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Applied and Environmental Microbiology, September 1999, p. 3901-3907, Vol. 65, No. 9
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Construction of Environmental DNA Libraries in
Escherichia coli and Screening for the Presence of Genes
Conferring Utilization of 4-Hydroxybutyrate
Anke
Henne,1
Rolf
Daniel,1,*
Ruth A.
Schmitz,1 and
Gerhard
Gottschalk1,2
Abteilung Allgemeine
Mikrobiologie1 and Göttingen
Genomics Laboratory,2 Institut für
Mikrobiologie und Genetik der Georg-August-Universität, 37077 Göttingen, Germany
Received 13 May 1999/Accepted 1 July 1999
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ABSTRACT |
Environmental DNA libraries from three different soil samples were
constructed. The average insert size was 5 to 8 kb and the percentage
of plasmids with inserts was approximately 80%. The recombinant
Escherichia coli strains (approximately 930,000) were
screened for 4-hydroxybutyrate utilization. Thirty-six positive E. coli clones were obtained during the initial screen, and
five of them contained a recombinant plasmid (pAH1 to pAH5) which
conferred a stable 4-hydroxybutyrate-positive phenotype. These E. coli clones were studied further. All five were able to grow with
4-hydroxybutyrate as sole carbon and energy source and exhibited
4-hydroxybutyrate dehydrogenase activity in crude extracts. Sequencing
of pAH5 revealed a gene homologous to the gbd gene of
Ralstonia eutropha, which encodes a 4-hydroxybutyrate
dehydrogenase. Two other genes (orf1 and orf6)
conferring utilization of 4-hydroxybutyrate were identified during
subcloning and sequencing of the inserts of pAH1 and pAH3. The deduced
orf1 gene product showed similarities to members of the
DedA family of proteins. The sequence of the deduced orf6 gene product harbors the fingerprint pattern of enoyl-coenzyme A
hydratases/isomerases. The other sequenced inserts of the plasmids recovered from the positive clones revealed no significant similarity to any other gene or gene product whose sequence is available in the
National Center for Biotechnology Information databases.
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INTRODUCTION |
Naturally occurring assemblages of
microorganisms often encompass a bewildering array of physiological,
metabolic, and genetic diversity. In fact, it has been estimated that
>99% of microorganisms observable in nature typically cannot be
cultivated by standard techniques (1). Thus, a large
fraction of the diversity in an environment is still unknown due to
difficulties in enriching and isolating microorganisms in pure culture.
Correspondingly, the diversity of enzymes catalyzing a certain reaction
is only partially known. The classical and cumbersome approach for
isolating enzymes from environmental samples is to enrich, isolate, and screen a wide variety of microorganisms for the desired enzyme activity. The enzyme is then recovered from the identified organism. An
alternative approach is to use the genetic diversity of the microorganisms in a certain environment as a whole to encounter previously unknown genes and gene products for various purposes. One
way to exploit the genetic diversity of various environments is the
construction of DNA libraries. The DNA used for the preparation of the
libraries is isolated from different soil samples without the culturing
of the organisms present. The DNA isolation methods for soils and
sediments are based either on recovery of bacterial cells and
subsequent lysis (14, 26) or on direct lysis of cells in the
sample followed by DNA purification (29). Higher yields of
DNA from soils and sediments are usually obtained with the direct lysis
method, because nonbacterial and extracellular DNA is also extracted
(24).
The main goal of this study was to investigate the potential of the
prepared libraries and to test the accessibility of the genetic
diversity in an environment by direct cloning of environmental DNA. In
this basic study, the DNA was prepared by the direct lysis method, and
environmental libraries were constructed using Escherichia coli as the host. Subsequently, the libraries were screened for the presence of genes conferring the utilization of 4-hydroxybutyrate. E. coli is unable to use 4-hydroxybutyrate as a carbon and
energy source for growth (28). Nevertheless, the organism
possesses two different coenzyme A (CoA)-independent succinate
semialdehyde dehydrogenases, which directly catalyze the oxidation of
succinate semialdehyde to succinate. These enzymes are involved in the
catabolism of 
-aminobutyric acid or of
p-hydroxyphenylvaleric acid (11, 12). One of the
succinate semialdehyde dehydrogenases is produced if succinate
semialdehyde is present (12). Therefore, the ability of
E. coli to grow with 4-hydroxybutyrate depends only on the presence and expression of a gene conferring 4-hydroxybutyrate dehydrogenase activity. The only known genes encoding a
4-hydroxybutyrate dehydrogenase are from Clostridium
kluyveri (4hbd) (23) and Ralstonia
eutropha (gbd) (28). The enzymes participate
in succinate plus ethanol fermentation and in 4-hydroxybutyrate
catabolism, respectively.
