 1/1,000 and 1/300 cells after 2AP treatment.
Figure
3B shows
the result of plating an even larger sample of
cells on the selective
medium. Now, only the mutator colonies
grow, as indicated by the blue
color of the colonies, which is,
upon magnification (Fig.
3C), really
due to thousands of Bgl
+ papillae from the X-Glu indicator.
Figure
3C also allows the
visualization of the microcolonies that
failed to develop into
true colonies. We verified that the surviving
colonies were predominantly
mutators by testing for increased frequency
of Rif
r mutants. Table
2
shows the results from several experiments.
It can be seen that
approximately 90% of the full-size colonies
that grow on the selective
plates after 2AP mutagenesis of strains
AS18 and AS18-29 are strong
mutators. Because both mutations that
need to revert to restore the
Lac
+ Met
+ phenotype are frameshifts, it is
expected that the mutators are
deficient in the mismatch repair system.
We have examined sample
mutators and found that all of the mutants
tested carry a mutation
in one of the four mismatch repair loci
(
mutHLS or
uvrD [see below]).

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FIG. 3.
Selection for mutators. (A) Strain AS18-29 was grown
overnight in LB broth with 2AP and plated on X-Glu plates. Here, one
mutator colony (see insert) is evident, as indicated by the numerous
blue Bgl+ papillae. (B) A photograph of a plate like that
diagrammed in Fig. 2. Two full-size mutator colonies grow on selective
plates onto which several thousand cells have been spread. Minute
microcolonies in the background are nonmutator colonies. The mutator
colonies appear blue because of thousands of blue Bgl+
papillae (see magnification in panel C). (C) A magnification of part of
the plate shown in panel B. Here, the nonmutator microcolonies are
evident, as are the blue Bgl+ papillae, representing the
microsatellite instability of the full-size mutator colony.
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TABLE 2.
Percentage of mutators among Lac+
Met+ colonies in 2AP cultures of AS18 and AS18-29 after the
plate selection described in the text and for Fig. 1 to 5
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We have carried out reconstruction experiments by mixing different
proportions of wild-type and
mutH derivatives of AS18-29
and
then plating them on selective medium. As Table
3 shows,
the selective plates are
sensitive to cell density. The cell lawn
eats up some of the limiting
nutrients, and the efficiency of
recovering a mutator goes down as the
cell density increases.
Placing up to 10,000 cells on a plate gives
optimal results. As
the number of cells approaches and then exceeds
10
5 per plate, the efficiency of recovery of mutators drops
significantly.
With 10
5 cells per plate, the efficiency
drops from 50 to 100% to 10%,
and with 10
6 cells, the
efficiency drops to 1% recovery. Despite this, we
can still detect
mutators that occur spontaneously, at levels
near 1 per 10
5
cells (see below).
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TABLE 3.
Efficiency of plating of mutH derivative of
AS18-29 in the presence of different densities of cells
of AS18-29a
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Detection of spontaneous mutators.
We employed strain AS18-29
to detect spontaneous mutators in cultures grown for three generations.
We examined 355 cultures, by plating 105 cells from each
culture, and an additional 344 cultures, by plating 104
cells from each culture. Colonies were detected on selection medium
without X-Glu and purified once before being tested for the frequency
of Rifr colonies. Because the frequency of spontaneous
mutators is on the order of 10
5 in the population, some
Lac+ Met+ colonies are due to spontaneous
mutations occurring in nonmutator cells. These colonies also appear on
the order of 10
5 in the population. As Table
4 shows, about 50% of the colonies detected were mutators. About 92% of the plates with 105
cells yielded no mutator colonies. Applying the 10% plating efficiency determined from reconstruction experiments (Table 3), we can calculate
the mutator frequency from the fraction of cultures with no mutators.
This gives a frequency of mutators of 0.8 × 10
5
(see Materials and Methods). For the cultures plated with only 105 cells per plate, which gives a plating efficiency of 50 to 100%, approximately 94% of the cultures yielded no mutator
colonies, which translates to 0.6 × 10
5 to 1.2 × 10
5 for the mutator frequency. These values are close
to estimates based on other measurements we have made, as described in
the Discussion.
Identification of mutators detected spontaneously.
