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Applied and Environmental Microbiology, December 2003, p. 7266-7272, Vol. 69, No. 12
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.12.7266-7272.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Uptake of Carbon Monoxide and Hydrogen at Environmentally Relevant Concentrations by Mycobacteria
Gary M. King*
Darling Marine Center, University of Maine, Walpole, Maine 04573
Received 2 July 2003/
Accepted 4 September 2003
 |
ABSTRACT
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Liquid
culture assays revealed a previously unreported capacity
for Mycobacterium bovis BCG, M. gordonae,
and M. marinum to oxidize CO and for M.
smegmatis to consume molecular hydrogen. M.
bovis BCG, M. gordonae, M.
smegmatis, and M. tuberculosis H37Ra oxidized CO at
environmentally relevant concentrations (<50 ppm);
H2 oxidation by M. gordonae and
M. smegmatis also occurred at environmentally
relevant concentrations (<10 ppm). CO was not consumed by
M. avium or M. microti, although
the latter appeared to possess CO dehydrogenase (CODH) genes based on
PCR results with primers designed for the CODH large subunit,
coxL. M. smegmatis and M.
gordonae oxidized CO under suboxic (10 and 1%
atmospheric oxygen) and anoxic conditions in the presence of nitrate;
no oxidation occurred under anoxic conditions without nitrate. Similar
results were obtained for H2 oxidation by M.
smegmatis. Phylogenetic analyses of coxL PCR products
indicated that mycobacterial sequences form a subclade distinct from
that of other bacterial coxL, with limited differentiation
among fast- and slow-growing
strains.
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INTRODUCTION
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Mycobacteria colonize soil and aquatic environments as well as various
vertebrate hosts (for examples see references3,
6,
10,
20, and
47). They have been
classified as slow or fast growing based on maximal growth rates in
culture (53,
57). Although many
strains require organic-rich or complex medium for optimal growth
(53), such conditions
seldom occur in situ. Thus, slow- and fast-growing strains express
traits that promote survival during nutrient starvation, when preferred
substrates are otherwise lacking, or when conditions lead to imbalanced
growth (for examples see references
8,
9,
12, and
51). In addition,
mycobacteria undoubtedly experience hypoxic and anoxic conditions with
or without nutrient limitation, which also must elicit adaptive
responses.
Numerous aspects of the molecular biology, physiology,
and ecology of bacterial survival responses have been explored for many
taxa, including Escherichia coli and other enteric bacteria
(31,
46), Bacillus
subtilis (11),
Pseudomonas (25,
54), Rhizobium
(56), and Vibrio
(39,
54), among others.
Phenomena such as sporulation, encystment, reductive cell division,
metabolic downshifts, and induction of various genetic systems have
been well documented
(30).
Mycobacterial
survival mechanisms and other adaptive responses have also been
investigated extensively
(8,
9,
12,
23,
24,
32,
38,
45,
51,
59). The nature of
latency, a form of long-term survival by the causative agents of
tuberculosis, has attracted particular attention, since some estimates
suggest that Mycobacterium tuberculosis and related
taxa infect as much as one third of the world's population
(57). These infections
involve persistence under nutrient-limited suboxic or anoxic conditions
within granulomas for periods of up to decades
(57). Reactivation of
latent mycobacteria leads to forms of tuberculosis that can be
difficult to treat (57).
Although significant progress has been made in understanding the
mechanisms of persistence by tubercle bacilli, much remains to be
learned.
Recently, Park et al.
(42) have shown that
several fast- and slow-growing mycobacteria (e.g., M.
smegmatis and M. tuberculosis H37Ra) grow
lithotrophically by using high CO concentrations. Earlier, Cho et al.
(4) documented very slow
growth on 100-ppm CO by Acinetobacter sp. strain JC1, which
has been described subsequently as a mycobacterium
(42). In contrast, growth
on high H2 and CO2 concentrations has been
reported for only one mycobacterial strain to date, M.
gordonae
(41).
The capacity
to use CO and H2 is intriguing, because H2 has
been proposed as a universal bacterial survival or maintenance
substrate (35). CO may
play a similar role. Both gases are ubiquitous, occurring in the
atmosphere at concentrations of about 0.5 to 0.6 ppm and 0.1 to 0.5
ppm, respectively (44).
