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Journal of Bacteriology, March 2001, p. 1707-1715, Vol. 183, No. 5
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.5.1707-1715.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Anaerobic Initial Reaction of n-Alkanes in a
Denitrifying Bacterium: Evidence for (1-Methylpentyl)succinate as
Initial Product and for Involvement of an Organic Radical
in n-Hexane Metabolism
Ralf
Rabus,1,*
Heinz
Wilkes,2
Astrid
Behrends,1
Antje
Armstroff,2
Thomas
Fischer,2
Antonio J.
Pierik,3 and
Friedrich
Widdel1
Max-Planck-Institut für Marine
Mikrobiologie, D-28359 Bremen,1 Institut
für Erdöl und Organische Geochemie, Forschungszentrum
Jülich GmbH, D-52425 Jülich,2 and
Laboratorium für Mikrobiologie, Philipps
Universität, D-35032 Marburg,3 Germany
Received 7 August 2000/Accepted 6 December 2000
 |
ABSTRACT |
A novel type of denitrifying bacterium (strain HxN1) with the
capacity to oxidize n-alkanes anaerobically with nitrate as the electron acceptor to CO2 formed
(1-methylpentyl)succinate (MPS) during growth on n-hexane
as the only organic substrate under strict exclusion of air.
Identification of MPS by gas chromatography-mass spectrometry was based
on comparison with a synthetic standard. MPS was not formed during
anaerobic growth on n-hexanoate. Anaerobic growth with
[1-13C]n-hexane or
d14-n-hexane led to a
1-methylpentyl side chain in MPS with one 13C atom or 13 deuterium atoms, respectively. This indicates that the 1-methylpentyl
side chain originates directly from n-hexane. Electron
paramagnetic resonance spectroscopy revealed the presence of an organic
radical in n-hexane-grown cells but not in
n-hexanoate-grown cells. Results point at a mechanistic
similarity between the anaerobic initial reaction of
n-hexane and that of toluene, even though n-hexane is much less reactive; the described initial
reaction of toluene in anaerobic bacteria is an addition to fumarate
via a radical mechanism yielding benzylsuccinate. We conclude that n-hexane is activated at its second carbon atom by a
radical reaction and presumably added to fumarate as a cosubstrate,
yielding MPS as the first stable product. When
2,3-d2-fumarate was added to cultures growing
on unlabeled n-hexane, 3-d1-MPS
rather than 2,3-d2-MPS was detected, indicating
loss of one deuterium atom by an as yet unknown mechanism.
 |
INTRODUCTION |
Alkanes as metabolites from
organisms (10) and constituents of petroleum
(49) and its refined products are widespread compounds in
our environment. Containing exclusively apolar
-bonds, alkanes are
among the chemically least reactive compounds. Bacteria and fungi that
utilize alkanes as growth substrates in the presence of molecular
oxygen have been known for about 100 years (14, 15).
Aerobic microorganisms all initiate the metabolism of alkanes by
monooxygenase reactions. These enzymes generate a highly reactive oxygen species by partial reduction of O2, resulting in the
introduction of a hydroxyl group into the alkane molecule by a radical
mechanism (22, 51). The alkanol formed is further oxidized
and metabolized via the
-oxidation pathway.
It was shown only relatively recently that special types of bacteria,
which are physiologically and phylogenetically distinct from previously
described aerobic hydrocarbon-degrading microorganisms, degrade
n-alkanes under strict exclusion of oxygen.
n-Alkanes were anaerobically oxidized in pure cultures using
sulfate (2, 3, 41, 43) or nitrate (18) as the
electron acceptor or in enrichment cultures with sulfate
(16) or nitrate (13, 39). Also, anaerobic
conversion of long-chain n-alkanes to methane and
CO2 in associations of enriched bacteria and archaea was
demonstrated (4, 55). Oxidation of the isoprenoid-like
alkane 2,5,9,13-tetramethylpentadecane (pristane) was demonstrated in a
nitrate-reducing bacterial community (13). None of the
hitherto isolated alkane-degrading anaerobic bacteria utilize aromatic
hydrocarbons such as toluene, whereas anaerobic bacteria that degrade
aromatic hydrocarbons do not utilize alkanes (24).
First investigations into the anaerobic metabolism of
n-alkanes were conducted with two phylogenetically related
sulfate-reducing bacteria, strains Hxd3 and Pnd3 (3).
Adaptation studies and analysis of cellular fatty acids with strain
Hxd3 suggested that anaerobic degradation of alkanes does not occur via
desaturation to 1-alkenes, a questionable mechanism that has been
speculated about in some early studies on the possibility of anaerobic
n-alkane degradation (for an overview, see reference
3). Strain Hxd3 formed mainly C-odd cellular fatty acids
during growth with n-hexadecane and C-even cellular fatty
acids during growth with n-heptadecane. One explanation for
these fatty acid patterns was the assumption of an alteration in the
carbon chain length during the initial anaerobic reactions by a C-odd
carbon unit, e.g., by terminal addition of a one-carbon moiety. In
strain Pnd3, however, cellular fatty acids were mainly C-even upon
growth with C-even alkanes and mainly C-odd upon growth with C-odd
alkanes; in addition, unidentified fatty acids were formed. The
findings suggested different modes of initial reactions in the two
n-alkane-degrading sulfate-reducing strains
(3). Still, a common principle in the mechanism of initial
reactions of n-alkanes in both strains was considered by
assuming that the site of carbon addition may also be the subterminal position in the chain (3). In a third isolate of an
n-alkane-degrading sulfate-reducing bacterium (strain
AK-01), the n-alkanes serving as growth substrates
influenced the pattern of cellular fatty acids in a similar manner as
in strain Pnd3; in addition, 2-, 4-, and 6-methyl-branched fatty acids
were identified (44). By labeling studies, the methyl
branch of the fatty acids was shown to be the original terminal carbon
of the n-alkane, suggesting addition of a carbon compound to
the subterminal position (carbon-2) of the n-alkanes; the
carboxyl group was not derived from bicarbonate (44).
