been identified on pJP 4. In addition to these plasmids,
several others have been identified. Based on sequence
similarities observed between them, it was suggested that
they may derive from a common ancestor (van der Meer
et al. 1992). This hypothesis was later reinforced by the
observation of independent recruitment of diverse gene
cassettes during the assembly of 2,4-D-degrading plasmids
in different bacterial strains (Vallaeys et al. 1999). It was
also shown that genetic recombination mediated by
transposable elements, insertion sequences (ISs) being their
simplest representative, played an important role in the
construction of pesticide-degrading pathways. These
transposable elements play the role of shuttle for degrading
genes favoring the construction of catabolic operon
(Box 16.2).
However, whatever the transfer mechanism involved,
successful transfer of pesticide-degrading genes between
different populations of soil-degrading community does not
necessarily mean that transferred genes are expressed in the
host. Indeed if chromosomal-borne regulatory elements
are not transferred to the new host, the expression of
pesticide-degrading genes might be compromised. In addition,
following HGT structural modifications of catabolic plasmid
to adapt to genetic environment of the host might also alter the
expression of pesticide-degrading genes. In that way, several
observations suggest that catabolic-plasmid dispersion
among different populations of the bacterial community is
accompanied by its structural and genetic diversification (van
der Meer et al. 1992). It has been demonstrated that different
catabolic plasmids, in particular those involved in the
degradation of halogenated aromatic compounds, are sharing
important sequence similarities. This observation reveals the
existence of conserved sequences, notably those involved in
the degradation. Recently, fine analyses of data issued from
large-scale sequencing program of the full genome of numerous microorganisms allowed the identification of those
conserved sequences which are often part of ICE elements
referring to group of mobile DNA elements, which are known
as conjugative transposons or plasmids or genomic islands
(van der Meer and Sentchilo 2003). These components have
particularly well been observed for clc element coding for
chlorobenzoate and chlorocatechol degradation. Indeed,
Springael et al. (2001) showed that Tn4371-like mobile
elements are involved in the mobility of clc genes. Later on,
Gaillard and collaborators (2006) showed that the clc element
responsible for 3- and 4-chlorocatechol degradation was part
of a mobile genomic island in Pseudomonas sp. strain B13
which was not only showing catabolic properties but also
exhibiting pathogenic characters. These observations are
again in favor of an ancestral origin of the different catabolic
plasmids that evolved following their transfer to different
hosts to adapt to their lifestyle. These evolutions are often
mediated by mobile genetic elements that are providing
Box 16.2: Pesticide Biodegradation: Genetic Basis.
The Examples of Hormone Herbicides
and s-Triazines
Guy Soulas* and Fabrice Martin-Laurent
2,4-D and Hormone Herbicides
The genes tfdA, B, C, D, E, and F encode the transformation of 2,4-D into chloromaleylacetate further
transformed into maleylacetate by a chromosome
encoded maleylacetate reductase. They were first
identified on a plasmid pJP4 of a 2,4-D-degrading
strain Cupriavidus necator JMP 134 (formerly
Alcaligenes eutrophus and Ralstonia eutropha) (Don
and Pemberton 1985). pJP4 is a member of the IncP1
family of plasmids which may be viewed as among the
most potent vehicles for the spread and accumulation
of multiantibiotic resistance and many kinds of accessory genes between a broad range of host bacteria.
DNA signature analysis demonstrated that recombination events have allowed them to rapidly adapt to
changing bacterial hosts and environmental conditions
(Norberg et al. 2011; Sen et al. 2011). The first step in
the degradation of 2,4-D is performed by an
α-ketoglutarate-dependent
2,4-D
dioxygenase,
encoded by the tfdA and tfdA-like genes. The analyses
of the sequences in isolated strains have defined the
existence of four groups of tfdA genes: classes I, II,
and III in β- and g-Proteobacteria (Mcgowan et al.
1998) and tfdAa genes in some a-Proteobacteria (Itoh
et al. 2002). The continuous exposure of soil
microcosms to different hormone herbicides produced
an impressive variety of new tfdA gene-related
sequences (Gazitu ´a et al. 2010). The abundance and
diversity of these sequences in soils may be explained
by the role of α-ketoglutarate dioxygenases in catabolism of natural, more common, compounds (Hogan
et al. 1997). The product of the tfdB genes performs
the crucial step responsible for the initial hydroxylation of the benzene ring. It catalyzes the FADdependent oxidative hydroxylation of 2,4-DCP and
its homologues, in the presence of O 2 and NADPH/
NADH as an electron donor. Many chlorophenol
hydroxylases have been isolated. Most of them display
high activity towards 2,4-DCP and 4-chloro-2methylphenol. A novel tfdB gene, designated as tfdBJLU, was identified (Lu et al. 2011). The gene product
shows only moderate sequence identity (48 % identity)
with other known TfdB proteins. TfdB-JLU exhibited
monooxygenase activity towards many chlorinated
phenols with the highest activity towards
(continued)
16 Applied Microbial Ecology and Bioremediation
693
several others have been identified. Based on sequence
similarities observed between them, it was suggested that
they may derive from a common ancestor (van der Meer
et al. 1992). This hypothesis was later reinforced by the
observation of independent recruitment of diverse gene
cassettes during the assembly of 2,4-D-degrading plasmids
in different bacterial strains (Vallaeys et al. 1999). It was
also shown that genetic recombination mediated by
transposable elements, insertion sequences (ISs) being their
simplest representative, played an important role in the
construction of pesticide-degrading pathways. These
transposable elements play the role of shuttle for degrading
genes favoring the construction of catabolic operon
(Box 16.2).