H2 and CO are also found within lung or respiratory gases at
concentrations of about 5 to 50 ppm and 2 to 5 ppm, respectively
(1,
2,
17,
19,
40,
43,
47,
58). The ability of
mycobacteria to consume these gases at environmentally relevant
concentrations was assessed by using stationary-phase cultures grown
with various media and oxic, suboxic, and anoxic conditions. In
addition, sequence data for a fragment of the large subunit of CO
dehydrogenase (coxL) were obtained to assess phylogenetic
relationships between mycobacteria and other CO
oxidizers.
 |
MATERIALS AND
METHODS
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Culture growth.
M. gordonae,
M. marinum, M. microti, and
M. tuberculosis H37Ra were obtained from the American
Type Culture Collection. M. avium, M.
bovis BCG, and M. smegmatis were obtained
from M. Glickam (Memorial Sloan-Kettering Cancer Center). Cultures were
grown in serum bottles (60 or 160 cm3) containing one of
three media: Middlebrook 7H9 with oleic acid-albumin-dextrose-catalase
(OADC) supplement (4.5 ml)
(53), Middlebrook 7H9
without OADC supplement (4.5 ml), or a pyruvate (25 mM), yeast extract
(0.05%), mineral salts medium (PYE) (9.5 ml)
(29). After sealing with
butyl rubber stoppers and crimp caps, media were inoculated with 0.5-ml
volumes of suitable cell suspensions. Cultures were incubated at
37°C (30°C for M. marinum and
M. smegmatis) with shaking at 125
rpm.
CO and H2
utilization.
M.
smegmatis and M. gordonae were grown
aerobically with PYE and Middlebrook 7H9 with OADC, respectively, as
described above. Stationary-phase cells were harvested by
centrifugation, washed with a 10 mM phosphate buffer (pH 6.5), and
resuspended in buffer to an optical density (600 nm) of about 1.0. Ten
milliliters of culture was transferred to 160-ml serum bottles that
were subsequently sealed with butyl rubber stoppers and crimp caps.
Bottle headspaces contained ambient air, nitrogen with either 0.2 or
2% oxygen (suboxic treatments), or nitrogen only (anaerobic
treatments). Some suboxic and anaerobic treatments were amended with
sodium nitrate to a final concentration of 10 mM. CO or hydrogen was
added to bottle headspaces at final concentrations of up to 1%.
Headspace subsamples were obtained at intervals by using a needle and
syringe; CO concentrations were determined by gas chromatography as
previously described
(26-28).
CO
uptake by M. bovis BCG, M. marinum,
M. microti, and M. tuberculosis
H37Ra was assessed by growing cultures in Middlebrook 7H9 with or
without OADC supplement as described above. CO was added to culture
headspaces at concentrations up to 1% 2 to 3 weeks
postinoculation. Since detergents were omitted from the growth medium,
cells clumped and adhered to the bottle walls, precluding optical
measurements of cell density. CO uptake was monitored as described
above.
PCR analyses.
Genomic DNA from 2- to 4-ml volumes
of mycobacterial cultures was extracted by using a bead-beating kit
(MoBio, Inc., Hayward, Calif.). Genomic extracts were used in a PCR
analysis as described by King
(29). Briefly, primers
OMPf
(5'-GGCGGCTT[C/T]GG[C/G]AA[C/G]AAGGT-3')
and O/Br
(5'-[C/T]TCGA[T/C]GATCATCGG[A/G]TTGA-3')
were used in 50-µl reaction volumes with standard
final concentrations for buffer, deoxynucleoside triphosphates, primers
(0.1 µM each), and magnesium ion (1.5 mM). Culture extracts
were used at final concentrations of approximately 1 to 10 ng. Positive
controls included DNA extracts from a known CO oxidizer,
Oligotropha carboxidovorans; negative controls included
extracts from an organism for which no CO oxidation has been observed
in vivo, Lutibacterium anuloederans
(5). Reactants were
denatured at 94°C in an Eppendorf Mastercycler thermocycler
(Brinkmann Instruments, Inc., Westbury, N.Y.) for 3 min prior to
addition of 0.5 U of MasterTaq DNA polymerase (Brinkmann Instruments,
Inc.) at 80°C. Each amplification cycle consisted of a 45-s
denaturation step at 94°C, a 60-s annealing step with the below
temperature profile, and a 90-s extension at 72°C. Annealing
temperatures varied according to a touchdown protocol, which was
initiated at 62°C for two amplification cycles followed by
1°C stepwise decreases in annealing temperature (two
amplification cycles for each step) to a final value of 58°C,
which was used for 30 amplification cycles. A final 20-min extension at
72°C completed amplification. PCR products were visualized with
ethidium bromide gel electrophoresis and were purified with MoBio PCR
clean-up kits. Purified DNA was sequenced bidirectionally using the PCR
primers with an ABI model 377 sequencer by the University of Maine
Sequencing Facility.