We mapped the mutation causing the mutator phenotype in 45 of the
spontaneous mutators detected in the above experiments, by P1
transduction (see Materials and Methods). All of the mutations fell
into one of the four mismatch repair genes. However, as Table 5 shows, the mutations were not
distributed equally among mutL, mutH,
mutS, and uvrD. Instead, 19 of the mutations were
in mutH, 18 were in mutL, 7 were in
mutS, and 1 was in uvrD.
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TABLE 5.
Position of the mutation resulting in the mutator
phenotype in each of the 45 independent mutators of
spontaneous origin
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Different combinations of markers are effective in selection.
The strain AS18-29 carries a mutation in the lac region on
an F' plasmid and a met mutation in the chromosome. The
selective medium is not limited to those markers, nor does it depend on having a mutation on an F' plasmid (data not shown). Several different combinations of markers were made for use in the successive selection medium. Some of the markers are derived from the experiment whose results are shown in Table 1. A second set of markers was derived by
first making a mutH derivative of AS18-29 and obtaining
auxotrophs (in the presence of methionine) induced by the mutator
effect of the mutH allele. Then, the mutH allele
was crossed out, and the reversion rates were compared. The new strains
from this selection carry mutations that are not limited to additions
or deletions at monotonous runs of G's or C's. They may contain
additions or deletions at runs of A's or T's, or at repeating
dinucleotides, as well as certain base substitutions. Table
6 shows the useful strains obtained from
this selection. One additional mutation used in some experiments (data
not shown) is the argE amber mutation derived from strain
XAC (43). This mutation reverts via base substitutions that
either restore the UAG codon to a sense codon or else create an amber
or ocher suppressor.
Triple selection.
We utilized strain AS210 (Table 6), which
carries frameshift mutations in lacZ, metE, and
leu. Even though three successive selections occur, colonies
were obtained on plates with limiting amounts of glucose, methionine,
and leucine. After mutagenesis with 2AP, 97% of the colonies (26 of
27) were found to be mutators, and 90% of the colonies detected
spontaneously were mutators. All of the mutator colonies tested had
defects in one of the mismatch repair genes. The plating efficiency of
a mutator on this medium, however, does not exceed 10%.
Mutator cascade.
Some mutators may not exhibit an increased
rate of mutations at certain sequences, such as frameshifts at runs of
identical bases of repeated sequences. However, they might show an
increased rate of mutation at a second mutator locus, the resulting
secondary mutators now being able to stimulate the specific sequence
change. This type of mutator cascade might be significant in creating certain phenotypes. We can examine this phenomenon by looking at our
tester strain, AS18-29, into which we have crossed a mutation at the
mutT locus. The resulting mutators show an increased
incidence of only one specific transversion, A:T
C:G (10),
because of the failure to hydrolyze the oxidatively damaged DNA
synthesis precursor 8-oxo-dGTP (38). That mutT
cells do not greatly increase mutations at the frameshifts we used to
monitor mutations in AS18-29 is evidenced in Table
7. Comparing the wild-type and
mutT derivatives of AS18-29 with respect to reversion of
either the lac, met, or bgl frameshift
mutation shows either only slight or no differences compared with the
mutH derivative of AS18-29, which shows an enormous increase
(Table 7). Yet, when we look at the incidence of mutations in the
mutHLS pathway that create mutators that can now stimulate the frameshifts in lac, met, and bgl,
we see that mutT increases the spontaneous level of these
mutators from 8 × 10
6 to 3 × 10
4.
In the
mutT derivative, approximately 1 of each 3,300 cells
has a mutation in the
mutHLS system. As a single cell
divides
and forms a colony, on average at some point between the 12th
and 16th cell division the first mutator arises and forms a very
thin
sector, representing the lineage of daughter cells in the
colony.
Occasionally, a
mutHLS mutator arises in the first cell
division, yielding a colony that is half
mutT alone and half
mutT mutH (or
mutL or
mutS). We can
visualize these sectors by decorating
them with blue papillae arising
from the Bgl
+ reversion event at the frameshift in the
bglA gene in AS18-24.
Figure
4
shows some of these sectors. Recall that the starting
mutT
derivative of AS18-29 cannot give rise to frequent Bgl
+
papillae. Figure
4A shows a colony that is half sectored for
the
mutHLS phenotype. Figure
4B shows a colony with a smaller
mutator sector.