However, whatever the transfer mechanism involved,
successful transfer of pesticide-degrading genes between
different populations of soil-degrading community does not
necessarily mean that transferred genes are expressed in the
host. Indeed if chromosomal-borne regulatory elements
are not transferred to the new host, the expression of
pesticide-degrading genes might be compromised. In addition,
following HGT structural modifications of catabolic plasmid
to adapt to genetic environment of the host might also alter the
expression of pesticide-degrading genes. In that way, several
observations suggest that catabolic-plasmid dispersion
among different populations of the bacterial community is
accompanied by its structural and genetic diversification (van
der Meer et al. 1992). It has been demonstrated that different
catabolic plasmids, in particular those involved in the
degradation of halogenated aromatic compounds, are sharing
important sequence similarities. This observation reveals the
existence of conserved sequences, notably those involved in
the degradation. Recently, fine analyses of data issued from
large-scale sequencing program of the full genome of numerous microorganisms allowed the identification of those
conserved sequences which are often part of ICE elements
referring to group of mobile DNA elements, which are known
as conjugative transposons or plasmids or genomic islands
(van der Meer and Sentchilo 2003). These components have
particularly well been observed for clc element coding for
chlorobenzoate and chlorocatechol degradation. Indeed,
Springael et al. (2001) showed that Tn4371-like mobile
elements are involved in the mobility of clc genes. Later on,
Gaillard and collaborators (2006) showed that the clc element
responsible for 3- and 4-chlorocatechol degradation was part
of a mobile genomic island in Pseudomonas sp. strain B13
which was not only showing catabolic properties but also
exhibiting pathogenic characters. These observations are
again in favor of an ancestral origin of the different catabolic
plasmids that evolved following their transfer to different
hosts to adapt to their lifestyle. These evolutions are often
mediated by mobile genetic elements that are providing
Box 16.2: Pesticide Biodegradation: Genetic Basis.
The Examples of Hormone Herbicides
and s-Triazines
Guy Soulas* and Fabrice Martin-Laurent
2,4-D and Hormone Herbicides
The genes tfdA, B, C, D, E, and F encode the transformation of 2,4-D into chloromaleylacetate further
transformed into maleylacetate by a chromosome
encoded maleylacetate reductase. They were first
identified on a plasmid pJP4 of a 2,4-D-degrading
strain Cupriavidus necator JMP 134 (formerly
Alcaligenes eutrophus and Ralstonia eutropha) (Don
and Pemberton 1985). pJP4 is a member of the IncP1
family of plasmids which may be viewed as among the
most potent vehicles for the spread and accumulation
of multiantibiotic resistance and many kinds of accessory genes between a broad range of host bacteria.
DNA signature analysis demonstrated that recombination events have allowed them to rapidly adapt to
changing bacterial hosts and environmental conditions
(Norberg et al. 2011; Sen et al. 2011). The first step in
the degradation of 2,4-D is performed by an
α-ketoglutarate-dependent
2,4-D
dioxygenase,
encoded by the tfdA and tfdA-like genes. The analyses
of the sequences in isolated strains have defined the
existence of four groups of tfdA genes: classes I, II,
and III in β- and g-Proteobacteria (Mcgowan et al.
1998) and tfdAa genes in some a-Proteobacteria (Itoh
et al. 2002). The continuous exposure of soil
microcosms to different hormone herbicides produced
an impressive variety of new tfdA gene-related
sequences (Gazitu ´a et al. 2010). The abundance and
diversity of these sequences in soils may be explained
by the role of α-ketoglutarate dioxygenases in catabolism of natural, more common, compounds (Hogan
et al. 1997). The product of the tfdB genes performs
the crucial step responsible for the initial hydroxylation of the benzene ring. It catalyzes the FADdependent oxidative hydroxylation of 2,4-DCP and
its homologues, in the presence of O 2 and NADPH/
NADH as an electron donor. Many chlorophenol
hydroxylases have been isolated. Most of them display
high activity towards 2,4-DCP and 4-chloro-2methylphenol. A novel tfdB gene, designated as tfdBJLU, was identified (Lu et al. 2011). The gene product
shows only moderate sequence identity (48 % identity)
with other known TfdB proteins. TfdB-JLU exhibited
monooxygenase activity towards many chlorinated
phenols with the highest activity towards
(continued)
16 Applied Microbial Ecology and Bioremediation
693