Amino acid sequences were deduced from
partial coxL sequences by using ExPAsy
(http://us.espasy.org/tools/dna.html)
and were aligned with other coxL sequences by using Clustal X,
with manual adjustments as necessary. The resulting alignments were
analyzed by using PAUP* 4.0b (Sinauer Associates, Inc., Sunderland,
Mass.) to determine phylogenetic relationships among taxa. After
excluding gapped positions, 367 residues were subjected to a
neighbor-joining algorithm (1,000 bootstrap replicates) for tree
construction.
Nucleotide sequence
accession numbers.
Sequences have been deposited in
GenBank under accession numbers
AY307917
and AY333106 to
AY333109.
 |
RESULTS
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CO
and H2 utilization.
M. smegmatis grew
with either 20% H2 plus 2% CO2 or
20% CO alone as carbon and energy sources (Fig.
1). Growth was slower for both of the former than for a mineral salts
medium containing 25 mM pyruvate. Although the CO-based medium
contained the greatest amount of substrate carbon (about 7 mmol versus
2.5 mmol for pyruvate and 0.8 mmol for H2 plus
CO2), cell yields were least for CO, with intermediate
yields for H2 plus CO2 based on absorbance data
(Fig. 1).

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FIG. 1. Growth
of M. smegmatis in mineral salts plus various carbon
and energy sources: pyruvate, H2 plus
CO2, and CO. Data are means of triplicates
± 1 standard
error.
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Washed,
stationary-phase M. smegmatis incubated in a mineral
salts buffer with oxic and suboxic headspaces or under anoxic
conditions in the presence of nitrate consumed 5 ppm CO at similar
initial rates (Fig.
2). CO was not consumed by cells incubated anaerobically without nitrate
(Fig. 2). CO was depleted
to concentrations of <0.05 ppm by cells incubated with air or
10% air; cells incubated with 1% air and under anoxic
conditions with nitrate reduced CO to 1.5 ± 0.2 ppm and 1.2
± 0.2 ppm, respectively, but these values did not differ
significantly between treatments (P > 0.05). Similar
results were obtained in a second trial, which showed that nitrate
addition did not alter CO uptake by cells incubated with 1% air
(data not shown). Nitrite concentrations of more than 1 mM were
observed in anoxic plus nitrate treatments (data not
shown).
H2 was also consumed readily by washed,
stationary-phase M. smegmatis incubated in a mineral
salts buffer. Initial uptake rates were similar for cultures incubated
under oxic and suboxic conditions and under anoxic conditions in the
presence of nitrate (Fig.
3). A slight decline that did not differ statistically from zero
(P > 0.05) occurred under during anoxic incubations
without nitrate. H2 was reduced to levels of
1 ppm
under oxic and suboxic conditions and to 2 ppm under anoxic conditions
with nitrate. When H2 was added to stationary-phase cultures
grown and maintained in PYE medium, uptake was substantially faster
(>90%) than that for cultures grown and maintained in
Middlebrook 7H9 medium with OADC supplement (Fig.
4). In addition, cells in PYE reduced H2 from initial
concentrations of >3,500 ppm to <2 ppm in 48
h, while cells in 7H9 with OADC only reduced H2 from about
3,100 ppm to 2,400 ppm during the same interval.

