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Applied and Environmental Microbiology, December 2003, p. 7236-7241, Vol. 69, No. 12
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.12.7236-7241.2003
Copyright © 2003, American
Society for
Microbiology. All Rights Reserved.
Targeting Methanopterin Biosynthesis To Inhibit Methanogenesis
Razvan Dumitru,1 Hector Palencia,2 Scott D. Schroeder,2 Bree A. DeMontigny,3 James M. Takacs,2 Madeline E. Rasche,4 Jess L. Miner,3 and Stephen W. Ragsdale1*
Departments
of Biochemistry,1
Chemistry,2
Animal
Science, University of Nebraska-Lincoln, Lincoln,
Nebraska,3
Department of Microbiology and Cell
Science, University of Florida, Gainesville,
Florida4
Received 3 June 2003/
Accepted 1 September 2003
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ABSTRACT
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This
paper describes the design, synthesis, and successful employment of
inhibitors of
4-(ß-D-ribofuranosyl)aminobenzene-5'-phosphate
(RFA-P) synthase, which catalyzes the first committed step in the
biosynthesis of methanopterin, to specifically halt the growth of
methane-producing microbes. RFA-P synthase catalyzes the first step in
the synthesis of tetrahydromethanopterin, a key cofactor required for
methane formation and for one-carbon transformations in methanogens. A
number of inhibitors, which are N-substituted derivatives of
p-aminobenzoic acid (pABA), have been synthesized and their
inhibition constants with RFA-P synthase have been determined. Based on
comparisons of the inhibition constants among various inhibitors, we
propose that the pABA binding site in RFA-P synthase has a relatively
large hydrophobic pocket near the amino group. These enzyme-targeted
inhibitors arrest the methanogenesis and growth of pure cultures of
methanogens. Supplying pABA to the culture relieves the inhibition,
indicating a competitive interaction between pABA and the inhibitor at
the cellular target, which is most likely RFAP synthase. The inhibitors
do not adversely affect the growth of pure cultures of the bacteria
(acetogens) that play a beneficial role in the rumen. Inhibitors added
to dense ruminal fluid cultures (artificial rumena) halt
methanogenesis; however, they do not inhibit volatile fatty acid (VFA)
production and, in some cases, VFA levels are slightly elevated in the
methanogenesis-inhibited cultures. We suggest that inhibiting
methanopterin biosynthesis could be considered in strategies to
decrease anthropogenic methane emissions, which could have an
environmental benefit since methane is a potent greenhouse
gas.
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INTRODUCTION
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Biological methane formation is a microbial process catalyzed by
methanogens, which are members of the Archaea domain, the
third kingdom of life
(23). Methanogens are
found in most anaerobic environments, including the rumen of
domesticated livestock
(24). The beneficial
effects of methanogenesis include the removal of H2 formed
during the oxidative metabolism of biomass, thus enhancing the
biodegradation process (equations
1 and
2). However, there are
several negative aspects of ruminant methanogenesis. Since methane
production in the rumen results in a loss of between 3 and 12%
of feed gross energy, inhibition of methanogenesis has long been
considered as a strategy to improve agricultural productivity
(25). Inhibition of
ruminal methanogenesis can enhance production of the volatile fatty
acids (VFAs) that are useful to the host
(10). Furthermore,
methane is a potent greenhouse gas and thus contributes to the problem
of global warming (4).
Ruminal methanogenesis produces about 80 million tons of methane per
year (11), second only to
the mining, processing, and use of coal, oil, and natural gas (100
million
tons).
 | (1) |
 | (2) |
The
objective of the research described here is to specifically inhibit a
key methanogenic enzyme that is not present in the animal or in ruminal
bacteria. We have targeted a biosynthetic enzyme,
4-(ß-D-ribofuranosyl)aminobenzene-5'-phosphate
(RFA-P) synthase, which catalyzes the first step in methanopterin
biosynthesis. The reduced form of methanopterin,
tetrahydromethanopterin, is involved in multiple steps in
methanogenesis; it also replaces the functions of tetrahydrofolic acid,
the predominant one-carbon carrier in eukaryotes and bacteria. Given
the importance of tetrahydromethanopterin in growth and in energy
production by methanogens, the inhibition of RFA-P synthase should
specifically halt methanopterin biosynthesis and thereby preclude
methanogenesis without adversely affecting the metabolism of ruminal
bacteria or the animal. The results described herein support this
expectation.