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MATERIALS AND METHODS |
Sample sites, bacterial strains, and plasmids.
For the
construction of environmental DNA libraries, soil samples from a sugar
beet field near Göttingen, Germany, a meadow near Northeim,
Germany, and the valley of the river Nieme, Germany, were collected.
E. coli DH5
(2) was used as host, and the
plasmid pBluescript SK+ (pSK+) (Stratagene, San
Diego, Calif.) was employed as vector for the cloning experiments.
E. coli JM109/pCK1, containing and expressing the gene
encoding 4-hydroxybutyrate dehydrogenase of C. kluyveri (23), was used as the positive control for growth
experiments and enzymatic analysis.
Media and growth conditions.
E. coli was routinely
grown in Luria-Bertani medium at 30°C (2). Tetrazolium
indicator plates (4) containing 4-hydroxybutyrate as test
substrate were employed for the screening procedure. The indicator
plates contained the following (grams per liter): sodium 4-hydroxybutyrate, 4.0; K2HPO4, 3.0;
KH2PO4, 7.0; proteose peptone, 2.0;
MgSO4, 0.1; and 2,3,5-triphenyl tetrazolium chloride,
0.025. Utilization of 4-hydroxybutyrate (4 g/liter) as a carbon source for recombinant E. coli strains was tested in M9 medium
(19) supplemented with a small amount of yeast extract (0.2 g/liter), MgSO4 (2 mM), and CaCl2 (0.1 mM). All
growth media for E. coli strains harboring plasmids also
contained 100 µg of ampicillin/ml to maintain the presence of the plasmids.
Preparation of cell extracts.
Cells at the stationary growth
phase from 500-ml cultures were harvested by centrifugation at
6,000 × g for 20 min, washed once with 100 mM
potassium phosphate buffer (pH 8.0), and resuspended in 2 to 3 ml of
the same buffer. The cells were disrupted by a 1-min sonication/ml of
sample in a type MK2 ultrasonic disintegrator with an amplitude of 14 µm. Sonication was done in periods of 15 s each, followed by a
break of 15 s. During this procedure the samples were cooled. The
extract was cleared by centrifugation at 16,000 × g
for 30 min at 4°C.
Enzyme assays.
4-Hydroxybutyrate dehydrogenase was assayed
at 30°C in a 97 mM 2-amino-2-methyl-1,3-propanediol-HCl buffer (pH
8.5), containing 1 mM NAD+ and 20 mM 4-hydroxybutyrate
(28). The reaction was started by the addition of
4-hydroxybutyrate and monitored at 334 nm (A334 = 6.3 mM
1 · cm1). For
determination of 3-hydroxybutyrate dehydrogenase activity 4-hydroxybutyrate was replaced by the same amount of racemic
3-hydroxybutyrate. Protein concentrations were measured by the method
of Bradford (6) with bovine serum albumin as a standard. All
enzyme activities are expressed according to the formula
micromoles/(minutes × milligrams of protein).
Molecular procedures.
The DNA isolation from soil samples
was based on the direct lysis method of Zhou et al. (29).