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FIG. 4.
Appearance of mutator subpopulations as colony sectors.
A mutT derivative of strain AS18-29 was plated on minimal
glucose plates with methionine and X-Glu. Mismatch-repair-deficient
(MMR ) sectors (e.g., mutH) are revealed by
frequent blue Bgl+ papillae (microsatellite instability).
(A) An MMR mutant has arisen at the first cell division,
resulting in half of the colony having microsatellite instability. (B)
An MMR mutant has arisen at approximately the fifth cell
division, resulting in a thinner sector of the colony displaying
microsatellite instability.
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When the subpopulation of
mutT-generated
mutHLS
mutators within a colony sector reaches a sufficient size, it can give
rise
to the first revertant able to overcome one of the growth
restrictions
imposed by the Lac

Met

Bgl

phenotype of the AS18-29 strain background. As
depicted in Fig.
1 and
2, this can then lead to a progression that
leads to the
development of a full-size mutator colony. As Fig.
5 diagrams,
in the case shown here, the
starting strain can grow to only a
certain size on medium with limiting
methionine and limiting glucose.
Then, the
mutHLS mutator
cell sector generates a Lac
+ revertant (for instance),
which can grow further, and then a
Met
+ cell that can grow
without restrictions arises. The rapidly growing
colony thus arises
from within a slow-growing colony, extends
out beyond the original
colony, and displays microsatellite instability
by throwing off
frequent blue papillae in the presence of X-Glu.
Figure
6 shows some of these colonies. Figure
6A
and B show single
colonies outgrowing the original slow-growing colony,
and Fig.
6C shows how the unrestricted growth can ultimately invade
other
surrounding slow-growing or nongrowing microcolonies.

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FIG. 5.
The effects of a mutator cascade are depicted in a
schematic diagram of a mutT derivative of strain AS18-29
(Lac Met Bgl ) growing on
lactose minimal medium with trace amounts of glucose and methionine and
the indicator X-Glu. The starting cell (A) forms a microcolony, in
which a mutH cell arises (B). As the microcolony grows,
exhausting the glucose in the medium, the subpopulation of
mutH cells also slowly proliferates (C), until a
Lac+ cell arises within the mutH subpopulation
(D). The Lac+ cells can grow further on the lactose in the
medium until the trace methionine is exhausted. If a Met+
cell appears (E), it can now grow without the restriction of limiting
methionine or glucose, expanding rapidly and showing microsatellite
instability by the appearance of many blue Bgl+ papillae
(F).
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FIG. 6.
Mutator cascade. The figure shows selection for the
growth of a mutator arising from a microcolony. The starting
microcolony is a mutT derivative of strain AS18-29. The
mutT mutator cannot revert the frameshift mutations in
lacZ and metE, but can generate mutations in the
mutH, -L, or -S genes, resulting in
mismatch-repair-deficient (MMR ) mutators that can revert
the frameshifts and break free of growth restrictions. (A and B)
MMR mutator colonies growing out from a microcolony. The
MMR mutators have many blue papillae, demonstrating
microsatellite instability (see legend to Fig. 4). (C) An
MMR mutator generated on a more crowded plate will grow
in an unrestricted fashion, proliferating over the plate and
overrunning the nonmutator microcolonies.
|
|
 |
DISCUSSION |
Mutator cells, defined as cells with higher rates of mutation than
those of wild type, were first detected in Drosophila
melanogaster in the early 1940's (54) and in bacteria
in the early 1950's (68). Now, mutations in more than 20 different genes in bacteria such as E. coli have been
shown to result in the mutator phenotype (see reviews in references
8, 13, 19, 44, and 64). Most of
these cause defects in repair or damage avoidance systems, although
some affect less well defined pathways (7, 42, 63). Higher
cells also display mutator phenotypes when certain genes are
inactivated, and this can lead to increased incidence of disease. For
instance, inheriting one copy of a defective gene involved in the human
counterpart to the bacterial mismatch repair system leads to increased
susceptibility to colon cancer, HNPCC-related endometrial cancer, and
ovarian cancer (4, 18, 30, 49; see review in
reference 37). The resulting tumor lines are
mutators that show increased repeat-tract instability (see reviews in
references 27 and 35) and higher
mutation rates in genes such as hprt (1, 3, 21).