In the first dedicated step of methanopterin
biosynthesis, RFA-P synthase catalyzes the conversion of
phosphoribosylpyrophosphate (PRPP) and p-aminobenzoate (pABA)
to CO2, inorganic pyrophosphate, and ß-RFA-P (Fig.
1). Rasche and White have partially purified and characterized the
methanogenic RFA-P synthase
(17), and the enzyme from
Archaeoglobus fulgidus has recently been purified to
homogeneity and cloned and heterologously overexpressed
(20). The reaction is
thought to proceed via the oxycarbenium intermediate and its adduct
with pABA (Fig. 1,
structures 4 and 5, respectively). We have focused on designing
competitive inhibitors that are structural analogs of pABA (Fig.
2). Analogs of pABA that inhibit RFA-P synthase are expected to be highly
selective because the amino group is the nucleophile in most
pABA-dependent reactions while the ring carbon 4 is the nucleophile in
the RFA-P synthase-catalyzed reaction.

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FIG. 2. A
series of analogs of pABA (structure 6), wherein R1 is a
nonpolar or polar group of varying steric demand, was synthesized via
the reductive amination of
pABA.
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The inhibitors described
herein both impair RFA-P synthase activity and arrest methanogenesis in
pure cultures of methanogens (some in the submicromolar range) and in
dense ruminal fluid cultures (artificial rumena). Supplying an excess
of the natural substrate pABA to the culture relieves the inhibition,
suggesting that RFA-P synthase is the cellular target. The inhibitors
do not adversely affect the growth of acetogenic bacteria, which play a
beneficial role in the rumen. Our results also indicate that ruminal
bacterial metabolism and ruminal dynamics in general are not adversely
affected since there is no inhibition and, under some conditions, a
slight elevation of VFA production in the methanogenesis-inhibited
artificial rumen system. Based on comparisons of the inhibition
constants among various inhibitors, we propose that the pABA binding
site in RFA-P synthase has a relatively large hydrophobic pocket near
the amino group.
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MATERIALS AND
METHODS
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Materials.
Sodium sulfide was purchased from
Sigma-Aldrich. Monobromobimane (Thiolyte) was purchased from
Novabiochem. All buffers, media ingredients, and other reagents were
acquired from Sigma-Aldrich. Solutions were prepared with nanopure
deionized water. N2 (99.98%),
N2-H2 (90:10 [vol/vol]), Ar
(99.8%), H2-CO2 (80:20
[vol/vol]), and CH4-N2 (0.2:99.8
[vol/vol]) were obtained from Linweld (Lincoln,
Nebr.).
Growth of
organisms.
Methanothermobacter
marburgensis (formerly Methanobacterium
thermoauotrophicum strain Marburg) (strain OCM82) was obtained
from the Oregon Collection of Methanogens and was cultured on
H2-CO2-H2S (80:20:0.1
[vol/vol/vol]) at 65°C in 15-ml Hungate tubes. Growth
was measured by the optical density at 580 nm (OD580).
Moorella thermoacetica (formerly Clostridium
thermoaceticum) (strain ATCC 39073) was grown at 55°C as
previously described (1).
Methanobrevibacter smithii (ATCC 35061) was grown at
37°C in 20-ml Hungate tubes containing 5 ml of media that
included 12.5 g each of cysteine HCl and Na2S per
liter as reducing agents and 1.1 mM vancomycin with shaking at 200 rpm
(16). The culture tubes
were pressurized initially and at 30-h intervals in
H2-CO2 (80:20 [vol/vol]) to 190 kPa,
and growth was assessed by measuring the
OD580.
