mobility, would be more adapted to survive in soil and to
colonize new ecological niches.
In rhizospheric Pseudomonas exhibiting antagonistic
activity toward fungal phytopathogens, the two-component
system GacA/GacS is involved in regulating the production
of secondary metabolites and the synthesis of exoenzymes
(chitinase, lipase, protease). Variants devoided of biocontrol
activity have mutations in gacA and gacS: point mutation,
insertion, and deletion. In some cases, revertants can be
observed (van den Broek et al. 2005). Strains mutated in
gacS display a shorter lag phase compared to the wild type.
In an environment like the rhizosphere, variants would be
more competitive and could adapt more easily to the heterogeneous and challenging rhizosphere ecosystem (van den
Broek et al. 2005).
9.4.3 Phase Change in Epigenetics Control
In contrast to the genetic mechanisms described
above, epigenetic regulation* of phase variation occurs
without modification of the DNA sequence. This involves
differentially methylated sequences in regulatory regions
of genes or operons that undergo phase variation operons.
The state of methylation of these sequences affects fixation
of a transcriptional regulator.
This epigenetic mechanism of phase variation was first
elucidated for the expression of pap (“pyelonephritisassociated”) pili among uropathogenic Escherichia coli.
In the “OFF” state, the global regulator Lrp is bound to
sites in the vicinity of the pap operon promoter, preventing
transcription. Transition to the “ON” state requires methylation of a GATC sequence present in the binding site;
methylation prevents binding of Lrp and allows the pap
operon to be expressed (Hernday et al. 2003).
Synthesis of pef pili in Salmonella typhimurium is also
regulated by methylation of specific sites in the promoter
region of the pef genes (Nicholson and Low 2000).
Historically, phase variation has been investigated mainly
in bacterial pathogens of humans and animals. However,
recent studies have shown that phase variation also occurs
in bacteria interacting with plants. When phase variation
involves proteins of the cell surface, it allows the bacterium
to evade the immune system. But it would be simplistic to
consider phase variation as a strategy intended solely to
evade the immune system. Phase variation can also modulate virulence; indeed, variants of R. solanacearum or
L. pneumophila are less virulent than the wild type (Poussier
et al. 2003). For these variants with reduced virulence, phase
variation could allow to save energy, preventing the cell to
synthesize some factors dispensable under certain
conditions. In other cases, the appearance of variants could
allow these cells to colonize new environments.
9.5
Antibiosis and Antibiotic Resistance*
The diversity of microorganisms has been estimated to range
between 10
3 and 10
6 taxa/g soil (Gans et al. 2005; Schloss
and Handelsman 2006). Among these, environmental
microorganisms compete for energy sources and nutrients.
Some organisms live symbiotically or coexist with other
species of microorganisms, many of which produce
antibiotics (Donadio et al. 2007). These are toxic molecules,
bactericidal or bacteriostatic, which limit the existence or the
number of other microorganisms in their neighborhood.
The number of different antibiotics from natural sources
is estimated at about 10
4 (Challis and Hopwood 2003).
However, only a small part or a few dozen of these
molecules are used for human and animal health including
antibiotics of synthetic origin, for example, as sulfonamides,
oxazolidinones, and quinolone (Table 9.6). Others are not
used for various reasons such as toxicity to the host or else
too short a lifetime in the body, problems that can be
circumvented by combinatorial chemistry (Fig. 9.18).
9.5.1 Biosynthesis of Antibiotics
The biosynthesis of polyketide antibiotics, aminoglycosides,
and peptides typically involves the enzymes of the family
polyketide synthase (PKS), glycosyltransferases (GT), and
nonribosomal peptide synthetases (NRPS). In bacteria, three
types of polyketide synthases (PKS I, II, III) have been
described: the PKS type I multifunctional enzymes are
organized into modules where each module has a specific
activity for the assembly of specific substrates to synthesize
ultimately the antibiotic. For example, for the synthesis of
erythromycin (Long et al. 2002), a molecule of propionate
and mevalonate is recognized by the adenylation domain
(AT), activated by binding to coenzyme A (CoA), and each
molecule is transferred to an transporter of acyl moieties or
acyl carrier protein (ACP). The condensation of the two
substrates that is accompanied by the release of a molecule
of CO 2 is catalyzed by another domain called keto-synthase
(KS). These activities are common to all modules of type I
PKS. The product of these reactions gives a keto acyl group
which may be reduced to an alcohol by a keto reductase
domain (KR), then dehydrated by a dehydratase domain
(DH), and finally reduced by an enoyl reductase domain
(ER), if they are present in the same module. Finally the
thioesterase domain (TE) catalyzes the final reaction by
cutting the thio-ester bond and thus releasing a free molecule
of lactone (Fig. 9.19). Among type II PKS enzyme, activities
are carried by different proteins that can iteratively catalyze
the biosynthesis of polyketides (Hopwood and Sherman
1990). The PKS type III or chalcone synthases lack an
320
P. Normand et al.
colonize new ecological niches.