Fifty grams of each environmental sample was mixed with 135 ml of DNA
extraction buffer (100 mM Tris-HCl [pH 8.0], 100 mM sodium EDTA, 100 mM sodium phosphate, 1.5 M NaCl, 1% [wt/vol] cetyltrimethylammonium
bromide) and 1 ml of proteinase K (10 mg/ml) in GS3 tubes by horizontal
shaking at 225 rpm for 30 min at 37°C. Next, 15 ml of 20% (wt/vol)
sodium dodecyl sulfate was added and the samples were incubated in a 65°C water bath for 2 h with gentle end-over-end inversion every 15 to 20 min. After centrifugation at 6,000 × g for 10 min at room temperature, the resulting supernatants were transferred into new GS3 tubes. The remaining soil pellets were extracted two more
times by suspending them in 45 ml of extraction buffer and 5 ml of 20%
sodium dodecyl sulfate. The subsequent incubation and centrifugation
were done as described above. Supernatants from all extraction steps
were combined and mixed with an equal volume of chloroform-isoamyl
alcohol (24:1 [vol/vol]). The aqueous phase was recovered by
centrifugation, and the DNA was precipitated with 0.6 volume of
isopropanol at room temperature for 1 h. A pellet of crude nucleic
acids was obtained by centrifugation at 9,000 × g for
20 min. After washing with 70% (vol/vol) ethanol, the DNA was
resuspended in 2 to 4 ml of deionized water. The final purification of
the DNA and the removal of coextracted humic substances were performed
with the Wizard Plus Minipreps DNA Purification System (Promega,
Heidelberg, Germany). The purified environmental DNA was partially
digested with BamHI or Sau3AI and, in order to
avoid cloning of very small DNA fragments, size fractionated by sucrose
density centrifugation (10 to 40% [wt/vol]). Fractions containing
DNA fragments of >2 kb were ligated into BamHI-digested pSK+ and the products were then transformed into E. coli DH5. This strain was employed for maintenance and
amplification of the environmental DNA libraries. All other
manipulations of DNA, PCR, and transformation of plasmids into E. coli were done according to routine procedures (2). The
Göttingen Genomics Laboratory (Göttingen, Germany) determined the DNA sequences. Sequence analysis was performed with the
Genetics Computer Group software package (10).
Nucleotide sequence accession numbers.
The nucleotide
sequences of the inserts of pAH1, pAH5, and pAH6 have been deposited in
the GenBank database under accession nos. AF148264 to AF148266.
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RESULTS AND DISCUSSION |
Construction of environmental DNA libraries.
Three different
soil samples (from a meadow, a sugar beet field, and the valley of the
river Nieme) were used for the construction of environmental DNA
libraries. The DNA was isolated from the samples by direct lysis of
microorganisms present without previous enrichment or extraction of
microbial cells. The extraction of DNA from the three different soils
resulted in coextraction of other soil components, which caused a
brownish color in the crude DNA solutions obtained. This color
indicates the presence of humic acids, which are typically coextracted
during direct preparation of DNA from soils (25). Further
purification of the DNA with the Wizard Plus Minipreps DNA Purification
System resulted in an almost complete decoloring of the DNA extracts.
Approximately 15 µg of DNA per g of soil was obtained. This yield is
in the same range as that described for the isolation of DNA from other soils (27, 29). The purified DNA was partially digested and size fractionated. DNA fragments of >2 kb were ligated into
pSK+ and then transformed into E. coli (see
Materials and Methods). Approximately 2,000 recombinant E. coli strains per µg of isolated soil DNA were obtained. The low
yield was probably caused by humic substances, which remain in the
purified environmental DNA and interfere with the restriction digestion
or the ligation reaction (25). The quality of the three
different environmental libraries produced was controlled by
determination of the average insert size and the percentage of
recombinant plasmids containing inserts. The three libraries revealed
average insert sizes of 5 to 8 kb. The percentage of plasmids
containing inserts was approximately 80%. No significant differences
between the three different soils were observed during the preparation
of the libraries.
Screening for genes conferring 4-hydroxybutyrate dehydrogenase
activity.