Ruminal organisms were cultured in a shaking
water bath (45 rpm) by a batch method
(5) that used a
bicarbonate- and phosphate-based buffer with added macro- and
microminerals, cellobiose (2 g/liter), Trypticase (2 g/liter), and 12.8
mM Na2S as a reductant. Five-milliliter cultures were
incubated in 9.4-ml glass vials that were sealed and crimped with
gas-tight septa. Fresh ruminal fluid was obtained from the rumena of
two fistulated steers maintained on a diet of 70% forage and
30% grain, strained through four layers of cheesecloth, and
added to buffer at 20% of final volume. The culture vials
(5.4-ml headspace) were pressurized initially and after 12 h
of incubation at 37°C in H2-CO2 (80:20
[vol/vol]) to 190 kPa. Candidate inhibitors were added to
triplicate cultures in logarithmically spaced concentrations between 10
and 0.01 mM. Each experiment included cultures containing a known
inhibitor of methanogenesis, 2-bromoethanesulfonate, as a positive
control. After 30 h of incubation, the vials were cooled to
22°C, the headspace pressure was measured with a manometer, and
500 µl of the gas phase was assayed for methane and hydrogen by
gas chromatography with a silica gel column equipped with a thermal
conductivity detector.
Purification and
assays.
RFA-P synthase was
partially purified as previously described
(17). The enzymatic assay
was performed in a reaction mixture with a total volume of 0.25 ml
containing 3 mM [14C]carboxyl-labeled pABA, 10 mM
PRPP, 25 mM MgCl2, and 100 mM TES
[N-tris(hydroxymethyl)-methyl-2-aminoethanesulfonic
acid] buffer, pH 4.8, and was initiated by adding enzyme
(typically, 0.04 mg). The 14C label is eliminated as
14CO2 during the reaction (Fig.
1). The reaction mixture
was quenched with 100 µl of 1 M citric acid, pH 3.5, and the
residual radioactivity in the reaction mixture was determined by liquid
scintillation counting. (For further details, see the figure
legends.)
The VFA concentration in the liquid phase of the
ruminal batch cultures was assayed after centrifuging the cells and
precipitating the proteins by adding one-fourth volume of 20%
metaphosphoric acid. The VFA concentration in the supernatant was
determined by gas chromatography with a Chromasorb WAW column and a
flame ionization detector. The VFA concentration was also determined in
parallel cultures in which ground brome hay replaced cellobiose, and
headspace was pressurized with only CO2 at inoculation of
the cultures.
Synthesis of
4-(alkylamino)benzoic acid derivatives.
Na(CN)BH3 (1.4 molar
equivalents) was carefully added to a nitrogen-blanketed mixture of
95% ethanol and acetic acid (90:10, vol/vol) containing 0.2 M
pABA (1 molar equivalent) and the requisite aldehyde (1.3 molar
equivalents). The resulting mixture was stirred at room
temperature for approximately 24 to 36 h. Afterwards, the
reaction mixture was diluted with water (ca. four times the volume of
ethanol) and extracted three times with ethyl acetate. The combined
organic layers were dried with anhydrous Na2SO4
and concentrated. The residue was purified by chromatography on silica
with a mixture of hexanes and ethyl acetate as eluent or by
crystallization from ethyl acetate. All compounds gave satisfactory
spectral analysis and elemental composition. The N-alkyl-pABA
derivatives are very stable compounds that are even resistant to
autoclaving. The same resistance results are obtained whether the
compounds are autoclaved or filter sterilized before addition to the
medium. The pABA derivatives were dissolved as a stock solution in
water before being added to the culture
medium.
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RESULTS AND DISCUSSION
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The goal
of the work described here was to test the concept that a specific
inhibitor of methanogenesis could be developed based on the inhibition
of an enzyme involved in the biosynthesis of a key cofactor,
methanopterin. As described here, we were successful in developing
inhibitors that target the first committed step in methanopterin
biosynthesis and halt the growth of methanogens without adversely
affecting bacteria involved in VFA production, as tested in pure
culture and in a rumen model system.
A previously identified
inhibitor, 4-(methylamino)benzoic acid
(17) (Fig.
2, structure 6,
R1 = Me), was reexamined and found to have an
inhibition constant (Ki) of 145 µM (Fig.
3). A number of pABA derivatives (Fig.
3) were tested for their
ability to inhibit the RFA-P synthase reaction with the substrates
(pABA and PRPP) at saturating concentrations. First, each compound was
tested at a concentration of 1 mM, and if inhibition was observed, its
concentration was varied to obtain a complete inhibition curve. Figure
4 shows representative results with 4-(isopropylamino)benzoic acid. The
data for all inhibitors fit well to a competitive inhibition equation.
