protein and its protein partners are usually involved in DNA
repair. However, due to its activity, RecA also allows the
integration of exogenous DNA. Proteins, such as MutS
and MutL in E. coli, have antagonistic activities to RecA.
The MutS/MutL/MutH proteins detect and correct
mismatches in double-stranded DNA during replication,
ensuring the fidelity of this process. The function of the
MutS/MutL/MutH system is very important because the
inactivation of mutS is responsible for the emergence of
strains with very high mutation rates (Taddei et al. 1996).
The relative level of expression of RecA compared to MutS/
MutL has important consequences for the cell: a higher level
of expression of RecA can increase the ability of the cell to
initiate homologous recombination and thus to integrate
foreign DNA. Stressful situations, through the modulation
of the protein levels, can change the capacity of
microorganisms to detect and repair point mutations and
thus to maintain the integrity of their genetic material. At
the population level, this phenomenon can lead to the emergence of individuals carrying beneficial adaptations. Then,
HGT may facilitate the dissemination of these adaptations to
a larger number of individuals.
The rate of homologous recombination varies from one
organism to another. For instance, it has been shown in vitro
that, under optimal conditions, it varies from 0.1 % in A. baylyi
to 25–50 % in B. subtilis and S. pneumoniae. Because it
requires a high level of sequence similarity between chromosomal and recombinant DNA, in most cases homologous
recombination allows acquiring new alleles but not new
genes. In some cases however, homologous recombination
may lead to a gain of genetic material and thus to an increase
of the size of the recipient cell genome. This may happen when
the flanking regions of the exogenous DNA fragment are very
similar to the sequence of the genome of the recipient cell. In
this case, homologous recombination is initiated through the
intermediary of the flanking regions leading to the integration
of exogenous DNA into the genome of the recipient.
DNA recombination can occur even if chromosomal and
exogenous DNA are not sufficiently similar to induce
homologous recombination. This involves another process
called nonhomologous (or illegitimate) recombination. Several genes acting in this mechanism have been identified in
E. coli. It involves double-strand breaks and reassembly via
the ends of DNA strands (Ikeda et al. 2004). In principle,
illegitimate recombination can lead to the integration of
exogenous DNA at any location of the recipient cell genome,
except when the illegitimate recombination occurs via the
activity of site-specific recombinases. Nevertheless, this process promotes the integration of new DNA fragments and
thus leads to an increase of the genome size of the recipient.
Laboratory experiments have shown that the frequency of
illegitimate recombination is very low in the case of linear
DNA and slightly higher in the case of circular DNA. The
low frequency of illegitimate recombination events could
result from selection pressures ensuring the conservation of
the integrity of the genome of the recipient cell.
The third mechanism of recombination is called
homology-facilitated illegitimate recombination (HFIR). It
requires the presence of a single small region of high similarity between exogenous and chromosomal DNA (de Vries
and Wackernagel 2002). Once recombination is initiated in
the region of high similarity, it continues in the adjacent
regions which present little or no similarity at all. As in the
case of illegitimate recombination, HFIR leads to a net gain
of DNA and thus can contribute to increase the size of the
recipient genomes. In the case of plasmids (or circular
DNA), this mechanism can result in their complete integration into the chromosome of the recipient cell. HFIR can
lead to the integration of fragments of relatively large size
(>1,000 bp). Experiments have shown that the effectiveness
of HFIR is relatively low. However, it can significantly
increase when more than one area of strong similarity are
shared by the exogenous and host DNA (for additional
details on HFIR, see Thomas and Nielsen 2005).
Irrespective of the mechanism of recombination
involved, the integration of exogenous DNA into the
genome of the host (Fig. 12.4e) or its maintenance as an
autonomous genetic element (Fig. 12.4f) do not mean that
the HGT has been successful. Indeed, the long-term persistence of the exogenous DNA in populations depends on
several factors (Fig. 12.4g), such as possible deleterious
effects resulting from its integration. Indeed, depending on
its location, the integration of the exogenous DNA can lead
to the disruption of important genes (or groups of genes or
operons) and thus cause deleterious effects on the recipient
cell and its offspring. In this case, due to natural selection,
the transferred DNA will disappear rapidly at the same time
as the cells that carry them. Stochastic phenomena* can
also lead to the disappearance of the exogenous DNA more
or less rapidly even if it carries alleles or genes conferring an
advantage to the receiving cell. Finally, natural selection
determines the long-term persistence of the exogenous
DNA in populations.
In conclusion, to be successful, HGT must go throughout each of these steps, and therefore, only a minority
succeeds. This means that there is a large difference
between the number of HGT events measured in terms of
amount of exogenous DNA entering into cells and the
number of HGT events that can be detected in presentday microbial genomes. These two concepts are often
wrongly confused.
12.3 Detection
The detection and quantification of HGT has been a hotly
debated issue in the scientific community for many years.