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FIG. 4. H2
uptake by M. smegmatis grown with pyruvate-mineral
salts (open symbols) or Middlebrook 7H9 with OADC (closed symbols).
Insert shows uptake at low concentrations. Data are means
of triplicates ± 1 standard error. The bar indicates
approximate respiratory H2 concentration
range.
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M.
gordonae grown in Middlebrook 7H9 with OADC and transferred to
a mineral salts buffer consumed CO present at initial headspace
concentrations from 15 to 25 ppm (Fig.
5). Uptake rates were similar for oxic and suboxic conditions and were
notably slower for anoxic conditions with nitrate; no uptake occurred
for anoxic incubations without nitrate (Fig.
5). CO was not consumed by
oxic M. gordonae grown and maintained in Middlebrook
7H9 with OADC (data not shown) or by similarly treated M.
microti (Fig.
6). In contrast, after an initial lag, M. marinum grown
and maintained in Middlebrook 7H9 with OADC consumed CO slowly over a
period of about 3 weeks, reducing headspace concentrations from about
1% to <0.2%.
CO was also consumed by
M. tuberculosis H37Ra and M. bovis
BCG grown and maintained in Middlebrook 7H9 with or without OADC (Fig.
7). Uptake was slower than that for M. marinum, with a
reduction in concentrations from about 1 to 0.6% over 4 weeks.
M. tuberculosis H37Ra grown and maintained in
Middlebrook 7H9 with OADC also consumed CO present at initial headspace
concentrations of about 50 ppm; again, uptake was slow, with a
21% reduction in CO over about 2.5 weeks (Fig.
7).

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FIG. 7. CO
uptake by M. tuberculosis H37Ra (squares) and
M. bovis BCG (circles) under various growth
conditions: Middlebrook 7H9, open symbols; Middlebrook 7H9 plus OADC,
closed symbols; M. tuberculosis H37Ra grown with
Middlebrook 7H9 and incubated with about 50 ppm CO ( ). Data
are means of triplicates ± 1 standard
error.
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PCR,
sequence, and phylogenetic analyses.
PCR products consistent with the size
of the target coxL fragment (1,260 to 1,290 bp) were obtained
from all mycobacterial extracts except those of M.
avium (Fig.
8). Inferred amino acid sequences derived from the PCR products contained
several motifs consistent with those of known coxL, including
the active site, AYRCSFR, and binding sites for the molybdopterin
cytosine dinucleotide cofactor (e.g., QGQ, HETT, and SRS).
Mycobacterial amino acid sequences also contained several potentially
unique motifs, including KTGWVYD, RLSVQTQ, and HGAGDLP, that appeared
to be suitable targets for the design of genus-specific primers or
probes.

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FIG. 8. PCR
products from genomic extracts of selected mycobacteria using
coxL primers. Expected fragment size was ca. 1,260 to 1,290
bp.
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Phylogenetic analyses indicated that mycobacterial
coxL sequences were related to but distinct from those of most
known CO oxidizers (Fig.
9). Mycobacterial sequences clustered together and formed a subclade with
high bootstrap support (100%) by using neighbor-joining (Fig.
9) and parsimony
algorithms (data not shown). Sequences for M.
tuberculosis H37Ra, M. tuberculosis H37Rv
(data not shown), M. bovis (data not shown), and
M. microti were essentially identical and were not
phylogenetically resolvable. However, coxL from mammalian
pathogens appeared distinct from that of other
taxa.

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FIG. 9. Unrooted
neighbor-joining tree from a phylogenetic analysis of an approximately
1,100-bp coxL sequence with 1,000 bootstrap
replicates. Bootstrap support of >50% is indicated at
nodes.
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DISCUSSION
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Results presented here
and reported by others document growth by several mycobacteria,
including M. smegmatis and M.
tuberculosis H37Ra (Fig.
1)
(42), on gas phase CO at
concentrations up 50%. A mycobacterium originally described as
Acinetobacter sp. strain JC1 also grows with CO concentrations
as low as 0.01% (100 ppm), albeit very slowly
(4). Similar observations
described here and published by others demonstrate growth on high
H2 concentrations by M. gordonae and
M. smegmatis (reference
41 and Fig.
