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Journal of Bacteriology, August 2000, p. 4632-4636, Vol. 182, No. 16
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Demonstration of a Novel Glycolytic Pathway in the
Hyperthermophilic Archaeon Thermococcus zilligii by
13C-Labeling Experiments and Nuclear Magnetic
Resonance Analysis
Karina B.
Xavier,1
Milton S.
da Costa,2 and
Helena
Santos1,*
Instituto de Tecnologia Química e
Biológica, Universidade Nova de Lisboa, 2780-156 Oeiras,1 and Departamento de
Bioquímica and Centro de Neurociências de Coimbra,
Universidade de Coimbra, 3000 Coimbra,2 Portugal
Received 3 March 2000/Accepted 26 May 2000
 |
ABSTRACT |
The operation of a novel glycolytic pathway was demonstrated in
nongrowing cells of Thermococcus zilligii by analysis of
the isotopic enrichment in the end products derived from fermentation of 13C-labeled glucose. The new pathway involved the
formation of formate, derived from C-1 in glucose, via cleavage of a
six-carbon carboxylic acid.
 |
TEXT |
Thermococcus zilligii,
formerly designated Thermococcus strain AN1, is a
hyperthermophilic archaeon with an optimum growth temperature of 75 to
80°C belonging to the order Thermococcales (9,
13). All the organisms of this order are hyperthermophiles and
obligate anaerobes that grow heterotrophically by fermenting peptides
and, in some cases, complex carbohydrates.
In recent years, several hyperthermophiles belonging to the domains
Archaea and Bacteria were examined to identify
their glycolytic pathways (3, 6, 11, 16-18, 21). This
interest was fueled by the expectation that novel metabolic pathways
and enzymes might operate under the extreme temperature conditions
required for growth of these organisms. For example, a modified version
of the Embden-Meyerhof (EM) glycolytic pathway, involving ADP-dependent hexokinase and phosphofructokinase, was found in the
Thermococcus and Pyrococcus species investigated
(6, 7, 17, 19).
The hyperthermophilic archaeon T. zilligii is an atypical
member of the thermococci. Unlike the other members of the genus Thermococcus, this species is not a marine organism and has
a relatively low tolerance for NaCl (200 mM); furthermore, it has the
lowest optimal temperature for growth among the species of the same
genus and an unusual lipid membrane composition (10); finally, glucose is a preferred substrate for growth as long as low
levels of peptides are provided. These differences prompted us to
select T. zilligii as a putatively interesting target to extend studies on carbohydrate metabolism in hyperthermophiles.
Here, we use 13C-labeling experiments with whole cells to
demonstrate the operation of a novel glycolytic pathway that involves the cleavage of a six-carbon compound to yield formate.
Analysis of end products derived from the metabolism of
[13C]glucose by cell suspensions.
T. zilligii
DSM2770 was grown at 75°C in a 5-liter fermentor in the medium
described by Lanzotti et al. (10) using 10 g of
tryptone (Difco, Detroit, Mich.) per liter as carbon source with
continuous bubbling of nitrogen gas and stirring at 39 rpm. Cells were
harvested by centrifugation (7,500 × g for 10 min at 27°C) at the end of the exponential phase and washed once with anaerobic 20 mM potassium phosphate buffer, pH 7.4, containing 2.5 g of NaCl per liter. The cells were then suspended in the same buffer,
and 4.5 ml of cell suspension (5 to 10 mg of protein/ml) was incubated
for 2 h at 75°C with selectively enriched
[13C]glucose (15 mM) in closed serum bottles under an
argon atmosphere. Samples were centrifuged, and the supernatants were
frozen and stored until analyzed by 1H and 13C
nuclear magnetic resonance (NMR). The major products, quantified by
1H NMR, were acetate (4 to 9 mM) and formate (0.5 to 2 mM).
Succinate, isobutyrate, propionate, and isovalerate were also produced,
but they were derived from internal reserves present in the cells, since these compounds were not isotopically enriched. Typically around
60% of acetate produced was derived from internal reserves. To
identify the type of glycolytic pathway operating in this organism, six
independent experiments were performed with glucose selectively labeled
in each of the six carbon atoms. The isotopic enrichments determined in
the end products, acetate and formate, are summarized in Table
1. The protein content in the sonicated
cell suspension was determined by the Bradford method (2).
The label in [1-13C]glucose ended primarily on formate
(78% labeled) and to a smaller extent on the methyl group of acetate.
The 13C NMR spectrum in Fig.