Indeed, at the end of the 1990s, the analysis of the first
12 Horizontal Gene Transfer in Microbial Ecosystems
453
repair. However, due to its activity, RecA also allows the
integration of exogenous DNA. Proteins, such as MutS
and MutL in E. coli, have antagonistic activities to RecA.
The MutS/MutL/MutH proteins detect and correct
mismatches in double-stranded DNA during replication,
ensuring the fidelity of this process. The function of the
MutS/MutL/MutH system is very important because the
inactivation of mutS is responsible for the emergence of
strains with very high mutation rates (Taddei et al. 1996).
The relative level of expression of RecA compared to MutS/
MutL has important consequences for the cell: a higher level
of expression of RecA can increase the ability of the cell to
initiate homologous recombination and thus to integrate
foreign DNA. Stressful situations, through the modulation
of the protein levels, can change the capacity of
microorganisms to detect and repair point mutations and
thus to maintain the integrity of their genetic material. At
the population level, this phenomenon can lead to the emergence of individuals carrying beneficial adaptations. Then,
HGT may facilitate the dissemination of these adaptations to
a larger number of individuals.
The rate of homologous recombination varies from one
organism to another. For instance, it has been shown in vitro
that, under optimal conditions, it varies from 0.1 % in A. baylyi
to 25–50 % in B. subtilis and S. pneumoniae. Because it
requires a high level of sequence similarity between chromosomal and recombinant DNA, in most cases homologous
recombination allows acquiring new alleles but not new
genes. In some cases however, homologous recombination
may lead to a gain of genetic material and thus to an increase
of the size of the recipient cell genome. This may happen when
the flanking regions of the exogenous DNA fragment are very
similar to the sequence of the genome of the recipient cell. In
this case, homologous recombination is initiated through the
intermediary of the flanking regions leading to the integration
of exogenous DNA into the genome of the recipient.
DNA recombination can occur even if chromosomal and
exogenous DNA are not sufficiently similar to induce
homologous recombination. This involves another process
called nonhomologous (or illegitimate) recombination. Several genes acting in this mechanism have been identified in
E. coli. It involves double-strand breaks and reassembly via
the ends of DNA strands (Ikeda et al. 2004). In principle,
illegitimate recombination can lead to the integration of
exogenous DNA at any location of the recipient cell genome,
except when the illegitimate recombination occurs via the
activity of site-specific recombinases. Nevertheless, this process promotes the integration of new DNA fragments and
thus leads to an increase of the genome size of the recipient.
Laboratory experiments have shown that the frequency of
illegitimate recombination is very low in the case of linear
DNA and slightly higher in the case of circular DNA. The
low frequency of illegitimate recombination events could
result from selection pressures ensuring the conservation of
the integrity of the genome of the recipient cell.
The third mechanism of recombination is called
homology-facilitated illegitimate recombination (HFIR). It
requires the presence of a single small region of high similarity between exogenous and chromosomal DNA (de Vries
and Wackernagel 2002). Once recombination is initiated in
the region of high similarity, it continues in the adjacent
regions which present little or no similarity at all. As in the
case of illegitimate recombination, HFIR leads to a net gain
of DNA and thus can contribute to increase the size of the
recipient genomes. In the case of plasmids (or circular
DNA), this mechanism can result in their complete integration into the chromosome of the recipient cell. HFIR can
lead to the integration of fragments of relatively large size
(>1,000 bp). Experiments have shown that the effectiveness
of HFIR is relatively low. However, it can significantly
increase when more than one area of strong similarity are
shared by the exogenous and host DNA (for additional
details on HFIR, see Thomas and Nielsen 2005).
Irrespective of the mechanism of recombination
involved, the integration of exogenous DNA into the
genome of the host (Fig. 12.4e) or its maintenance as an
autonomous genetic element (Fig. 12.4f) do not mean that
the HGT has been successful. Indeed, the long-term persistence of the exogenous DNA in populations depends on
several factors (Fig. 12.4g), such as possible deleterious
effects resulting from its integration. Indeed, depending on
its location, the integration of the exogenous DNA can lead
to the disruption of important genes (or groups of genes or
operons) and thus cause deleterious effects on the recipient
cell and its offspring. In this case, due to natural selection,
the transferred DNA will disappear rapidly at the same time
as the cells that carry them. Stochastic phenomena* can
also lead to the disappearance of the exogenous DNA more
or less rapidly even if it carries alleles or genes conferring an
advantage to the receiving cell. Finally, natural selection
determines the long-term persistence of the exogenous
DNA in populations.
In conclusion, to be successful, HGT must go throughout each of these steps, and therefore, only a minority
succeeds. This means that there is a large difference
between the number of HGT events measured in terms of
amount of exogenous DNA entering into cells and the
number of HGT events that can be detected in presentday microbial genomes. These two concepts are often
wrongly confused.
12.3 Detection
The detection and quantification of HGT has been a hotly
debated issue in the scientific community for many years.
Indeed, at the end of the 1990s, the analysis of the first
12 Horizontal Gene Transfer in Microbial Ecosystems
453