To test the potential of the environmental libraries,
the recombinant E. coli strains of three different libraries
were screened for utilization of 4-hydroxybutyrate. Since E. coli has two CoA-independent succinate semialdehyde
dehydrogenases, the use of 4-hydroxybutyrate as carbon and energy
source depends only on the presence and heterologous expression of a
4-hydroxybutyrate dehydrogenase-encoding gene. The screening was
performed on tetrazolium indicator plates (4) containing
4-hydroxybutyrate as test substrate. Tetrazolium in its oxidized state
is soluble in water and appears colorless or faintly yellow in
solution. Upon oxidation of the test substrate, it is reduced. This
yields to the formation of a insoluble deep red formazan, which is
precipitated in the cells. The reduction of tetrazolium is a result of
electrons passing from the test substrate, through the enzymatic
machinery of central metabolism, the electron transport chain, and
ultimately on to tetrazolium (4). Thus, E. coli
colonies capable of catabolizing 4-hydroxybutyrate reduce tetrazolium
and produce a deep red formazan, whereas colonies failing to catabolize
4-hydroxybutyrate remain uncolored.
To estimate the number of tested
E. coli clones and to
identify positive clones, simultaneously, the recombinant
E. coli strains
were directly plated on tetrazolium indicator plates
after transformation
of the environmental libraries. Thirty-six of
approximately 930,000
E. coli clones were positive during
the initial screen (Table
1). Most of
these clones
28
were obtained from library I, but
the time necessary
for the appearance of the phenotype was much
longer than for positive
clones of the other two libraries (Table
1). To confirm the
4-hydroxybutyrate-positive phenotype of the
clones, the recombinant
plasmids were isolated and retransformed
into
E. coli and
the resulting
E. coli strains were screened again
on
tetrazolium indicator plates containing 4-hydroxybutyrate as
an
additional carbon source. Only five different recombinant plasmids,
designated pAH1 to pAH5, conferred a stable 4-hydroxybutyrate-positive
phenotype to the resulting recombinant
E. coli strains.
Since
all 36 initial clones harbored plasmids with inserts, the high
percentage of false-positive clones was not caused by plasmid
loss.
Sometimes the appearance of false-positive colonies on tetrazolium
indicator plates is due to crossfeeding by positive clones, which
excrete catabolism intermediates in the culture medium (
4).
Three of the plasmids conferring a stable phenotype were obtained
from
library I, one was obtained from library II, and one was
obtained from
library III (Table
1). The insert sizes of pAH1
to pAH5 were in the
range of 1,000 to 4,500 bp (Table
2). The
corresponding
E. coli strains (
E. coli/pAH1 to
E. coli/pAH5) were
studied further.
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TABLE 2.
Characterization of pAH1 to pAH5 and the corresponding
E. coli clones: insert sizes, growth rates with
4-hydroxybutyrate as sole carbon and energy source, and specific
activities of 4-hydroxybutyrate and 3-hydroxybutyrate dehydrogenase in
crude extracts
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Physiological and biochemical characterization of the
4-hydroxybutyrate-positive E. coli clones.
The five
positive E. coli clones obtained after the screening
procedure were tested for growth in M9 medium containing
4-hydroxybutyrate as the sole carbon and energy source. In contrast to
the negative control, E. coli/pSK+, which
harbors the plasmid used as cloning vector, all five recombinant E. coli strains showed growth under these conditions. One
clone (E. coli/pAH1) revealed a similar growth rate and the
other four had a slower growth rate than the positive control E. coli JM109/pCK1, which harbors the 4hbd gene from
C. kluyveri (Table 2). Enzymatic analysis revealed
4-hydroxybutyrate dehydrogenase activity in crude extracts of all
recombinant E. coli strains (Table 2). The recorded
activities of E. coli/pAH2 to E. coli/pAH4 (0.04 U/mg) were lower than the one in crude extracts of E. coli
JM109/pCK1 (0.12 U/mg). The activity of E. coli/pAH5 was
slightly higher than that of the positive control. E. coli/pAH1, exhibiting a growth rate similar to that of the
positive control, showed in crude extracts the highest specific
4-hydroxybutyrate dehydrogenase activity of all tested strains (0.35 U/mg). The four clones exhibiting a slow growth rate on
4-hydroxybutyrate also showed 3-hydroxybutyrate dehydrogenase activity,
whereas E. coli/pAH1 revealed no significant activity (Table
2). Thus, the 4-hydroxybutyrate-positive phenotype of E. coli/pAH2 to E. coli/pAH5 might be due to a side
activity of a 3-hydroxybutyrate dehydrogenase.
