Box 16.3 (continued)
dehydrochlorinase encoding gene linA whose products
are involved in the initial lindane dechlorination step
does not exhibit any sequence similarity with genes in
databases (Imai et al. 1991) in spite of the use of very
sensitive bioinformatics tools including PSI-BLAST
(cf. Sect. 17.7.5). These data can be seen as the first
indication of an unknown molecular origin of the linA
gene that led to the hypothesis of a molecular shuffling
to explain emergence of this gene in bacteria isolated
from different polluted sites. However, validation of
this hypothesis requires that bacterial populations
in nonpolluted soils do not contain a functional
(continued)
Box 16.3 (continued)
linA gene. It also requires presence in one or several
bacteria hosts of the various DNA fragments whose
shuffling could create this gene. Experimental
confirmation of this hypothesis led to define several
investigation steps that were applied to linA from
S. francense as models (Boubakri et al. 2006). Step 1:
Bioinformatics analysis of the linA gene to define
its structure. Step 2: Analysis of not polluted soil
metagenomes to detect presence of linA gene
fragments and concomitantly to confirm absence of
a complete and functional linA gene. Step 3: Experimental demonstration that a functional linA gene can
(continued)
Cl
Cl
Cl
Cl
Cl
Cl
HCl
HCl
+ HCl
HCl
HCl
HCl
HCl
HCl
NAD
+
NADH+H
+
H 2 O
H 2 O
H 2 O
H 2 O
O 2
O 2
O 2
HCl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
2GSH
2GSH
GS-SG+HCl
GS-SG+HCl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
OH
OH
OH
OH
OH
OH
HO
HO
HO
TCA
HO
HO
O
O
O
C
C
H 3 C
HO
HO
O
COOH
COOH
NAD
+
NADH+H
+
NADH+H
+
NAD
+
COOH
COOH
COOH
CO - CoA
CoA
CoA
CoA
COOH
COOH
COOH
COOH
COOH
CHO
C O
HO
HO
Spontaneous
Spontaneous
succinate
succinyl-CoA
Spontaneous
Spontaneous
Cl
Cl
Cl
Cl
OH
Cl
Cl
Cl
LinA
LinEb
LinE
LinA
LinB
LinB
LinD
LinE
LinF
LinF
LinJ
LinGH
LinEb
LinE
LinD
LinC
(LinX)
Upstream
Pathway
Downstream
Pathway
1
2
3
5
9
12
16
?
11
13
19
18
14
15
17
10
8
7
4
6
Dead-end
Dead-end
Box Fig. 16.6 Scheme of the degradation pathways of lindane in
Sphingobium
japonicum
UT26.
Enzymes:
LinA:
Dehydrochlorinase; LinB: halidohydrolase; LinC and LinX:
Dehydrogenases; LinD: Dechlorinase; LinE: Dioxygenase; LinF:
Maleylacetate reductase; in GHI: succinyl-CoA transferase; LinJ:
b-ketoadipyl-CoA thiolase. The enzymes of the “track upstream”
(“upstream pathway”) are expressed and constitutively active. 2,5DCHQ (8) then initiates the dowstream pathway by activation of the
LinR regulator that induces the expression of genes linD, linE, and
LinR (Nagata et al. 2007) (Copyright: Springer)
706
J.-C. Bertrand et al.
dehydrochlorinase encoding gene linA whose products
are involved in the initial lindane dechlorination step
does not exhibit any sequence similarity with genes in
databases (Imai et al. 1991) in spite of the use of very
sensitive bioinformatics tools including PSI-BLAST
(cf. Sect. 17.7.5). These data can be seen as the first
indication of an unknown molecular origin of the linA
gene that led to the hypothesis of a molecular shuffling
to explain emergence of this gene in bacteria isolated
from different polluted sites. However, validation of
this hypothesis requires that bacterial populations
in nonpolluted soils do not contain a functional
(continued)
Box 16.3 (continued)
linA gene. It also requires presence in one or several
bacteria hosts of the various DNA fragments whose
shuffling could create this gene. Experimental
confirmation of this hypothesis led to define several
investigation steps that were applied to linA from
S. francense as models (Boubakri et al. 2006). Step 1:
Bioinformatics analysis of the linA gene to define
its structure. Step 2: Analysis of not polluted soil
metagenomes to detect presence of linA gene
fragments and concomitantly to confirm absence of
a complete and functional linA gene. Step 3: Experimental demonstration that a functional linA gene can
(continued)
Cl
Cl
Cl
Cl
Cl
Cl
HCl
HCl
+ HCl
HCl
HCl
HCl
HCl
HCl
NAD
+
NADH+H
+
H 2 O
H 2 O
H 2 O
H 2 O
O 2
O 2
O 2
HCl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
2GSH
2GSH
GS-SG+HCl
GS-SG+HCl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
OH
OH
OH
OH
OH
OH
HO
HO
HO
TCA
HO
HO
O
O
O
C
C
H 3 C
HO
HO
O
COOH
COOH
NAD
+
NADH+H
+
NADH+H
+
NAD
+
COOH
COOH
COOH
CO - CoA
CoA
CoA
CoA
COOH
COOH
COOH
COOH
COOH
CHO
C O
HO
HO
Spontaneous
Spontaneous
succinate
succinyl-CoA
Spontaneous
Spontaneous
Cl
Cl
Cl
Cl
OH
Cl
Cl
Cl
LinA
LinEb
LinE
LinA
LinB
LinB
LinD
LinE
LinF
LinF
LinJ
LinGH
LinEb
LinE
LinD
LinC
(LinX)
Upstream
Pathway
Downstream
Pathway
1
2
3
5
9
12
16
?
11
13
19
18
14
15
17
10
8
7
4
6
Dead-end
Dead-end
Box Fig. 16.6 Scheme of the degradation pathways of lindane in
Sphingobium
japonicum
UT26.
Enzymes:
LinA:
Dehydrochlorinase; LinB: halidohydrolase; LinC and LinX:
Dehydrogenases; LinD: Dechlorinase; LinE: Dioxygenase; LinF:
Maleylacetate reductase; in GHI: succinyl-CoA transferase; LinJ:
b-ketoadipyl-CoA thiolase. The enzymes of the “track upstream”
(“upstream pathway”) are expressed and constitutively active. 2,5DCHQ (8) then initiates the dowstream pathway by activation of the
LinR regulator that induces the expression of genes linD, linE, and
LinR (Nagata et al. 2007) (Copyright: Springer)
706
J.-C. Bertrand et al.