1,
respectively).
However, growth with high substrate concentrations
does not necessarily predict responses to environmentally relevant
concentrations or conditions. For example, Acinetobacter sp.
strain JC1 appears unable to grow by using ambient laboratory CO
concentrations (4);
indeed, its biomass decreases markedly over time when incubated with
ambient CO. A comparable phenomenon has been described for
methane-oxidizing bacteria, most of which cannot grow on or even
consume ambient methane concentrations under typical culture conditions
(18).
In this
study, uptake assays (Fig.
2 to
7) revealed that oxic
stationary-phase cultures of fast- and slow-growing mycobacteria
utilize CO and H2 at concentrations observed in natural
systems (i.e., <1 to 5 ppm for CO and H2
[21,
22,
26 to
28,
60]), including
ambient air and human respiratory gases (<2 to 5 ppm for CO
[1,
2,
19,
40,
44,
58] and <2
to 50 ppm for H2
[17,
43]). CO and
H2 uptake also occur during incubations with suboxic
conditions and anoxic conditions with nitrate (Fig.
2,
3, and
5). Results from the
latter incubations suggest that ambient atmospheric CO and
H2 may not support mycobacterial uptake but that activity
occurs at higher levels found naturally in respiratory gases and some
aquatic systems.
Although nitrate dissimilation has been observed
for only a few CO oxidizers incubated with high substrate
concentrations (15),
results presented here suggest that nitrate-dependent anaerobic CO and
H2 uptake at low concentrations represent potentially
important adaptive responses. Clearly, anoxic conditions occur
frequently in many natural systems
(13). Moreover, anaerobic
metabolism, and nitrate respiration in particular, appears to be
especially significant for mycobacterial persistence in granuloma
tissues. For example, Fritz et al.
(14) have shown that
M. bovis BCG deficient in nitrate respiration could
not persist in mice used as a tuberculosis model. Accordingly, CO- and
H2-dependent nitrate dissimilation may contribute to
mycobacterial persistence during periods of anaerobiosis in natural
systems and animal hosts.
CO and H2 uptake at low,
naturally occurring concentrations may also contribute to mycobacterial
maintenance metabolism under oxic conditions during periods when
supplies of preferred organic substrates are limited. Substrate
limitation typifies aquatic and soil systems
(30,
34) from which
mycobacteria are routinely isolated. Substrate deprivation also
characterizes conditions that occur within granuloma tissues
(8). Accordingly,
mycobacteria possess several mechanisms for coping with substrate
limitation, including the stringent response
(45). CO and
H2 uptake during stationary phase and decreased CO and
H2 uptake by M. smegmatis cultures grown
with a relatively rich medium (e.g., see Fig.
4) are consistent with
known responses to substrate availability and represent a potentially
important but previously unrecognized adaptive response.
Due to
certain similarities with virulent M. tuberculosis
(e.g., strain H37Rv), M. bovis BCG, M.
marinum, M. smegmatis, and M.
tuberculosis H37Ra have been proposed as model organisms for
understanding aspects of latency and other phenomena
(38,
49,
52,
55,
59). For example,
responses of M. tuberculosis H37Rv to anaerobiosis
and substrate deprivation are similar to those of M.
bovis BCG and M. smegmatis, all of which
share a number of genes involved in adaptation to stress
(38).
Several of
the strains in this study may also serve as model organisms for
understanding CO and H2 metabolism. Although M.
bovis BCG and M. tuberculosis H37Ra consume
CO more slowly than other strains (for example, compare Fig.
2 to Fig.
7), which is consistent
with relatively slow growth on CO as reported for M.
tuberculosis H37Ra
(42), both consume high
and environmentally relevant CO concentrations when grown with
Middlebrook 7H9 containing or lacking OADC supplement. M.
marinum uses CO similarly, albeit with faster uptake rates
(Fig. 6), while in
contrast, M. gordonae and M.
smegmatis CO utilization appears more sensitive to culture
conditions. Collectively these organisms encompass a range of responses
to CO, H2, and culture conditions that provide a framework
for understanding activity by pathogenic M.
tuberculosis.