So far, no metabolites have been detected that could represent the
direct product of the initial anaerobic reaction of an n-alkane. The present study was undertaken to identify such
a metabolite and to gain insights into the mechanism of its formation. For the experiments, the recently isolated denitrifying strain HxN1
(18) was chosen. In contrast to other
n-alkane-degrading anaerobic bacteria, strain HxN1 grows
relatively rapidly (doubling time of 11 h under optimal conditions) and
does not adhere to the insoluble alkane phase, so that cells can be
harvested easily. Strain HxN1 utilizes n-alkanes with
relatively short chains (C6 through C8) that
are oxidized to CO2; other anaerobic
n-alkane-degrading strains grow preferentially with chain
lengths between C8 and C18. Recently,
two-dimensional gel electrophoresis of cell extracts of strain HxN1
revealed specific formation of proteins during growth on
n-hexane that were not formed on n-hexanoate.
These proteins were therefore supposed to be specifically involved in initial reaction steps of n-alkanes. In the N terminus, one
of these proteins exhibited a similarity to the small subunit (BssC) of
benzylsuccinate synthase in denitrifying bacteria (A. Behrends, P. Ehrenreich, J. Heider, T. Hurek, S. Ratering, and F. Widdel, unpublished data). This enzyme activates toluene anaerobically by addition of the methyl group to fumarate, yielding benzylsuccinate (24), and there is evidence for the involvement of a
glycyl radical in this reaction (17, 31; C. Leutwein,
A. J. Pierik and J. Heider, personal communication). Hence, we
expected a parallel between the mechanism of the initial reaction of
n-alkanes and that of toluene in anaerobic bacteria. Still,
a reaction of an alkane in the absence of oxygen would present a novel
type of biochemical mechanism, because a saturated hydrocarbon is much less reactive than toluene. In this paper, we report the identification of (1-methylpentyl)succinate (MPS) formed during strictly anaerobic growth of strain HxN1 with nitrate and with n-hexane as the
only organic substrate. Furthermore, an electron paramagnetic resonance (EPR) signal characteristic of a glycyl radical was detected in n-hexane-grown cells of strain HxN1. We therefore propose
the formation of MPS from n-hexane and fumarate via a
radical mechanism as the initial reaction in strain HxN1.
 |
MATERIALS AND METHODS |
Organism and cultivation.
The denitrifying strain HxN1 has
been subcultured since its isolation from an enrichment culture
(18). It was cultivated under anoxic conditions in
chemically defined, bicarbonate-buffered medium with nitrate (9 mM) as
the electron acceptor, as described previously (18, 38).
Freshly prepared sodium ascorbate (4 mM) was added as the reductant and
allowed to scavenge traces of oxygen by incubation for >1 day of the
medium before anaerobic inoculation (18). Cultures were
grown in stopper-sealed flat glass bottles (500 ml) containing 400 ml
of medium under a head space of N2-CO2 (90:10,
vol/vol). Since pure n-hexane is inhibitory, it was diluted
(5% [vol/vol]) in sterile, deaerated 2,2,4,4,6,8,8-heptamethylnonane as an inert, nontoxic carrier phase (18) before addition
to the culture (10 ml of mixture per bottle) by means of an
N2-flushed plastic syringe;
[1-13C]n-hexane was applied in the same
manner. d14-n-Hexane was mixed with
an equal volume of unlabeled n-hexane, and the isotopomer mixture was applied in the carrier phase like unlabeled
n-hexane alone. The hydrocarbons were filter sterilized
(regenerated cellulose, 0.2-µm pore size; Schleicher & Schuell,
Dassel, Germany) before addition. Sodium n-hexanoate
(caproate) in control experiments was added from an autoclaved stock
solution (final concentration, 3 mM). Cells were passaged (inoculum
size, 5% [vol/vol]) with n-hexane or
n-hexanoate as organic substrates at least 10 times before
the cultures for the experiments described were inoculated. Cultures
with n-hexane were incubated on a slowly rotating shaker (50 rpm) nearly horizontally, with the orifices below the medium surface,
so that contact of the overlying, hydrophobic
n-hexane/carrier phase mixture with the stoppers was
avoided. The incubation temperature was 28°C. In labeling experiments
with potential cosubstrates, cultures were grown on n-hexane
to an optical density at 660 nm (OD660) of 0.1. Then,
disodium 2,3-d2-fumarate or
2,2,3,3-d4-succinate was added (final
concentration, 10 mM), and the culture was allowed to grow to a higher
OD. All cultures were used for the described investigations (see
following sections) immediately after depletion of nitrate and formed
nitrite; the final OD660 was usually 0.3 to 0.4. The
presence of nitrate and nitrite was examined by using disposable test
strips (Merck, Darmstadt, Germany).
Analysis of metabolites.
Cultures for metabolite analysis
were heated in closed bottles in a water bath to 85°C for 15 min to
inactivate eventually present enzymes that may catalyze reactions with
oxygen during further handling in the air. Also, release (or additional
release) of metabolites into the medium was expected from this
treatment. In the case of n-hexane-grown cultures, the
aqueous phase was separated from the overlying carrier phase via a
separatory funnel. The heated cells were removed by centrifugation
(7,000 × g, 20 min) to avoid possible interference
with phase separation during subsequent ether extraction. The
supernatant from each culture (400 ml) was extracted with diethyl ether
(80 ml), first at pH 7.5 and subsequently at pH 1.5 (adjusted with
phosphoric acid); extraction at each pH was performed three times. The
three corresponding ether extracts were pooled, dried over anhydrous
Na2SO4, and stored at 4°C in glass bottles
sealed with Teflon-coated screw caps until further analysis. Directly
before analysis, each ether extract was evaporated to dryness, taken up
in 1 ml of dichloromethane, and methylated using an etheral solution of
diazomethane that was freshly prepared from Diazald (Sigma-Aldrich,
Deisenhofen, Germany) according to standard procedures (Technical
Bulletin AL113; Aldrich Chemical Co., Milwaukee, Wis.).