Molecular analysis.
The inserts of pAH1 to pAH5 were sequenced
and compared to the sequences in the National Center for Biotechnology
Information (NCBI) databases. The only genes encoding a
4-hydroxybutyrate dehydrogenase available in the databases are from
C. kluyveri (4hbd) and R. eutropha
(gbd) (23, 28). The 4hbd gene (1,116 bp) and the gbd gene (1,146 bp) encode polypeptides of 371 and 382 amino acids with predicted molecular masses of 41,755 and 40,495 Da, respectively. Both enzymes belong to the family of type III
alcohol dehydrogenases, which are also known as iron-containing dehydrogenases. This family is very heterogeneous and distinct from the
long-chain zinc-containing (type I) or short-chain zinc-lacking (type
II) enzymes (for a review, see reference 21).
Sequencing of the 3,211-bp insert of pAH5 (Fig.
1C) revealed an open reading frame (1,137 bp) which is very similar to the
gbd gene of
R. eutropha. Therefore, that open reading frame was
also designated
gbd. The presumptive gene is preceded by a weak
potential
ribosome binding site, appropriately spaced from the
start codon (Fig.
2). The deduced gene product (378 amino
acids)
with a predicted molecular mass of 39,324 Da is 69.8% identical
(76.7% similar) to 4-hydroxybutyrate dehydrogenase of
R. eutropha.
The
gbd gene product also revealed homology
to the 4-hydroxybutyrate
dehydrogenase of
C. kluyveri
(32.3% identity; 41.0% similarity)
and to other type III alcohol
dehydrogenases, including, e.g.,
Adh2 of
Zymomonas mobilis
(
8), DhaT of
Citrobacter freundii (
9),
and FucO of
E. coli (
7). No significant
similarities
to type I and type II alcohol dehydrogenases were found.
For the
detection of type III alcohol dehydrogenases, two specific
fingerprint
patterns are available in the PROSITE database
(
13). The first
one is
[STALIV]-[LIVF]-x-[DE]-x(6,7)-P-x(4)-[ALIV]-x-[GST]-x(2)-D-[TAIVM]-[LIVMF]-x(4)-E
and the second one is
[GSW]-x-[LIVTSACD]-[GH]-x(2)-[GSAE]-[GSHYQ]
- x - [LIVTP] - [GAST] - [GAS] - x(3) - [LIVMT] - x - [HNS] -[GA]-x-[GTAC].
The
gbd gene product showed both fingerprint patterns (amino
acids
172 to 200 and 258 to 279), except that the second one was not
fully retained (Fig.
2). 4-Hydroxybutyrate dehydrogenase requires
NAD(H) as a cofactor, but the highly conserved NAD(H) binding
fingerprint pattern G-X-G-X-X-G (
15) was not present in the
amino acid sequence. This is also characteristic for most type
III
alcohol dehydrogenases. To confirm that
gbd encodes a
4-hydroxybutyrate
dehydrogenase, the gene was subcloned. The resulting
E. coli strain
exhibited 4-hydroxybutyrate dehydrogenase
activity (data not shown).
Thus,
gbd encodes a
4-hydroxybutyrate dehydrogenase.
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FIG. 1.
(A) Restriction map of the insert of pAH1. Arrow
represents length, location, and orientation of the orf1
gene. (B) Restriction map of the insert of pAH3 and localization of the
insert of pAH6. Arrow represents length, location, and orientation of
the orf6 gene. (C) Restriction map of the insert of pAH5.
Arrow represents length, location, and orientation of the
gbd gene.
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FIG. 2.
Partial nucleotide sequence of the insert of pAH5. Only
one strand is shown. The gene encoding 4-hydroxybutyrate dehydrogenase
(gbd) has been translated by using the one-letter amino acid
code; amino acid symbols are written below the first nucleotides of the
corresponding codons. Putative ribosome binding site is underlined. The
two conserved regions of the protein, which match the fingerprint
patterns for type III alcohol dehydrogenases, are boxed. Matching amino
acids of the consensus sequences for both regions according to the
PROSITE database (13) are given in bold letters above the
DNA sequence. The sequence of the gbd gene has been
submitted to GenBank under accession no. AF148264.