1 shows clearly the resonances due to
formate and acetate at 171.4 and 23.6 ppm, respectively. The percentage of labeling in each compound was estimated from the 1H NMR
spectrum of the same supernatant (Fig. 1, trace B). In each of the
triplet of resonances, the central line (8.45 and 1.91 ppm for formate
and acetate, respectively) is due to the unlabeled group, while the two
lateral lines, with equal intensity, are due to the protons directly
attached to 13C atoms
(2JCH = 195 and 127 Hz for
formate and acetate, respectively). A very low isotopic enrichment in
formate (4%) was observed when [6-13C]glucose was
metabolized, and no significant isotopic enrichment of formate was
derived from any other carbon in glucose. Both carbon atoms in acetate
were labeled from [2-13C]glucose, but the percentage of
enrichment was about twofold higher on the methyl group than on the
carboxylic group. On the other hand, acetate derived from
[6-13C]glucose was labeled exclusively on the methyl
group. Metabolism of [4-13C]glucose resulted in no
significant incorporation of 13C label in the methyl group
of acetate, and the enrichment on the carboxylic group was very low.
Finally, the label ended on the carboxylic group of acetate when
[3-13C]glucose or [5-13C]glucose was
metabolized.
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TABLE 1.
Percentage of 13C labeling on the
fermentation products derived from the metabolism of
[13C]glucose by cell suspensions of T. zilligii grown on tryptonea
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FIG. 1.
NMR spectra of the supernatant containing the end
products derived from the fermentation of [1-13C]glucose
by T. zilligii. The cell suspension (4.5 ml and 7-mg/ml
protein concentration) was incubated with 15 mM
[1-13C]glucose for 2 h at 75°C. (A)
13C NMR spectrum acquired on a Bruker DRX500 spectrometer
using a 5-mm selective probe head (spectral width, 31 kHz; data size,
64,000; repetition delay, 61 s; pulse width, 7 µs). Proton
decoupling was applied during the acquisition time (1 s). (B)
1H NMR spectrum acquired on the same spectrometer with
water presaturation (spectral width, 5 kHz; data size, 64,000;
repetition delay, 17 s; pulse width, 7 µs). In the
13C NMR spectrum, resonances arising from nonmetabolized
[1-13C]glucose are apparent in the region between 60 and
100 ppm. In the representation of the 1H NMR spectrum, the
strong intensity resonance due to the unlabeled methyl group of acetate
has been truncated.
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The labeling patterns of acetate expected when glucose is metabolized
by well-known glycolytic pathways, the EM and Entner-Doudoroff
(ED)
pathways and the pentose phosphate pathway (PPP), are summarized
in
Fig.
2. The PPP is usually found to
operate simultaneously
with the EM or the ED pathway since it does not
have a strictly
catabolic role. The labeling pattern expected for the
operation
of the pentose phosphoketolase (PPK) pathway, a major
glycolytic
route in some lactic acid bacteria (
5), has also
been included
in Fig.
2. The labeling in formate is not shown in Fig.
2, but
if this product was derived from pyruvate by the action of
pyruvate-formate-lyase,
an enzyme responsible for the formation of
formate in many anaerobic
organisms, the label would originate from the
carboxylic group
of pyruvate (
4).

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FIG. 2.
Expected labeling pattern of acetate and CO2
from selectively labeled glucose via EM, ED, and PPK pathways and the
PPP. The numbers show the fate of each carbon from glucose. The
labeling on acetate derived from the metabolism of
[2-13C]glucose and [3-13C]glucose via the
PPP takes into account the scrambling of label due to eventual
recycling of fructose-6-phosphate.
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The utilization of an ED glycolytic pathway by
T. zilligii
was ruled out by the absence of labeling on the methyl group of
acetate
derived from the metabolism of [3-
13C]glucose (Table
1
and Fig.
2). On the other hand, the detection
of
13C
enrichment on the methyl group of acetate derived from
[1-
13C]glucose showed that
T. zilligii
utilizes an EM glycolytic pathway.
However, the operation of this
pathway alone is not reconcilable
with the labeling pattern observed on
acetate derived from [2-
13C]glucose or
[3-
13C]glucose, leading to the conclusion that at least
two glycolytic
pathways are operating. Metabolism of
[2-
13C]glucose led to the formation of a mixture of the
two single-labeled
isotopomers of acetate,
13CH
3COOH and
CH
313COOH, whereas metabolism of
[3-
13C]glucose led to the formation of acetate labeled on
the carboxylic
group (Table
1). The operation of the EM pathway alone
would
lead to labeling exclusively on the carboxylic group of acetate
derived from [2-
13C]glucose and to complete loss of label
from [3-
13C]glucose (Fig.
2); therefore, the results
cannot be explained
by the operation of the EM pathway
alone.
The labeling observed on the methyl group of acetate derived from
[2-
13C]glucose and on the carboxylic group of acetate
from [3-
13C]glucose is consistent with the cleavage of
the C-2-C-3 bond
in a five-carbon compound, a splitting pattern
expected for the
operation of either the PPP or the PPK pathway.