Gas chromatographic-mass spectrometric (GC-MS) analysis of methylated
culture extracts was performed on a type 5890 gas chromatograph (Hewlett Packard, Waldbronn, Germany) connected to a type 95SQ mass
spectrometer (Finnigan MAT/ThermoQuest, Egelsbach, Germany). The gas
chromatograph was equipped with a KAS 3 injection system (Gerstel,
Mülheim, Germany) and a BPX5 fused silica capillary column
50 m long, 0.22-mm inner diameter, and 0.25-µm film thickness. Helium was used as the carrier gas. The oven temperature was programmed from 60 to 340°C (8-min isotherm) at a heating rate of 3°C/min. The
mass spectrometer was operated in electron impact mode at an electron
energy of 70 eV and a source temperature of 260°C. Full-scan mass
spectra were recorded over a mass range from 50 to 600 Da at a scan
rate of 0.74 s per decade, with an interscan delay of 0.2 s
and a scan cycle rate of 1 s.
Identity of metabolites with synthetic MPS or (1-ethylbutyl)succinic
acid (EBS) was verified by coinjection of the methyl
esters. Each
coinjection was performed twice using two different
gas chromatography
columns. In addition to the column used for
GC-MS analysis (see above),
an Ultra 1 fused silica capillary
column (50 m long, 0.22-mm inner
diameter, and 0.33-µm film thickness)
was used, with hydrogen as the
carrier gas. All coinjection analyses
were performed on the same model
of gas chromatograph and with
the same temperature program as described
for GC-MS; however,
peaks were detected via flame ionization.
5

-Androstane served
as an internal standard for quantification of
extracted
metabolites.
EPR spectroscopy.
Cells for EPR analysis were harvested from
six cultures (400 ml each) freshly grown with n-hexane or
n-hexanoate. All steps were performed under strictly anoxic
conditions either inside an anoxic chamber (Coy, Ann Arbor, Mich.) with
a fresh oxygen-scavenging catalyst, or under gassing of tubes with pure
N2 (52). Cells from 2.4 liters of culture
volume were centrifuged (7,000 × g, 20 min) and
resuspended in anoxic water (10 ml) containing sodium dithionite
(0.1 mM) to a final volume of approximately 5 ml. One part of this
concentrated suspension was disrupted by passage through a French
pressure cell (9.5-mm piston, 120 MPa). Removal of cell debris by
centrifugation (20,000 × g, 20 min) yielded the crude
extract. From this, another aliquot was used to sediment membranes
(100,000 × g, 60 min); this supernatant is referred to
as the soluble extract. Protein in lysed cells and extracts was
quantified by the method of Bradford (12) with bovine
serum albumin as the standard. Aliquots (each approximately 0.25 ml) from the cell suspension, the crude extract, and the soluble extract were transferred to anoxic EPR tubes, sealed under N2, and
immediately frozen and stored in liquid N2.
EPR spectroscopy was carried out using an EMX-6/1 X-band EPR
spectrometer (Bruker, Karlsruhe, Germany) with a standard TE102
rectangular cavity and an ESR-900 helium flow cryostat with variable
temperature (Oxford Instruments, Oxford, U.K.). EPR spectra were
recorded under nonsaturating conditions and present averages of
5 to 20 scans. Data acquisition was done with the software supplied
by Bruker
(WINEPR acquisition program, version 2.3.1); data manipulation
(determination of
g values, subtraction, baselining, and
integration)
was done with the WINEPR program version 2.11. Spin
integration
with correction for
g anisotropy in field-swept
spectra (
1)
was performed using a solution of 10 mM
CuSO
4, 2 M NaClO
4, and
10 mM HCl as the
standard.
Chemical synthesis of MPS and EBS.
MPS and EBS as standard
compounds were synthesized from succinic acid dimethyl ester and
2-hexanone or 3-hexanone, respectively. The reaction sequences involved
Stobbe condensation of the carbonyl compounds with succinic acid
dimethyl ester, dehydration yielding the unsaturated intermediate, and
catalytic hydrogenation with Raney nickel, analogous to the synthesis
of 3-hydroxybenzylsuccinate described elsewhere (35). This
procedure of chemical synthesis yields racemic diastereomers of MPS and
EBS. Methylation of the substituted succinic acids using a solution of
diazomethane in diethyl ether yielded the respective dimethyl esters.
The diastereomer mixtures of the dimethyl esters of MPS and EBS were
isolated as colorless oily liquids from the reaction mixture by column
chromatography on silica gel with a dichloromethane-methanol mixture
(99:1). Structures were confirmed by 1H and 13C
nuclear magnetic resonance (NMR) spectra recorded on a Varian Gemini300
instrument (Varian, Darmstadt, Germany). Signals from (1-methylpentyl)succinic acid dimethyl ester (mixture of
diastereomers) were as follows: 1H NMR (300 MHz,
CDCl3, trimethylsilane [TMS]):
= 3.697 (s, 3H), 3.693 (s, 3H), 3.676 (s, 3H), 3.673 (s, 3H), 2.92-2.67 (m, 4H), 2.43-2.31 (m, 2H), 1.86-1.95 (m, 1H), 1.72-1.84 (m, 1H), 1.15-1.35 (m,
12H), 0.84-0.92 (m, 12H) ppm; 13C NMR (75 MHz,
CDCl3, TMS):
= 175.10, 174.68, 173.12, 172.96, 51.72, 51.68, 51.53, 46.03, 45.61, 35.03, 34.50, 34.01, 33.55, 33.27, 31.32, 29.39, 29.28, 22.67, 16.85, 16.19, and 13.98 ppm. Signals from
(1-ethylbutyl)succinic acid dimethyl ester (mixture of diastereomers)
were as follows: 1H NMR (300 MHz, CDCl3, TMS):
= 3.690 (s, 6H), 3.684 (s, 6H), 2.87-3.05 (m, 2H), 2.69-2.79 (m, 2H), 2.29-2.36 (m, 2H), 1.62-1.72 (m, 2H), 1.15-1.38 (m, 12H),
0.85-0.94 (m, 12H) ppm; 13C NMR (75 MHz, CDCl3,
TMS):
= 175.34, 173.18, 51.79, 51.70, 43.07, 41.21, 33.17, 32.97, 31.99, 31.78, 24.17, 23.70, 20.41, 20.26, 14.24, 14.19, 11.81, and 11.65 ppm.