Loeb had already postulated that creation of a mutator cell would be an
early step in some cases of carcinogenesis, since a mutator can
generate the multistep mutations faster than can a normal cell with
lower mutation rates (27, 36). How then do mutators arise in
a population of cells, and how do they proliferate?
Clearly, spontaneous mutants constantly arise in a population, and some
of these are mutators. The balance of selective advantage and
disadvantage will affect the proportion of mutators in any given
environment, but the continued generation of new spontaneous mutations
will provide a constant source. Using the selection system described in
this work and discussed further below allows us to measure the
proportion of cells in a growing population of E. coli
cells that have defects in one of the four mismatch repair genes. This
number of just under 10
5 (0.8 × 10
5)
mutants is in a population growing in broth for about 33 generations. This number is in agreement with estimates from our previous study (39), in which Lac+ frameshift mutants detected
at 2 × 10
7 were scored to reveal that 0.5% (5 × 10
3) were mutators. These values predict that mutants
that are both Lac+ and defective in one of the four
mismatch repair loci are present at 10
9 in the population
(the product of these latter two frequencies). However, since the
Lac+ revertant rate in each mutator subpopulation is close
to 10
4 (9, 30), then the mutators are
estimated to be in the population at 10
9 divided by
10
4, or close to 10
5. (Interestingly, a
subsequent analysis of mismatch repair mutators in Salmonella
typhimurium shows that they occur spontaneously an order of
magnitude less frequently than found here for E. coli [32]).
Looking at the distribution of mutations among the four mismatch repair
loci (Table 5) that leads to a combined rate of 0.8 × 10
5 mutators in the population makes us realize how these
measurements can vary, depending on the specific gene being monitored.
The mutant frequencies for each of the four loci are as follows:
mutH, 3.4 × 10
6; mutL,
3.2 × 10
6; mutS, 1.2 × 10
6; uvrD, 1.8 × 10
7. It
is not clear why only 1 of 45 mutations is in the uvrD gene. Reconstruction experiments indicate that the efficiency of plating of
strains with uvrD mutations in the selection employed is the same as for strains with mutations in mutH (data not shown),
suggesting that the effect is due to rates of mutations themselves, but
it is possible that other hidden experimental biases conspire to reduce
the appearance of UvrD mutants.
We should note at this point that mutagenesis from any of a number of
sources serves to increase the proportion of mutators to near or above
10
3 (see, for instance, reference 39).
However, in addition to mutagenesis, selection for mutant phenotypes
can serve to increase the frequency of mutators in a population.
Chemostat experiments show that extensive continued growth in a
full-nutrient environment can still lead to the selection of fitter
strains and increase the proportion of mutators, since they can give
rise to fitter variants more rapidly than can the wild type (6, 9,
20, 46, 61, 65). Computer simulations also argue that mutators are selected for in continued growth in chemostats (67). In fact, some mutators were originally found by procedures designed to
screen mutagenized cells after single or successive selections (12, 23, 24, 34) or by observation of cells selected for a
specific phenotype (60, 61). Several investigators have found that natural isolates of bacteria have several percent mutators (22, 28, 31), suggesting that populations in the wild might be undergoing constant selection. Cebula and coworkers have argued that
the several percent mutators found among E. coli and
Salmonella strains isolated from patients might be related
to pathogenicity (31), although others have disputed this
correlation (41).
In a previous study (39), we showed how quickly the
proportion of mutators can rise in a population, and how several
successive selections can result in the entire surviving population
being mutator. This underscores the consequences of certain
chemotherapies, in which the resistant cells may be enriched for
mutators. In the previous work (39), the successive
selections involved transferring cells to different media. We have
extended that study in the work reported here by designing a single
medium that selects for several phenotypes in succession. Cells with
multiple nutrient requirements are challenged to form colonies by
eventually overcoming each of the growth barriers. In the most studied
case, strain AS18-29, carrying frameshifts in the lacZ gene
on the F plasmid and in the chromosomal metE gene, must
revert both mutations in order to form full-size Lac+
Met+ colonies. A second strain adds a third growth
requirement via a frameshift mutation in the chromosomal leu
operon. The medium contains very small amounts of glucose as a carbon
source and small amounts of methionine (and also of leucine when
relevant). This permits a microcolony of nearly 105 cells
to form, which if derived from a mutator cell will contain enough cells
to have a mutant that can now use, for example, the lactose in the
medium as a carbon source to initiate a new microcolony of
105 cells before it exhausts the methionine. A mutator cell
will now have a second mutation in this new microcolony that reverses the metE mutation, allowing it to form a full-size colony
(in the case of the derivative with the mutation in leu, a
third round of successive microcolony formation would be required).