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E. coli/pAH1 exhibited the highest 4-hydroxybutyrate
dehydrogenase activity and harbored the plasmid with the smallest
insert
(1,002 bp). DNA sequence analysis of the insert revealed one
potential
gene, designated
orf1, within the sequence (Fig.
1A). A potential
ribosome binding site, appropriately spaced from the
start codon,
preceded the presumptive gene (Fig.
3). The
orf1 gene (678 bp)
codes for 225 amino acids with a predicted molecular mass of 23,603
Da.
The amino acid sequence deduced from
orf1 was compared with
deduced amino acid sequences available in the NCBI databases.
This
search showed similarities (44.4 and 33.0% identity and 56.1
and
40.6% similarity) to hypothetical transmembrane proteins from
Synechocystis PCC6803 (SLR0305; 22,200 Da) (
16)
and
E. coli (YdjZ; 26,200 Da) (
3), respectively,
which are members of the
DedA family of proteins. The members of this
family contain multiple
predicted transmembrane regions and have not
been functionally
characterized so far. Hydropathy analysis
(
18) of the deduced
orf1 protein sequence also
revealed four to five hydrophobic and
probably membrane-spanning
regions (data not shown).
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FIG. 3.
Nucleotide sequence of the insert of pAH1. Only one
strand is shown. The orf1 gene has been translated by using
the one-letter amino acid code; amino acid symbols are written below
the first nucleotides of the corresponding codons. Putative ribosome
binding site is underlined. The sequence of the orf1 gene
has been submitted to GenBank under accession no. AF148265.
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The sequences of the inserts of pAH2 to pAH4 revealed no significant
similarity to genes encoding 4-hydroxybutyrate dehydrogenases
or to any
other sequence available in the databases, except for
a part of the
insert of pAH3 (see below). This result indicates
that the constructed
DNA libraries harbor genes from a wide variety
of microorganisms, which
mostly have not been investigated or
even cultivated so
far.
To identify the DNA regions on pAH2 to pAH4 which are responsible for
the utilization of 4-hydroxybutyrate by the corresponding
recombinant
E. coli strains, the inserts were partially subcloned
by
restriction digestion with various enzymes or by PCR by using
primers
derived from sequencing and subsequent ligation into pSK
+.
The resulting constructs were transformed into
E. coli, and
the recombinant
E. coli strains were screened again on
tetrazolium
indicator plates containing 4-hydroxybutyrate as an
additional
carbon source. This method was successful for the insert of
pAH3.
The plasmid recovered from the corresponding positive
E. coli strain was designated pAH6. All attempts to subclone a DNA
region
conferring 4-hydroxybutyrate utilization of pAH2 and pAH4
failed.
Both plasmids were not studied here any further because of the
low 4-hydroxybutyrate dehydrogenase activities in crude extracts
of the
corresponding recombinant
E. coli strains.
The plasmid pAH6 contained a 913-bp
SacI-
BamHI
insert (Fig.
1B). The corresponding recombinant
E. coli
strain (
E. coli/pAH6)
was able to grow in M9 medium
containing 4-hydroxybutyrate as
the sole carbon and energy source and
showed 4-hydroxybutyrate
dehydrogenase activity in crude extracts in
the same range as
for the original clone (
E. coli/pAH3)
(data not shown). The sequence
of the insert of pAH6 (Fig.
4) harbored a single large open reading
frame (852 bp) designated
orf6 (Fig.
1B) which was preceded
by
a potential ribosome binding site, appropriately spaced from the
start codon (Fig.
4). The deduced gene product (283 amino acids),
with
a predicted molecular mass of 31,750 Da, showed the signature
pattern
for members of the enoyl-CoA hydratase/isomerase family
of proteins
(amino acids 126 to 146; Fig.
4). Enoyl-CoA hydratase
and enoyl-CoA
isomerase are both involved in fatty acid metabolism.