Chemicals.
Chemicals were of analytical grade and mostly
obtained from Fluka (Deisenhofen, Germany) or Merck (Darmstadt,
Germany). Purity of n-hexane was
99.5%.
d14-n-Hexane,
2,2,3,3-d4-succinic acid, 2-hexanone,
3-hexanone, and succinic acid dimethyl ester were purchased from
Sigma-Aldrich (Deisenhofen, Germany).
[1-13C]n-Hexane and
2,3-d2-fumaric acid were purchased from Campro Scientific (Berlin, Germany). 2,2,4,4,6,8,8-Heptamethylnonane was from
Alfa/Johnson Matthey (Karlsruhe, Germany). Acids used as substrates
(n-hexanoic acid, labeled fumaric acid, and labeled succinic
acid) were titrated to yield aqueous solutions (1 M, pH 8) of sodium
salts prior to addition to the medium. Diethyl ether of analytical
grade was obtained from Riedel-de Haën (Seelze, Germany).
Calculation of free energies.
G° values of
reactions were calculated from Gf° values. The
Gf° values (in kilojoules per mole) of the
following species are given in the literature: fumarate2
(aq),
604.2 (48); methane (g),
50.8 (48);
n-hexane (lq),
4.3 (47); and toluene (lq),
+114.2 (48). Gf° values of
substituted succinates, which are not given in the literature, were
calculated from increments using two different algorithms (34,
47). The Gf° values obtained (in
kilojoules per mole) were as follows: methylsuccinate2
(aq),
681.6 and
685.5; MPS2
(aq),
647.3 and
644.0; and benzylsuccinate2
(aq),
525.4 and
521.1.
Respective Gf° values calculated via increments for succinate2
(aq) as a test case were
687.5 and
690.0, compared to the literature value of
690.2 kJ/mol
(48). The equilibrium constant was calculated as
K = exp(
G°/RT), where R is the gas
constant and T is the absolute temperature.
 |
RESULTS |
Identification of MPS as a metabolite specifically formed from
n-hexane.
GC-MS analysis of ether extracts from
cultures of strain HxN1 grown with n-hexane and subsequently
pasteurized without access to air revealed 12 pronounced peaks of
metabolites in the supernatant. These were not detectable in cultures
grown with n-hexanoate. Peaks were only detectable if the
culture (pH of about 7.5) was acidified before ether extraction,
indicating that metabolites were carboxylates. No significant portions
of metabolites were left in the cell pellet of the heat-treated culture.
Because of the hypothesized initial reaction of
n-alkanes
with fumarate yielding an alkyl-substituted succinate (see the
introduction),
we focused in the present study on the identification of
dicarboxylic
acids. Methyl esters of these eluted in the gas
chromatogram after
33 min (Fig.
1) behind
peaks of various monocarboxylic acids (not
shown). The mass spectra
corresponding to the three depicted peaks
(Fig.
1) were very similar
and thus provided evidence for a close
structural relationship between
them (Table
1). The relatively
simple
fragmentation patterns were essentially in agreement with
the structure
of C
6 alkyl-substituted succinic acid dimethyl esters.
Weak
but definite and specific signals at
m/z 173 (M
+ 
C
4H
9; from compounds 2 and 3 in Fig.
1) and
m/z 187 (M
+ 
C
3H
7; from compound 1 in Fig.
1) pointed at
methyl esters of
MPS and EBS, respectively. Details of the
fragmentation pattern
are shown for MPS dimethyl ester in Fig.
2A. To confirm the interpretation
of the
GC-MS results, authentic standards of MPS and EBS dimethyl
esters were
synthezised. Based on coinjection on two different
GC columns and
identity of the mass spectra, MPS and EBS dimethyl
esters were
identified unambiguously. No evidence for the presence
of
n-hexylsuccinate (as dimethyl ester), another
hypothetical
transformation product of
n-hexane (see
Discussion), was obtained.
On the basis of structural considerations it
is very unlikely
that
n-hexylsuccinate dimethyl ester, which
is expected to have
a mass spectrum similar to those of MPS and EBS
dimethyl esters,
would coelute with either of these two compounds.
However, this
assumption has to be verified by synthesis and analysis
of an
authentic standard of
n-hexylsuccinate dimethyl ester.
The concentration
of MPS in the supernatant of the heat-treated culture
was approximately
5 µM.

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FIG. 1.
Partial gas chromatograms of methylated extracts from
heat-treated, acidified cultures of strain HxN1 after anaerobic growth
with nitrate as the electron acceptor and with n-hexanoate
(A) or n-hexane (B) as the only organic substrate. Both
chromatograms were recorded at the same detection sensitivity. Mass
spectrometric data from peaks are shown in Table 1; the mass spectrum
of compound 3, which was essentially the same as of compound 2, is
shown in Fig. 2A. Compounds 2 and 3 are interpreted as separable
diastereomers of MPS dimethyl ester; possible diastereomers of compound
1, viz., of EBS dimethyl ester, were not separable on the gas
chromatography column. Asterisks (*) indicate chiral carbon atoms;
assignment of the absolute stereochemistry of diastereomers was not
achieved in the present study.
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TABLE 1.
Mass spectral data and structural assignment of
metabolites (after methylation) formed during growth of strain HxN1
on n-hexane and nitrate under anoxic conditions
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FIG. 2.
Mass spectra of methylated MPS (diastereomer
corresponding to peak 3 in Fig. 1B) from anaerobic cultures of strain
HxN1 grown with nitrate as the electron acceptor and unlabeled and/or
deuterium-labeled organic substrates. The following experiments were
conducted (panel of recorded mass spectra indicated in parentheses):
unlabeled n-hexane (A); mixture of unlabeled
n-hexane and d14-n-hexane
(A, B, C, and D); and unlabeled n-hexane and
2,3-d2-fumarate or
2,2,3,3-d4-succinate (A and C).