In rhizospheric Pseudomonas exhibiting antagonistic
activity toward fungal phytopathogens, the two-component
system GacA/GacS is involved in regulating the production
of secondary metabolites and the synthesis of exoenzymes
(chitinase, lipase, protease). Variants devoided of biocontrol
activity have mutations in gacA and gacS: point mutation,
insertion, and deletion. In some cases, revertants can be
observed (van den Broek et al. 2005). Strains mutated in
gacS display a shorter lag phase compared to the wild type.
In an environment like the rhizosphere, variants would be
more competitive and could adapt more easily to the heterogeneous and challenging rhizosphere ecosystem (van den
Broek et al. 2005).
9.4.3 Phase Change in Epigenetics Control
In contrast to the genetic mechanisms described
above, epigenetic regulation* of phase variation occurs
without modification of the DNA sequence. This involves
differentially methylated sequences in regulatory regions
of genes or operons that undergo phase variation operons.
The state of methylation of these sequences affects fixation
of a transcriptional regulator.
This epigenetic mechanism of phase variation was first
elucidated for the expression of pap (“pyelonephritisassociated”) pili among uropathogenic Escherichia coli.
In the “OFF” state, the global regulator Lrp is bound to
sites in the vicinity of the pap operon promoter, preventing
transcription. Transition to the “ON” state requires methylation of a GATC sequence present in the binding site;
methylation prevents binding of Lrp and allows the pap
operon to be expressed (Hernday et al. 2003).
Synthesis of pef pili in Salmonella typhimurium is also
regulated by methylation of specific sites in the promoter
region of the pef genes (Nicholson and Low 2000).
Historically, phase variation has been investigated mainly
in bacterial pathogens of humans and animals. However,
recent studies have shown that phase variation also occurs
in bacteria interacting with plants. When phase variation
involves proteins of the cell surface, it allows the bacterium
to evade the immune system. But it would be simplistic to
consider phase variation as a strategy intended solely to
evade the immune system. Phase variation can also modulate virulence; indeed, variants of R. solanacearum or
L. pneumophila are less virulent than the wild type (Poussier
et al. 2003). For these variants with reduced virulence, phase
variation could allow to save energy, preventing the cell to
synthesize some factors dispensable under certain
conditions. In other cases, the appearance of variants could
allow these cells to colonize new environments.
9.5
Antibiosis and Antibiotic Resistance*
The diversity of microorganisms has been estimated to range
between 10
3 and 10
6 taxa/g soil (Gans et al. 2005; Schloss
and Handelsman 2006). Among these, environmental
microorganisms compete for energy sources and nutrients.
Some organisms live symbiotically or coexist with other
species of microorganisms, many of which produce
antibiotics (Donadio et al. 2007). These are toxic molecules,
bactericidal or bacteriostatic, which limit the existence or the
number of other microorganisms in their neighborhood.
The number of different antibiotics from natural sources
is estimated at about 10
4 (Challis and Hopwood 2003).
However, only a small part or a few dozen of these
molecules are used for human and animal health including
antibiotics of synthetic origin, for example, as sulfonamides,
oxazolidinones, and quinolone (Table 9.6). Others are not
used for various reasons such as toxicity to the host or else
too short a lifetime in the body, problems that can be
circumvented by combinatorial chemistry (Fig. 9.18).
9.5.1 Biosynthesis of Antibiotics
The biosynthesis of polyketide antibiotics, aminoglycosides,
and peptides typically involves the enzymes of the family
polyketide synthase (PKS), glycosyltransferases (GT), and
nonribosomal peptide synthetases (NRPS). In bacteria, three
types of polyketide synthases (PKS I, II, III) have been
described: the PKS type I multifunctional enzymes are
organized into modules where each module has a specific
activity for the assembly of specific substrates to synthesize
ultimately the antibiotic. For example, for the synthesis of
erythromycin (Long et al. 2002), a molecule of propionate
and mevalonate is recognized by the adenylation domain
(AT), activated by binding to coenzyme A (CoA), and each
molecule is transferred to an transporter of acyl moieties or
acyl carrier protein (ACP). The condensation of the two
substrates that is accompanied by the release of a molecule
of CO 2 is catalyzed by another domain called keto-synthase
(KS). These activities are common to all modules of type I
PKS. The product of these reactions gives a keto acyl group
which may be reduced to an alcohol by a keto reductase
domain (KR), then dehydrated by a dehydratase domain
(DH), and finally reduced by an enoyl reductase domain
(ER), if they are present in the same module. Finally the
thioesterase domain (TE) catalyzes the final reaction by
cutting the thio-ester bond and thus releasing a free molecule
of lactone (Fig. 9.19). Among type II PKS enzyme, activities
are carried by different proteins that can iteratively catalyze
the biosynthesis of polyketides (Hopwood and Sherman
1990). The PKS type III or chalcone synthases lack an
320
P. Normand et al.