Figure 3 shows the
inhibition constants and the standard deviations for the pABA
derivatives that were tested. Several of the new inhibitors have
Ki values below 20 µM. pABA derivatives
bearing n-propyl, isopropyl, and isobutyl nitrogen
substituents strongly inhibit the enzyme. These results suggest that
the pABA binding site in RFA-P synthase has a relatively large
hydrophobic pocket near the amino group. It is not clear why complete
inhibition of the enzyme is not achieved; the final percentage of
inhibition varied from 60 to 85%. The 2-hydroxyethyl and several
aromatic derivatives, e.g., the furanyl-, thiophenyl-, phenyl-, and
2-pyridylmethyl derivatives, are particularly effective inhibitors.
With the exception of the isobutyl derivative, branched, unbranched,
and cyclic alkyl derivatives of four or more carbon atoms are
ineffective. The N,N-dimethylamino analog of pABA is neither a
substrate nor an inhibitor of the enzyme.

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FIG. 3. pABA
analogs evaluated for RFA-P synthase inhibition and methanogen growth
inhibition. Ki values for RFA-P synthase inhibition
[µM (± standard deviation)] are given in
bold. Methanogen growth inhibition data are given in brackets for
complete inhibition or delayed growth (growth lag in hours). NI, no
inhibition at 1 mM
concentration.
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FIG. 4. Inhibition
of RFA-P synthase by pABA analog. Partially purified RFA-P synthase
(17) was reacted with
[14C]carboxyl-labeled pABA and PRPP in the
presence and absence of 4-(isopropylamino)benzoic acid.
Elimination of 14CO2 associated with RFA-P
formation followed. The solid line shows the fit of the data to a
competitive inhibition
equation.
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Each of the pABA
analogs shown in Fig. 3
was then tested for its ability to inhibit methanogenesis and the
growth of the methanogen M. marburgensis (Fig.
3 and
5A; Table
1). As in the enzyme inhibition experiments, the cultures were first
grown in the presence of 1 mM analog. The cultures that did not alter
growth were not pursued further and, as shown in Fig.
3, were scored as
noninhibitory. Analogs that inhibited growth at 1 mM were studied
further in various concentrations to obtain complete inhibition curves.
The concentrations at which growth was completely inhibited are shown
in Fig. 3, and the results
of a representative experiment with isopropylaminobenzoate are shown in
Fig.
5A. These presumed active-site-directed inhibitors extend the lag phase
and decrease the final cell density in a dose-dependent manner.
Methanogens are known to produce methane even in stationary phase;
however, these derivatives inhibit methanogenesis in parallel with cell
growth (Table 1).
Insignificant amounts of methane were measured in the headspace of
M. marburgensis cultures whose growth was completely
inhibited. Several N-substituted pABA derivatives that inhibit growth
at high concentrations (0.5 to 1 mM) do not inhibit the synthase
reaction. These compounds probably exert their effect by a mechanism
unrelated to the RFA-P synthase and have not been further studied.
Figure 3 shows that the
best inhibitors of RFA-P synthase also are the most potent inhibitors
of M. marburgensis. At 100 nM, the most potent inhibitor
currently, 4-[(2-pyridylmethyl)amino]benzoic acid, completely
arrests the growth of and methane formation by M.
marburgensis. Inhibition is fully reversed by supplementing the
medium with pABA, indicating a competitive interaction between pABA and
the inhibitor at the cellular target, which is most likely RFAP
synthase. When the cells were grown in the presence of inhibitor for 5
days (instead of the standard incubation for 2 days), the OD continued
to decrease to zero.
One might wonder why we used this
thermophilic methanogen instead of a ruminal microbe. These studies,
which involve hundreds of biological assays, require the use of a
rapidly growing and robust methanogen like M. marburgensis
that can be cultured to fairly high cell density. In our experience,
the ruminal methanogen Methanobrevibacter ruminantium does not
meet these requirements. To rule out the hypothesis that inhibition is
exclusive to this one strain, we performed two types of experiments.