In
E. coli (gene
fadB) and
Pseudomonas fragi (gene
faoA), both
enzymes are part of a multifunctional enzyme
which contains both
a 3-hydroxyacyl-CoA dehydrogenase domain and a
3-hydroxybutyryl-CoA
epimerase domain (
20). Database
searches revealed a weak similarity
(34.8% identity; 40.7%
similarity) of Orf6 to the
crt gene product
of
Clostridium acetobutylicum. CrT (261 amino acids) is a
3-hydroxybutyryl-CoA
dehydratase (crotonase) involved in butyrate
formation (
5)
and is evolutionarily related to enoyl-CoA
hydratases/isomerases.
In addition, the
orf6 gene product
revealed 34.6% identity (48.1%
similarity) to the C-terminal region
of the 3-hydroxyacyl-CoA
dehydrogenase (HbD2) of
Archaeoglobus
fulgidus (
17). Sequence
analysis suggested the
participation of CoA in the enzyme reaction,
but the addition of CoA,
acetyl phosphate, ATP, or combinations
of these substrates to the assay
mixture had no significant effect
on 4-hydroxybutyrate dehydrogenase
activity.
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FIG. 4.
Nucleotide sequence of the insert of pAH6. Only one
strand is shown. The orf6 gene has been translated by using
the one-letter amino acid code; amino acid symbols are written below
the first nucleotides of the corresponding codons. Putative ribosome
binding site is underlined. The conserved region of the protein, which
matches the fingerprint pattern for enoyl-CoA hydratases/isomerases, is
boxed. Matching amino acids of the consensus sequence for this region
([LIVM]-[STA]-x-[LIVM]-[DENQRHSTA]-G-x(3)-[AG]
(3)-x(4)-[LIVMST]-x-[CSTA]-[DQHP]-[LIVMFY]) (13) are
given in bold letters above the DNA sequence. The sequence of the
orf6 gene has been submitted to GenBank under accession no.
AF148266.
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Since
E. coli/pAH1,
E. coli/pAH3 and the subclone
E. coli/pAH6 exhibited 4-hydroxybutyrate dehydrogenase
activity in crude
extracts, the
orf1 and
orf6
gene products may represent new types
of 4-hydroxybutyrate
dehydrogenases. Interestingly, the recorded
specific 4-hydroxybutyrate
dehydrogenase activities in crude extracts
of the strains containing
orf1 were threefold higher than those
in crude extracts of
the positive control,
E. coli/pCK1 (Table
2). Another
possibility is that the
orf1 and
orf6 gene
products
facilitate the utilization of 4-hydroxybutyrate in a way that
is not yet understood. The characterization of the purified gene
products will unravel the function of both
enzymes.
The results presented show that it is possible to prepare DNA libraries
and to clone directly functional genes from environmental
soil samples.
To our knowledge, no other report of such an approach
has been
published. The cloning of genes from environmental soil
samples
described by other authors involved a PCR step, i.e.,
cloning of genes
encoding
-ketoacyl synthases (KS
) (
22)
or
16S rRNA (
1). The sequences of the primers used were derived
from conserved regions of known genes or protein families. Thus,
the
identification of entirely new genes or gene products by PCR-based
methods is very limited. Our direct cloning approach illustrates
another way to access and to exploit the immense pool of genes
from
microorganisms which have not been cultivated so far. The
existence of
sequence information prior to cloning is not required.
In addition, the
existing environmental libraries can be employed
for screening of
various targets. This has significant implications
for microbial
biotechnology in the
future.
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ACKNOWLEDGMENTS |
The work was supported by the Fonds der Chemischen Industrie and
by the Akademie der Wissenschaften, Göttingen, Germany.
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FOOTNOTES |
*
Corresponding author. Mailing address: Institut
für Mikrobiologie und Genetik der Georg-August-Universität,
Grisebachstr. 8, 37077 Göttingen, Germany. Phone: 49-551-393827. Fax: 49-551-393793. E-mail: rdaniel{at}gwdg.de.
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Applied and Environmental Microbiology, September 1999, p. 3901-3907, Vol. 65, No. 9
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Copyright © 1999, American Society for Microbiology. All rights reserved.
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Abstract
Introduction