However, a major
contribution of the PPP can be ruled out because of
the lack of
labeling of the methyl group of acetate derived from
[3-
13C]glucose (Table
1 and Fig.
2). Altogether, the
results described
until now allow us to conclude that
T. zilligii metabolizes glucose
via the simultaneous operation of an
EM pathway and a pathway
that leads to a labeling pattern of acetate
consistent with the
operation of a PPK
pathway.
Labeling experiments with [13C]pyruvate to elucidate
the origin of formate.
Pyruvate-formate-lyase is a well-known
enzyme that catalyzes the formation of formate from pyruvate.
Therefore, it was conceivable that the labeled formate could derive
from the metabolism of [1-13C]pyruvate, if this were an
intermediate in the metabolism of [1-13C]glucose by the
unknown glycolytic pathway. Experiments with pyruvate labeled on either
C-1 or C-3 were carried out according to the procedure described above
for glucose.
Pyruvate (15 mM) was metabolized at a much higher rate than was glucose
by cell suspensions of
T. zilligii (4.5 ml containing
6 mg
of protein/ml), but a much lower proportion of formate was
formed from
pyruvate metabolism, suggesting that the activity
of
pyruvate-formate-lyase, if it exists, is very low. When
[3-
13C]pyruvate was supplied, 90% of the label provided
was recovered
in the methyl group of acetate and formate was not
labeled (Table
2). On the other hand,
when the label was provided in [1-
13C]pyruvate, the pool
of formate was partially labeled (20%), but
the total label recovered
in formate accounted for only 0.5% of
the label utilized. Most
probably, the remaining label in [1-
13C]pyruvate was lost
as
13CO
2, due to the activity of
pyruvate:ferredoxin oxidoreductase
(
1,
8), since no other
labeled product was found. This high
concentration of labeled
13CO
2 led us to hypothesize that the labeling
of formate in this
experiment could be due to the activity of
formate-hydrogen-lyase
that interconverts
CO
2-H
2 and formate. Evidence for the operation
of this enzyme was obtained when cell suspensions were incubated
with
unlabeled glucose and labeled bicarbonate. Indeed, under
these
conditions the pool of formate was partially labeled (Table
2).
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TABLE 2.
Percentage of 13C labeling on the
fermentation products derived from the metabolism of different
substrates by cell suspension of T. zilligii grown
on tryptonea
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The observation that formate was a minor product of pyruvate metabolism
(the acetate/formate ratio was approximately 50),
in contrast to what
was observed from glucose metabolism (the
acetate/formate ratio was
approximately 6), led us to carry out
an experiment in which
[1-
13C]pyruvate would be cometabolized with unlabeled
glucose to simulate
the physiological conditions occurring during
glucose metabolism.
The production of formate doubled (the
acetate/formate ratio was
25), but the isotopic enrichment of the
formate pool remained
low compared to the very high incorporation of
13C on formate derived from [1-
13C]glucose
(78%) (Table
2). Therefore, we concluded that pyruvate
was not a
precursor of the formate detected from the metabolism
of glucose in
T. zilligii.
We propose that the metabolism of glucose in
T. zilligii
proceeds via the simultaneous operation of an EM pathway and a novel
pathway involving cleavage of a six-carbon carboxylic acid to
yield
formate and a pentose phosphate, which is subsequently cleaved
between
C-2 and C-3 (Fig.
3). Further evidence
for this pathway
was obtained from the identification, by
31P NMR, of xylulose-5-phosphate as a major phosphorylated
metabolite
in ethanolic extracts of
T. zilligii cells
metabolizing glucose
(Fig.
4). The
proposed metabolic scheme is in complete agreement
with the
comprehensive set of
13C-labeling data; the low isotopic
enrichment in formate derived
from [6-
13C]glucose and in
the carboxyl group of acetate derived from [4-
13C]glucose
(Table
1) is explained by scrambling of label in the
EM branch at the
level of triose-phosphate isomerase and aldolase,
as previously
reported for other microorganisms (
12,
20).
The barely
detectable isotopic enrichment in formate when
[4-
13C]glucose was metabolized resulted from the activity
of formate-hydrogen-lyase
upon labeled CO
2 produced via the
two glycolytic branches (Fig.
3).

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FIG. 3.
Proposed glycolytic pathway in T. zilligii.
HK, hexokinase; PFK, phosphofructokinase; P, phosphate. The numbers
show the fate of each carbon from glucose.
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FIG. 4.