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|
Both MPS and EBS possess two chiral carbon atoms and can in principle
exist as two racemic diastereomers. The two adjacent
peaks that were
observed with the methylated culture extract (compounds
2 and 3, Fig.
1) as well as with the synthetic standard had essentially
the same mass
spectra and were therefore assigned to the two diastereomeres
of MPS
dimethyl ester. In contrast, synthetic EBS dimethyl ester
yielded only
one peak, suggesting that diastereomers were not
separable on the
columns used; it is therefore presently unknown
whether EBS from strain
HxN1 consists of diastereomers like MPS.
Assignment of the
configuration to the two diastereomers of MPS
was not possible due to
the lack of standards of the pure diastereomers.
At present it is also
unknown whether the diastereomers of MPS
from strain HxN1 are
racemic.
Labeling studies.
To examine the formation of MPS in more
detail, cultures were provided with labeled n-hexane or with
labeled fumarate or succinate as possible precursors of the
dicarboxylate moiety in MPS. Growth of cultures was not affected when
unlabeled n-hexane was completely replaced by
[1-13C]n-hexane. In contrast, when
d14-n-hexane was provided as the only
organic substrate, no growth occurred within 2 weeks. Growth tests with
mixtures of unlabeled n-hexane and
d14-n-hexane at various ratios
revealed a 1:1 mixture (equal volumes) as the highest portion of
deuterated n-hexane that still allowed growth; this ratio
was therefore applied for labeling studies. Addition of 2,3-d2-fumarate or
2,2,3,3-d4-succinate to cultures growing with n-hexane did not impede growth; in contrast, these
dicarboxylic acids even stimulated growth, because strain HxN1 uses
them readily as carbon sources and electron donors (Behrends et al., unpublished).
Assignment of the structures obtained from the labeling experiments was
always straightforward due to the observation of relevant
fragments in
the mass spectra. In all these experiments, the diastereomers
of MPS
dimethyl ester exhibited the same labeling
patterns.
Utilization by strain HxN1 of [1-
13C]
n-hexane
as the only organic substrate yielded isotope peaks in the
fragmentation patterns
of extracted MPS methyl ester (not shown) that
indicated full
preservation of the label in the 1-methylpentyl side
chain.
Growth with the mixture of
n-hexane and
d14-
n-hexane yielded two
polydeuterated MPS isotopomers in addition to monodeuterated
and
unlabeled MPS isotopomers. The former two displayed a significantly
shorter retention time and could be clearly separated by gas
chromatography
from the isotopically lighter compounds. In contrast,
complete
separation of the two polydeuterated isotopomers or the two
lighter
isotopomers from each other could not be achieved with the gas
chromatographic method used. Nevertheless, the labeling patterns
of the
polydeuterated and the lighter isotopomers of MPS dimethyl
ester could
be resolved by careful selection of mass spectra from
the ascending and
descending parts of the gas chromatographic
peaks. One of the
polydeuterated products (Fig.
2B compared to
Fig.
2A) showed the
presence of 14 deuterium atoms and preservation
of 13 deuterium atoms
in the fragment (
m/z 170) carrying the 1-methylpentyl
side chain of MPS. Fragments at
m/z 148 and 115 (Fig.
2B) localized
the remaining deuterium atom at carbon-2 or carbon-3,
whereas
the crucial fragment at
m/z 170 allowed a
definite localization
at carbon-3 of the succinate moiety. Hence, there
was always a
hydrogen atom and never a deuterium atom at carbon-2 of
the succinate
moiety. The mass spectrum of the other polydeuterated
isotopomer
of MPS showed the presence of 15 deuterium atoms (Fig.
2D).
Again,
13 deuterium atoms were present in the fragment carrying the
1-methylpentyl
side chain. The two remaining deuterium atoms were
located at
carbon-3 of the succinate
moiety.
Upon addition of 2,3-
d2-fumarate to cultures
utilizing unlabeled
n-hexane, an unlabeled and a
monodeuterated isotopomer of
MPS dimethyl ester (Fig.
2A and C) were
detected and identified
as described in the experiment with the mixture
of
n-hexane and
d14-
n-hexane (see above). Also in
this experiment, the deuterium
in the labeled MPS could be definitely
localized at carbon-3 of
the succinate moiety, due to the crucial
fragment at
m/z 157 (Fig.
2C). Location of the
deuterium atom at any position other than
carbon-3 of the succinate
moiety would not be in agreement with
the observed fragmentation
pattern. When 2,2,3,3-
d4-succinate
was added
instead of 2,3-
d2-fumarate, the same products
(MPS and
3-
d1-MPS) but no MPS isotopomers
containing more than one deuterium
atom were
detected.
Evidence for the presence of a glycyl radical.
Dense cell
suspensions, crude extract, and soluble extract from strain HxN1 grown
on either n-hexane or n-hexanoate were studied by
EPR spectroscopy. A characteristic intense EPR signal was observed in
cells of n-hexane-grown cultures. (Fig.
3B). In crude and soluble extracts of
n-hexane-grown cells, a signal with identical EPR parameters
could also be observed, with intensity losses of 7 and 27%,
respectively (data not shown). The g value (2.0032), line
width, relaxational behavior (P1/2 at 77 K is
0.05 mW), and strong hyperfine coupling to a single proton (1.5 ± 0.1 mT) are indicative of an organic radical centered at the
-carbon
of an amino acid. With n-hexanoate-grown cells, the signal
indicative of such an organic radical was less than 4% of the signal
from n-hexane-grown cells (Fig. 3A), and only a very weak
nonhyperfine resolved isotropic signal at g = 2.004
with a line width of 1.7 ± 0.2 mT was present. The signal
persisted in the crude and soluble extract, with similar amplitude and
EPR parameters (not shown), and is tentatively assigned to a soluble
flavoprotein in the semiquinone form. Quantification of the intense EPR
signal by double integration and correction for the assumed presence of
a flavin semiquinone background signal as in
n-hexanoate-grown cells (only 10 to 20% of the double
integral) indicated a concentration of the radical of 5 µM in the
cell suspension. The protein content in the undiluted soluble extracts
was 12.4 and 9.4 mg/ml for cells grown on n-hexanoate and
n-hexane, respectively.