Full-size colonies can be picked and analyzed or directly visualized by using reversion of a frameshift mutation in the bgl operon
to decorate mutators with scores of blue papillae. The results, shown in Fig. 3, reveal that cells having to overcome several growth requirements in succession on a single defined medium give rise to
mutator colonies. After mild mutagenesis, 90 to 100% of the colonies
on this medium are mutators with defects in the mismatch repair system,
depending on whether two or three growth requirements are employed.
Even without a mutagen, spontaneous mutators constitute 50% of the
colonies of cells that break through the growth restrictions.
It is interesting to compare the emergence of mutator colonies on
plates selecting for overcoming several successive growth restrictions
with the emergence of a cancer cell that undergoes successive mutations
to break free of growth restrictions, particularly in the case of colon
cancer. In both cases, frameshift mutations at runs of mono- or
dinucleotides are involved in creating mutants. In the case of the
bacterial strain shown here, the frameshift mutations restore the
normal gene, whereas in the carcinogenesis model, frameshifts
inactivate certain genes. Many colon cancer cell lines have mutations
in the APC gene (25), the rII gene encoding the negative growth suppressor transforming growth factor
II (40, 50), and the apoptosis-associated BAX
gene (55). The APC gene contains runs of A
residues and an AG dinucleotide repeat that are frameshifted in
sequenced mismatch-repair-deficient tumor lines (25). In
these lines, most of the mutations inactivating transforming growth
factor
are at a run of 10 A's or at a threefold repeat of a GT
sequence in the rII gene (40), and frameshifts at
a run of eight G's are found in the BAX gene
(55). It is easy to see the parallels between successive
selections that enrich for mismatch-repair-deficient strains in
bacteria and those in human tumor lines that have to overcome several
growth restrictions.
Figures 4 to 6 portray the events that occur when a mutHLS
mutator cell arises within a colony of cells growing very slowly under
restrictive conditions. As all the cells grow, the patch of cells
derived from the mutHLS mutator cell (Fig. 4) reaches a
sufficient size to allow the appearance of a mutant that can overcome
subsequent growth restrictions (Fig. 5), proliferate during
unrestricted growth, and exhibit repeat-tract instability (Fig. 6). In
this series of experiments, the appearance of the mutHLS
mutator is accelerated by the presence of a different mutator, in this
case mutT, that cannot revert the frameshifts (Table 7) to
overcome the growth restrictions but that can generate mutations that
inactivate the mutH, mutL, or mutS
gene. This produces a mutator cascade, where one mutator induces a
second one. We have also found similar results with the mutA
mutators, which result from miscoding tRNAs (data not shown). It will
be interesting to see whether any examples of such a mutator cascade
are found among tumor lines, or whether any cancer susceptibilities are found to result from the inheritance of a defective copy of a different
repair gene that by itself leads to a mutator effect without
microsatellite instability but which can generate
mismatch-repair-deficient mutators. There is precedent for inactivation
of the mismatch repair genes as a second step in the development of
colon cancer. A significant fraction of sporadic colon cancer tumor
lines that show microsatellite instability suffer inactivation of
mismatch repair genes as a consequence of the epigenetic gene silencing produced by hypermethylation of both copies of the relevant promoters (29).
 |
ACKNOWLEDGMENT |
This work was supported by grant GM32184 to J.H.M. from the
National Institutes of Health.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Microbiology and Molecular Genetics and The Molecular Biology
Institute, University of California, Los Angeles, CA 90095. Phone:
(310) 825-8460. Fax: (310) 206-3088. E-mail:
jhmiller{at}mbi.ucla.edu.
 |
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Journal of Bacteriology, March 1999, p. 1576-1584, Vol. 181, No. 5
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Copyright © 1999, American Society for Microbiology. All rights reserved.
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