First, although our studies of other strains are not as extensive, the
best inhibitors for M. marburgensis also inhibit the
methanogenesis and growth of M. smithii, a mesophilic human
intestinal methanogen (data not shown). Second, as described below, we
did observe the inhibition of methanogenesis in an artificial rumen
system (containing all the naturally occurring ruminal microbes) with
the same inhibitors that prevent growth of M.
marburgensis.
Acetogenesis is an anaerobic and
hydrogenotrophic bacterial process (equation
3) that competes with
methanogenesis in many anaerobic habitats, including the rumen
(13,
14). Acetogenic bacteria
are beneficial since ruminant animals can use acetate as a nutrient.
Each of the inhibitors was tested for its effect on the growth of the
acetogenic bacterium M. thermoacetica. Methanopterin is not
required for survival of bacteria; accordingly, none of the RFA-P
synthase inhibitors described here affect the growth of M.
thermoacetica at concentrations as high as 1 mM (Fig.
5B). Acetogenic bacteria,
which use the Wood-Ljungdahl pathway, demand high levels of folate
since they contain 1,000-fold higher amounts of tetrahydrofolate
enzymes than most other organisms. Folic acid is not added to the
medium beyond the amount present in yeast extract. That these compounds
do not adversely affect the growth of acetogens at concentrations of
over 100-fold higher than those required to inhibit methanogens
suggests that these pABA derivatives do not inhibit folate
biosynthesis. Although acetogens are the only class of bacteria that
have been specifically tested in pure culture with the RFA-P synthase
inhibitors, results with the artificial rumen indicate that bacterial
metabolism in general is not adversely affected (see
below).
 | (3) |
We
tested the effect of the inhibitors on methane formation and VFA
production in an artificial rumen. Ruminal fluid, obtained from
fistulated steers, was cultured in the presence of inhibitors of the
RFA-P synthase or the cultured methanogen. Ruminal fluid is a complex
medium containing more than 60 species of bacteria at a density
exceeding 1011 cells/g plus numerous species of archaea,
protozoa, and fungi. Remarkably, at least three of the active pABA
derivatives inhibit (P < 0.01) methanogenesis in the
artificial rumen. Methane production is completely inhibited by 5 mM
4-(ethylamino)benzoate or 9 mM 4-(isopropylamino)benzoate, and 5 mM
4-(2-hydroxyethylamino)benzoate inhibited methane production to
2.5% of the control level. As a control, 1 mM
bromoethanesulfonate, an inhibitor of methyl-coenzyme M reductase,
completely inhibited (P < 0.01) methane production in
all experiments. We suspect that a higher concentration of the pABA
analog than of the enzyme is required to inhibit growing cultures
because of competition with pABA produced by the cells.
We
determined the effect of some of the effective inhibitors on VFA
production in the ruminal fluid culture (Fig.
6). VFA production by ruminal organisms is not depressed by adding an
RFAP synthase inhibitor at concentrations that completely block
methanogenesis. For example, when 7 mM 4-ethylaminobenzoate was added
to the artificial rumen system, acetate (P < 0.05) and
propionate (P < 0.10) levels were elevated relative to
the controls unexposed to the inhibitors. These results are consistent
with the studies with pure cultures of acetogenic bacteria and indicate
that the inhibitors do not adversely affect other ruminal bacteria or
ruminal dynamics. These experiments are important because a strategy
for reducing methane emissions from ruminal livestock will only be
practical if it does not adversely affect ruminal dynamics or the
health of the host. This requirement was a key factor in the strategy
of targeting RFAP synthase, which should be specific to methanogens.
The slight increases in acetate and propionate are consistent with the
expectation that inhibition of ruminal methanogenesis will enhance the
conversion of fibrous feedstuffs into metabolites that are useful to
the host rather than lost to the environment. VFAs produced by ruminal
bacteria constitute the ruminant animal's primary energy
source.

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FIG. 6. Effect
of a pABA-based RFAP synthase inhibitor on VFA production in a mixed
culture of ruminal organisms. Fresh, strained ruminal contents (0.8 ml)
were incubated at 37°C for 30 h in 10-ml vials
(n = 4 for 0 dose; n = 2 for all
other doses) with 3.2 ml of McDougal's buffer containing Ti
citrate, Trypticase, and bromegrass hay ground to pass through a
1-mm-pore-size screen. Headspace was pressurized to 10 kPa with
CO2 at time zero and again after 18 h. VFA
concentration was determined by gas chromatography and flame ionization
detection. Dose effects were analyzed by analysis of variance (overall
F-test, P < 0.13), and a least significant difference
test was used for mean separation. Error bars represent standard errors
of the means. a, increased concentration of acetate versus the level of
the control (P < 0.05); b, increased concentration of
propionate versus the level of the control (P <
0.10).