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|
FIG. 3.
EPR spectra of suspensions of cells of strain HxN1 grown
anaerobically with n-hexanoate (A) and n-hexane
(B) as the only organic substrates and nitrate as the electron
acceptor. The relative amplitudes were normalized for equal
concentrations of soluble protein. Conditions for recorded EPR spectra:
60 K; microwave power, 13 µW; modulation amplitude, 0.45 mT;
microwave frequency, 9.46 GHz; modulation frequency, 100 kHz.
|
|
 |
DISCUSSION |
Supposed initial reaction of n-hexane.
MPS was
identified as a prominent metabolite in cultures of strain HxN1 grown
anaerobically with n-hexane and nitrate. In parallel
cultures grown on n-hexanoate, MPS was not detectable, indicating that this compound is specifically formed during
n-hexane metabolism. The finding of the 13C
label from [1-13C]n-hexane in the
1-methylpentyl side chain proves that this moiety originates from the
n-alkane. This assumption is further confirmed by the
observed preservation of 13 deuterium atoms from
d14-n-hexane in the 1-methylpentyl
side chain of MPS. If n-hexane is the only organic
substrate, the dicarboxylate moiety in MPS also has to be derived, at
least in part, from the carbon of n-hexane; this transformation has to involve various metabolic steps that may include
oxidation/reduction, cleavage, and carboxylation reactions. The origin
of the dicarboxylate moiety of MPS is best explained if a
C4 dicarboxylic acid is assumed to be the direct precursor. Such an assumption agrees well with the hypothesized mechanistic relationship between the initial reactions of n-alkanes and
of toluene in denitrifying bacteria (see the introduction). Toluene is
activated by addition of the methyl group to fumarate as a cosubstrate,
yielding benzylsuccinate (7, 9, 24, 31). In analogy to
this, the formation of MPS can be explained by an addition of
n-hexane with its subterminal carbon atom to fumarate (Fig.
4). Another metabolite, EBS, was
identified in cultures of strain HxN1, and the amount of EBS extracted
was 100-fold lower than that of MPS. It is true that a low pool size of
a metabolite under nonequilibrium conditions in active cells does not
necessarily indicate that the compound is of minor relevance.
Nevertheless, there are hints that EBS is a by-product (formed by
"accidental" reaction) rather than a true intermediate and that MPS
is the principal product of the initial reaction of n-hexane
degradation. Monocarboxylic organic acids (with fewer carbon atoms than
MPS and EBS) detected in extracts from n-hexane-grown
cultures and tentatively identified as possible subsequent metabolites
contain methyl branches rather than ethyl branches (H. Wilkes, R. Rabus, T. Fischer, A. Armstroff, A. Behrends, and F. Widdel,
unpublished data).

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|
FIG. 4.
Proposed initial reaction of n-hexane with
fumarate yielding MPS during anaerobic growth of denitrifying strain
HxN1. Deuterium-labeled positions in a parallel experiment with
2,3-d2-fumarate added to an
n-hexane-utilizing culture are indicated in grey.
|
|
Experiments with the mixture of unlabeled
n-hexane and
d14-
n-hexane demonstrated the
formation of isotopomers of MPS with
one and two deuterium atoms at
carbon-3 of the succinate moiety.
These results suggest that the
deuterium at carbon-3 of MPS originates
via two different routes.
First, the deuterium atom that has to
be removed from
d14-
n-hexane to enable formation of
the new C-C
bond may be attached at carbon-3 of the succinate moiety in
MPS
rather than being diluted in a general pool of hydrogen ions.
Such
a deuterium transfer would be in accordance with a radical
mechanism
(see next section) and the assumed mechanistic similarity
with the
initial reaction of toluene in anaerobes. The proposed
reaction
mechanism of toluene includes abstraction of a hydrogen
(or deuterium)
atom from toluene (or methyl-
d3-toluene),
addition
of the benzyl radical formed to carbon-2 of fumarate, and
final
recombination of the hydrogen (or deuterium) atom with the
radical
at carbon-3, yielding benzylsuccinate (
6,
24).
Second, formation
of
d15-MPS with two deuterium
atoms at carbon-3 indicates conservation
of the label from
d14-
n-hexane in fumarate as the
assumed cosubstrate
via presently uncertain metabolic reactions
(without or with partial
proton/deuteron exchange with
H
2O).
The formation of two diastereomers of MPS in strain HxN1 is remarkable,
since most enzymatic reactions are highly stereoselective.
MPS has two
chiral carbon atoms (Fig.
1), so that two racemic
diastereomers (viz.,
four stereoisomers) do in principle exist.
Formation of all four
stereoisomers in an enzymatic reaction is
highly unlikely. However,
each of the two observed diastereomers
of MPS from strain HxN1 may
represent only one enantiomer. Formation
of two pure, nonracemic
diastereomers would occur in an initial
reaction with stereoselectivity
with respect to only one of the
two newly formed chiral centers. In the
initial reaction of toluene,
the formation of benzylsuccinate (which
has only one chiral center)
was shown to be stereospecific, with
addition of the benzyl moiety
at the
re face of fumarate
yielding
R-(+)-benzylsuccinate (
6,
32). In view
of this and other highly stereoselective biochemical
reactions of
fumarate, such as hydration to malate (
50), it
is likely
that MPS formation is also stereospecific at the fumarate
carbon (viz.,
at either the
si or
re face). One may therefore
envision that the MPS-forming enzyme exhibits relaxed stereospecificity
with respect to carbon-2 of the
n-hexane moiety.
Confirmation
of this hypothesis requires unequivocal assignment of the
absolute
configurations of MPS
stereoisomers.
The formation of 3-
d1-MPS upon addition of
2,3-
d2-fumarate to
n-hexane-utilizing
cultures of strain HxN1 indicates a loss
of the deuterium atom/ion at
the carbon atom that is linked to
the alkane chain. Such a loss is not
in agreement with the formal
addition of the 1-methylpentyl group to
the double bond of fumarate
in analogy with the presently assumed
mechanism of toluene activation.