Phosphomonoester region of the 31P NMR
spectrum of an ethanol extract from T. zilligii. The cell
suspension was incubated at 75°C with 15 mM glucose for 2 h and
extracted for 30 min with 70% ethanol. The final pH of the sample was
6.9. The spectrum was acquired on a Bruker DRX500 spectrometer using a
10-mm quadruple nucleus probe head (repetition delay, 1.8 s; pulse
width, 16 µs, corresponding to 55° flip angle; proton decoupling
during acquisition only). Assignments were made by spiking the extracts
with the pure compounds at pH 6.9 and 8.2. Abbreviations: X-5-P,
xylulose-5-phosphate; G-6-P, glucose-6-phosphate.
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The kinases in the EM glycolytic branch are ADP dependent.
Cell extracts of T. zilligii catalyzed the ADP-dependent
phosphorylation of glucose and fructose-6-phosphate. The specific activities of the ADP-dependent hexokinase and phosphofructokinase in
cell extracts of T. zilligii were 0.14 and 0.07 U/mg of
protein, respectively (cell extract preparation and enzyme assays were performed as previously described [15, 17].
ADP-dependent kinases have been found in other members of the
Thermococcales, and recently an ADP-dependent
phosphofructokinase was purified from T. zilligii
(14). At least, with respect to the ADP dependency of the
kinases, the EM branch of T. zilligii is similar to the EM
pathway described for Pyrococcus furiosus,
Thermococcus litoralis, and Thermococcus celer
(6, 17).
The relative contribution of the two glycolytic branches depends on
the presence of glucose during growth.
All the experiments
described above were carried out on cells grown on tryptone medium
without glucose. Interestingly, the labeling pattern of end products
derived from 13C-labeled glucose was different when glucose
(5 g/liter) was added to the medium in addition to tryptone (5 g/liter)
(Table 3). The relative fluxes of carbon
metabolized via the two branches could be calculated from the ratio of
the concentrations of the two acetate isotopomers,
13CH3COOH and
CH313COOH, obtained from the experiments with
[2-13C]glucose. In fact, the labeling on the methyl group
is due to the operation of the novel pathway, whereas the labeling on
the carboxylic group is due to metabolism via the EM pathway (Fig. 3).
A relative contribution of 2:1 (novel pathway versus EM pathway) was
calculated for cells grown on tryptone. When
[2-13C]glucose was metabolized by cells grown in the
presence of glucose (Table 3) the
13CH3COOH/CH313COOH
ratio was approximately 0.5, indicating the inversion of the relative
contributions of the two branches. The presence of glucose in the
growth medium appears to repress the enzymes of the novel glycolytic
pathway (also compare formate production in Tables 1 and 3). However,
even under these growth conditions the contribution of this pathway is
still important.
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TABLE 3.
Percentage of 13C labeling on the
fermentation products derived from the metabolism of
[13C]glucose by cell suspensions of T. zilligii grown on glucosea
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Concluding remarks.
We demonstrate the operation of a novel
glycolytic strategy in T. zilligii with two branches
diverging at the level of glucose-6-phosphate (Fig. 3). Glucose is
phosphorylated by an ADP-dependent hexokinase to glucose-6-phosphate
which is subsequently degraded by two glycolytic branches: an EM-type
glycolytic pathway and a new route where formate is produced by a
reaction involving cleavage of the C-1 carboxylic group of a six-carbon
compound to yield formate and a pentose phosphate. By analogy with the
pyruvate-formate-lyase reaction, we suggest that the six-carbon
compound is an
-ketoacid, such as 2-keto-3-deoxy-6-phosphogluconate,
derived from 6-phosphogluconate. The contribution of the novel
glycolytic branch was twice as high as that of the EM-type pathway when
cells were grown on tryptone, and the inverse relationship was found
for cells grown in the presence of glucose. This is the first report of
a glycolytic pathway involving the formation of formate from C-1 in
glucose. It is noteworthy that the most atypical member of the
Thermococcales, T. zilligii, possesses also this
unusual glycolytic feature.
 |
ACKNOWLEDGMENTS |
This work was supported by the European Community Biotech Programme
(Extremophiles as Cell Factories, BIO4-CT96-0488) and by PRAXIS XXI and
FEDER, Portugal (PRAXIS/2/2.1/BIO/1109/95).
We thank Mónica Dias for performing some of the labeling
experiments and Peter Schönheit for vivid discussions.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Instituto de
Tecnologia Química e Biológica, Universidade Nova de
Lisboa, Apartado 127, 2780-156 Oeiras, Portugal. Phone:
351-214469800. Fax: 351-214428766. E-mail:
santos{at}itqb.unl.pt.
 |
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Journal of Bacteriology, August 2000, p. 4632-4636, Vol. 182, No. 16
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Copyright © 2000, American Society for Microbiology. All rights reserved.
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