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During the past 30 years, various strategies for
inhibiting methanogenesis have been considered. Davies et al.
(3) successfully inhibited
methanogenesis with a series of 2,4-bis
(trichloromethyl)benzo[1,3] dioxins in mixed ruminal
cultures, in acute intraruminal models, and in chronic (4-week)
experiments with sheep and cattle. Concurrent with
significantly less methanogenesis, VFA production was in some cases
unchanged, and in other cases it was increased. Feed efficiency during
14 weeks of treatment was improved in cattle fed the methanogenesis
inhibitors. Eli Lilly markets monensin, an ionophore and gram-positive
antibiotic that decreases methanogenesis
(21), which is fed to
nearly all feedlot cattle in the United States. An increase in VFA
production was observed when methanogenesis was inhibited by the
ionophore monensin (2,
15,
21). The increased feed
efficiency achieved by feeding monensin to cattle was interpreted as a
result, at least in part, of decreased methanogenesis
(21). However, monensin,
unlike the RFA-P synthase inhibitors, impairs all H2-forming
microbial processes, which negatively impacts beneficial processes like
acetogenesis as well as methanogenesis. Other nonspecific inhibitors of
methanogenesis include nitrogen oxides (nitrate, nitrite, NO, and
N2O), which have been studied in rice field soils
(12,
18).
Bromoethanesulfonate, a specific inhibitor of a key enzyme in methane
formation (methyl-coenzyme M reductase)(7), has been tested in an
infused sheep rumen; however, resistance develops within a few days
(10). Future studies will
be required to determine if methanogens develop resistance to these
RFA-P synthase inhibitors.
Our studies are based on (and so far
are consistent with) the hypothesis that treating animals with a
specific inhibitor of methanogenesis will have a beneficial effect on
the animal by increasing the levels of VFAs in the rumen. Hackstein et
al. have proposed that methanogens form a symbiotic relationship with
mammals, birds, and reptiles and that the development of a
gastrointestinal system that can house methanogens is evolutionarily
advantageous (8,
9). The ability to
specifically inhibit methanogenesis would allow long-term monitoring of
an animal's growth rate, feed efficiency, ruminal function, and
overall health and offer a test of Hackstein's
hypothesis.
The global atmospheric methane burden has doubled
over the past 200 years to reach its present value of 1.75 ppm. The
continuing rise in methane levels is due predominantly to greenhouse
gas emissions from human activities and contributes to climate change.
It has been noted by the U.S. Environmental Protective Agency that,
unlike other methane emission sources for which there are technologies
or practices aimed specifically at reducing emissions, no control
options are currently available for reducing enteric fermentation
(22). Based upon the
results discussed above, these inhibitors of RFA-P synthase hold
promise for use as antimicrobial agents in ruminant livestock to reduce
methane emissions.
 |
ACKNOWLEDGMENTS
|
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We thank Xun-Tian Jiang,
Ryan Dull, Damireddi Sahadeva Reddy, and Gregory C. Theriot for
assistance in preparing some of the derivatives used in these
studies.
The work was supported by grants from the Agricultural
Research Division of the University of Nebraska (to S.W.R., J.M.T., and
J.L.M.), the National Institutes of Health (grant R41-GM64297 to
S.W.R., J.M.T., and J.L.M.), and the National Science Foundation (grant
MCB-9876212 to
M.E.R.).
 |
FOOTNOTES
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* Corresponding
author. Mailing address: Department of Biochemistry, Beadle Center,
University of Nebraska, Lincoln, NE 68588-0664. Phone: (402) 472-2943.
Fax: (402) 472-7842. E-mail:
sragsdale1@unl.edu. 
 |
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Applied and Environmental Microbiology, December 2003, p. 7236-7241, Vol. 69, No. 12
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.12.7236-7241.2003
Copyright © 2003, American
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