Such a formal addition of unlabeled
n-hexane to 2,3-
d2-fumarate
would
yield 2,3-
d2-MPS, which was, however, never
detected. Two
explanations for the loss of deuterium at carbon-2 of MPS
may
be envisioned. (i) Fumarate is not the actual cosubstrate but
is
converted to another, presently unknown compound that is the
direct
reactant and that has not kept the hydrogen or deuterium
at the
reacting carbon atom. (ii) Fumarate is the actual cosubstrate,
but the
deuterium or hydrogen atom at the reacting carbon-2 exchanges
with
external hydrogen species in an unknown, eventually ionic
reaction step
immediately before, during, or after the formation
of the novel C-C
bond. It is unlikely that the observed loss of
deuterium at carbon-2 of
MPS occurs via a D/H exchange at deuterated
fumarate in a reversible
(back and forth) reaction at succinate
dehydrogenase. Such a reaction
would yield a mixture of 2,3-
d2-,
2-
d1-, and unlabeled fumarate and, upon formal
addition of
n-hexane
to the double bond, a mixture of
2,3-
d2-, 2-
d1-, and
3-
d1-labeled
as well as unlabeled MPS; however,
such a mixture of MPS isotopomers
has never been detected. In
conclusion, our experiments indicate
that the hydrogen atom of not only
the hydrocarbon substrate but
also of the assumed cosubstrate fumarate
is involved in the mechanism
of MPS formation. In the presently
proposed mechanistic model
of the initial reaction of toluene, the
hydrogen atoms of fumarate
are assumed to be maintained
(
24), even though this has not
been proven. Experiments
with labeled fumarate and unlabeled toluene
are needed to prove whether
and to what extent the mechanisms
of
n-alkane and toluene
activation differ in some details. An
activated succinate derivative is
unlikely as the direct cosubstrate
in the initial reaction of
n-hexane; the loss of three of the
four deuterium atoms from
2,2,3,3-
d4-succinate suggests succinate
oxidation to fumarate prior to a reaction with
n-hexane.
In view of the observed benzylsuccinate formation in a variety of
toluene-degrading anaerobic microorganisms, such as denitrifying
(
7,
9,
37), sulfate-reducing (
8,
37), and
anoxygenic
phototrophic bacteria (
54), one may assume that
the initial
reaction of
n-alkanes in various groups of
anaerobes also follows
the same principle, with fumarate as the direct
reactant. Different
responses of the fatty acid patterns in strains of
sulfate-reducing
bacteria to growth with long-chain
n-alkanes (
3) may be due
to different sites of
initial attack and fumarate addition at
the carbon chain. The formation
of methyl-branched fatty acids
in sulfate-reducing strain AK-01 grown
on long-chain
n-alkanes
and indication of subterminal carbon
addition to the chain (
44)
may also be considered a result
of an addition to fumarate analogous
to that in strain HxN1. A more
detailed and comparative study
of metabolic pathways is needed to
elucidate the further metabolism
of MPS and initial reaction products
of other
n-alkanes.
Significance of the identified radical.
The distinct EPR
signal in n-hexane-grown cells and its virtual absence in
n-hexanoate-grown cells of strain HxN1 provide evidence for
the specific involvement of a radical in the anaerobic initial reaction
of n-hexane. The observed signal is from a radical species
which has a strong coupling to a single hydrogen atom. The average
g value, line shape, and magnitude of the hyperfine coupling
is atypical for radicals at carbon side chains of amino acids (viz., at
amino acids other than glycine), flavin radicals, or sulfur-centered
radicals. To our knowledge, there are presently no biochemically
purified cell components other than glycyl radical enzymes which
exhibit such an EPR signal. However, it cannot be excluded that a
1-methylpentyl radical rather than a glycyl radical is present in a
protein that is specifically formed during growth of strain HxN1 on
n-hexane. It is true that
-carbon-centered radicals may
occur at amino acids other than glycine (40); however, these would not have the observed strong hyperfine coupling to a single
hydrogen atom. In anaerobic bacteria, signals like the present one have
thus far only been observed in the case of glycyl radical enzymes
(42). Such enzymes are pyruvate formate-lyase (27-29), anaerobic ribonucleotide reductase (36,
45, 46, 53), and the toluene-activating benzylsuccinate synthase
(C. Leutwein, A. J. Pierik, and H. Heider, personal
communication). Before the EPR measurement with benzylsuccinate
synthase, evidence for the presence of a glycyl radical in
benzylsuccinate synthase was provided by sequence similarity with other
glycyl radical enzymes (17, 31), and polypeptide
fragmentation upon exposure to oxygen (31). Hence, the EPR
spectrum obtained from n-hexane-grown cells of strain HxN1
is in favor of the presence of a glycyl radical in this bacterium and
further substantiates the assumed parallel between the initial
reactions of n-alkanes and toluene in anaerobes. A small
n-hexane-induced protein in strain HxN1 with N-terminal sequence similarity to the small subunit (BssC) of benzylsuccinate synthase (Behrends et al., unpublished) may be part of the assumed n-alkane-activating enzyme. Still, a definite assignment of
the EPR signal to a glycyl radical would be premature at present and has to be substantiated by further experiments, such as EPR
measurements upon growth with labeled glycine and purification of the
radical-bearing species.
The determined concentration of the radical in cells of strain HxN1
allows an estimation of the cellular content of the radical-harboring
protein. Using the presently determined protein content in the
soluble
cell extract and a molecular mass of 60 kDa as an average
value for
cytoplasmic proteins, it can be estimated that the radical
enzyme in
n-hexane-metabolizing cells of strain HxN1 amounts to
3.6%
(by mass) of the soluble protein; the amount would be 6%
if 100 kDa
was used as the average molecular mass of glycyl radical
enzymes as the
basis for the estimation. Two other catabolic glycyl
radical enzymes,
pyruvate-formate lyase in fermentatively growing
Escherichia
coli and benzylsuccinate synthase in toluene-degrading
Thauera aromatica, were also proportionately
significant proteins,
with a cellular content of 2 to 3% (
30,
31). The rather high
content of all these proteins may
compensate for the relatively
low specific activity of radical enzymes
that catalyze and control
intricate anaerobic
reactions.