Neither M. avium, which
causes a tuberculosis-like disease in immunocompromised individuals
(6), nor M.
microti, which causes a tuberculosis-like disease in rodents
and humans (37), appear
to oxidize CO under the conditions used in this study (Fig.
6; results for M.
avium not shown). Results for M. avium are
consistent with the absence of CODH genes from itsgenome
(http://ncbi.nlm.nig.gov/cgi-bin/Entrez/genom_table_cgi)
and the lack of a coxL product from PCR of genomic extracts
(Fig. 8). Results for
M. microti are somewhat enigmatic, since it yields a
coxL PCR product (Fig.
8), the sequence of which
is virtually identical to that of the coxL PCR product from
M. tuberculosis H37Ra (Fig.
9). Assuming M.
microti contains a complete cox operon, lack of CO
uptake indicates that its controls of expression differ from controls
for other mycobacteria. Further analysis of the differences between
M. microti and other mycobacteria may prove useful
for understanding the diversity of mycobacterial responses to substrate
limitation and the environmental factors that govern those
responses.
At present the range of physiological responses to CO
and the taxonomic diversity of mycobacterial CO oxidizers are unknown.
Evidence from genome sequences
(7,
16) and enzymatic assays
(42) indicate that
M. bovis and M. tuberculosis do not
contain ribulose-1,5-bisphosphate carboxylase (rubisco), a key enzyme
involved in lithotrophic CO2 fixation. This may account in
part for differences in CO oxidation (e.g., compare Fig.
2 to Fig.
7) and growth rates
(42). However, it is not
yet clear whether other slow-growing mycobacteria also lack rubisco or
differ in other respects from fast-growing mycobacteria.
Results
presented here suggest that CO utilization occurs commonly among
slow-growing mycobacteria, with some exceptions (e.g., M.
avium and perhaps M. microti). A recent
report suggests that many fast-growing strains also oxidize CO
(42). Collectively, these
taxa form a subgroup distinct from proteobacterial CO oxidizers, which
in turn form groups generally consistent with 16S phylogeny (Fig.
9). Whether mycobacterial
CO oxidizers as a group can be differentiated further from their
proteobacterial counterparts based on physiological traits remains to
be seen. Genomic evidence suggests that the cox operon in
M. tuberculosis is organized similarly to that of a
well-known
-proteobacterial carboxydotroph, Oligotropha
carboxidovorans (33,
48,
50), but this does not
imply physiological similarities. For example, O.
carboxidovorans fixes CO2 lithotrophically by using
rubisco (36), an enzyme
absent from M. tuberculosis. Interestingly, rubisco
is also absent from at least one
-proteobacterial CO oxidizer,
Silicibacter pomeroyi (M. A. Moran, personal
communication).
In summary, this is the first report of CO
utilization by slow- and fast-growing mycobacteria at ambient or
near-ambient concentrations and is the first report of mycobacterial CO
oxidation under suboxic and anoxic conditions. It is also the first
report of H2 utilization by M. smegmatis
and of CO utilization by M. bovis BCG and M.
marinum, both of which serve as model organisms for aspects of
tuberculosis. The results establish CO and H2 as substrates
that may contribute to mycobacterial maintenance metabolism during
periods of limited heterotrophic substrate
availability.
 |
ACKNOWLEDGMENTS
|
|---|
I thank M. Glickman
(Memorial Sloan-Kettering Cancer Center) for gifts of M.
bovis BCG, M. avium, and M.
smegmatis. I also thank M. Glickman and C. Nathan (Cornell
University) for helpful input.
This study was supported in part
by the C. S. Darling Endowment and NSF LExEn grant
00-85495.
 |
FOOTNOTES
|
|---|
* Mailing address: Darling Marine Center, University of Maine, Walpole, ME 04573. Phone: (207) 563-3146, ext. 207. Fax: (207) 563-3110. E-mail: gking{at}maine.edu. 
Contribution 385 from the Darling Marine Center. 
 |
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Applied and Environmental Microbiology, December 2003, p. 7266-7272, Vol. 69, No. 12
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