If a 1-methylpentyl radical is generated in strain HxN1, this reaction
does not necessarily have to occur by direct reaction
of the glycyl
radical with
n-hexane. The glycyl radical in
pyruvate-formate
lyase of
E. coli is regarded as a storage
radical. A thiyl radical
subsequently generated from a cysteyl residue
is supposed to perform
the actual attack on the substrate
(
5). Purification of the
MPS-forming enzyme from strain
HxN1 and structural investigations
are needed to prove the assumed
involvement of a glycyl
radical.
Energetic aspects of anaerobic initial reactions of
hydrocarbons.
Even if the mechanisms of the initial reactions of
n-alkanes and toluene in anaerobes follow the same
principle, the activation steps are not energetically equivalent. The
energetic expenditure for homolytic (and also heterolytic) cleavage of
a C-H bond is higher with an alkane than with the methyl group of
toluene. The resulting alkyl radical cannot be stabilized like the
benzyl radical with its
-electron system. The C-H bond energies at
the secondary carbon atom of an n-alkane and the methyl
group of toluene are 401 and 368 kJ/molmol, respectively
(33). However, these absolute values are not direct
indicators of the actual activation energies of the hydrocarbons,
because the transition state and its bond energies (such as that of
transiently bonded H· radical) at the enzyme are unknown.
These values only indicate that the bond energy to be overcome in the
case of n-hexane is 33 (= 401
368) kJ/mol higher
than in the case of toluene. The bond energy to be overcome for the
activation of an n-alkane at the primary (terminal) carbon
(C-H bond energy, 419 kJ/mol) would be higher by as much as 51 kJ/mol
in comparison to activation of toluene. This may explain why enzyme
evolution has not favored n-hexane activation at the
terminal carbon. A similar principle has been observed in the anaerobic
synthesis of diabolic acid (15,16-dimethyltriacontanedioic acid), the
only known reaction (19, 21) that resembles the anaerobic
initial reaction of an alkane. Diabolic acid, a major lipid component
in Butyrivibrio fibriosolvens, is formed by radical
condensation of two n-hexadecanoic (palmitic) acid molecules
at the subterminal carbon atom of their apolar residues. The reaction
is assumed to proceed via simultaneous formation of a radical at each
chain and hence differs in some detail from the suggested anaerobic
alkane activation. Furthermore, radical formation in the synthesis of
diabolic acid has been suggested to involve coenzyme B12
(21), whereas the glycyl radicals investigated so far are
generated with S-adenosylmethionine (20, 23).
Among chemical reactions, the addition of alkanes (e.g., of propane at
carbon-2) to alkenes via a radical mechanism (33) has some similarity to the suggested route of MPS formation. However, the more
rapid chemical reaction is performed at 500°C and 10 MPa and yields
an uncontrolled variety of products. In addition, an ionic mechanism
for alkane-alkene addition catalyzed by very strong acids is known
(33).
Irrespective of the high energy barrier during alkane activation, the
net reaction of
n-hexane and fumarate yielding MPS is
energetically favorable, with a standard free energy change
(
G°)
of

35 to

39 kJ/mol (depending on the algorithm
used for calculation
of the
Gf° value for
MPS); this corresponds to an equilibrium
constant of 10
6.1
to 10
6.8. The
G° value for the reaction of
toluene with fumarate yielding
benzylsuccinate is

31 to

35 kJ/mol.
This is in agreement with
the observation that benzylsuccinate
formation needs no coupling
to an energy-yielding reaction such as ATP
hydrolysis (
9,
31),
and the same may be true for MPS
formation. Hence, fumarate with
its

-bond is not only an acceptor to
bind the unstable intermediate
of hydrocarbon activation (viz., the
postulated radical), but
also a compound that "forces" the reaction
to the side of the
product. A reaction of fumarate with any
hydrocarbon, even with
methane as the least reactive one, would be
energetically feasible
(exergonic). A hypothetical reaction with
methane yielding methylsuccinate
would have a
G° value
of

26.6 to

30.5 kJ/mol. However, there
are no hints of such a
reaction from studies of the anaerobic
oxidation of methane in
sediments. Anaerobic utilization of methane
could not be demonstrated
in any pure culture, including strain
HxN1. Presently, the oxidation of
methane in anoxic habitats is
assumed to include a reversal of the
steps of methanogenesis in
archaea and scavenge of the product by
associated sulfate-reducing
bacteria (
11,
25,
26).
 |
ACKNOWLEDGMENTS |
R. Rabus, H. Wilkes, and A. Behrends contributed equally to this study.
We thank H. Heider, University of Freiburg, for fruitful discussions
and for communicating results from EPR analysis of Thauera aromatica prior to their publication. We are indebted to C. Bolm and M. Kesselgruber, RWTH Aachen, for NMR spectra of synthetic standards and stimulating discussions. We thank U. Disko and F. J. Keller at Forschungszentrum Jülich and D. Lange and C. Probian at
MPI for Marine Microbiology for experimental assistance. We are
grateful to R. K. Thauer, MPI for Terrestrial Microbiology, for
enabling our measurements with the EPR spectrometer.
This work was supported by the Max-Planck-Gesellschaft and the Fonds
der Chemischen Industrie.
 |
ADDENDUM IN PROOF |
A recent examination of metabolites in an anaerobic
sulfate-reducing enrichment culture growing on n-dodecane
also provided evidence for the formation of alkyl-substituted
succinates (K. G. Kropp, I. A. Davidova, and J. M. Suflita, Appl.
Environ. Microbiol. 66:5393-5398, 2000).
 |
FOOTNOTES |
*
Corresponding author. Mailing address:
Max-Planck-Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359 Bremen, Germany. Phone: 49-421-2028-736. Fax: 49-421-2028-790. E-mail: rrabus{at}mpi-bremen.de.
This article is dedicated to Wolfgang Buckel on the occasion of his
60th birthday.
 |
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Journal of Bacteriology, March 2001, p. 1707-1715, Vol. 183, No. 5
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.5.1707-1715.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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