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Journal of Bacteriology, December 2001, p. 7017-7026, Vol. 183, No. 24
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.24.7017-7026.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Cytochromes c550,
c552, and c1 in
the Electron Transport Network of Paracoccus
denitrificans: Redundant or Subtly Different in
Function?
Marijke F.
Otten,1
John
van der Oost,2
Willem N. M.
Reijnders,1
Hans
V.
Westerhoff,1,3
Bernd
Ludwig,4 and
Rob J. M.
Van Spanning1,*
Department of Molecular Cell Physiology, Faculty of
Biology, BioCentrum Amsterdam, Free University, 1081 HV
Amsterdam,1 Department of Microbiology,
Wageningen University, 6703 CT Wageningen,2 and
Department of Mathematical Biochemistry, Swammerdam Institute
of Life Sciences, BioCentrum Amsterdam, University of Amsterdam, 1018 TV Amsterdam,3 The Netherlands, and
Biozentrum der Universitaet, D-60439 Frankfurt,
Germany4
Received 24 July 2001/Accepted 19 September 2001
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ABSTRACT |
Paracoccus denitrificans strains with mutations in
the genes encoding the cytochrome c550,
c552, or c1 and
in combinations of these genes were constructed, and their growth
characteristics were determined. Each mutant was able to grow
heterotrophically with succinate as the carbon and free-energy source,
although their specific growth rates and maximum cell numbers fell
variably behind those of the wild type. Maximum cell numbers and rates of growth were also reduced when these strains were grown with methylamine as the sole free-energy source, with the triple cytochrome c mutant failing to grow on this substrate. Under
anaerobic conditions in the presence of nitrate, none of the mutant
strains lacking the cytochrome bc1 complex
reduced nitrite, which is cytotoxic and accumulated in the medium. The
cytochrome c550-deficient mutant did
denitrify provided copper was present. The cytochrome
c552 mutation had no apparent effect on the
denitrifying potential of the mutant cells. The studies show that the
cytochromes c have multiple tasks in electron transfer.
The cytochrome bc1 complex is the electron
acceptor of the Q-pool and of amicyanin. It is also the electron donor
to cytochromes c550 and
c552 and to the cbb3-type oxidase. Cytochrome
c552 is an electron acceptor both of the
cytochrome bc1 complex and of amicyanin, as
well as a dedicated electron donor to the
aa3-type oxidase. Cytochrome
c550 can accept electrons from the
cytochrome bc1 complex and from amicyanin, whereas it is also the electron donor to both cytochrome
c oxidases and to at least the nitrite reductase during
denitrification. Deletion of the c-type cytochromes also
affected the concentrations of remaining cytochromes c,
suggesting that the organism is plastic in that it adjusts its
infrastructure in response to signals derived from changed electron
transfer routes.
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INTRODUCTION |
Many bacteria that live in soil,
sewage or sludge possess a genome that encodes a highly branched
respiratory network. The encoded network comprises various types of
dehydrogenase and of terminal oxidoreductase, which are capable of
electron input and output flow, respectively, during oxidative
phosphorylation (4). Such versatility allows these
bacteria to use a variety of electron donors and terminal electron
acceptors once they become available in their natural habitats. The
genes or gene clusters that encode the different redox enzymes are
usually tightly regulated. They are expressed only under the growth
conditions at which they are required. One of the best-studied
organisms in that respect is Paracoccus denitrificans. This
gram-negative bacterium is able to grow heterotrophically with a
variety of organic carbon and free-energy sources, as well as
autotrophically, by using hydrogen, or so-called C1 substrates such as
methylamine or methanol, as free-energy sources (2, 3, 17, 41,
42, 46). The electron transport chain used for aerobic
heterotrophic growth possesses a full complement of proteins with
counterparts in the mitochondrial respiratory chain (20,
41). Upon depletion of the organic substrates, the bacterium
induces hydrogenase and methanol or methylamine dehydrogenases, as well
as their dedicated electron acceptors, provided that their substrates
are present (16, 49).
P. denitrificans is able to reduce molecular oxygen at a
wide range of oxygen concentrations. This flexibility is the result of
its potential to synthesize three types of terminal oxidase (9,
10, 32, 33, 35), which all belong to the superfamily of heme
copper oxidases (15, 38, 44). The one that is most expressed at atmospheric oxygen concentrations is the
aa3-type cytochrome c
oxidase, which has a relatively low affinity for oxygen (31,
36). Its expression level decreases with decreasing oxygen
concentrations (5). The second type of oxidase is the cbb3-type cytochrome c oxidase,
which has a relatively high affinity for oxygen and which is
increasingly synthesized at decreasing oxygen concentrations (10,
31). The third type of oxidase is a
ba3-type quinol oxidase, which is the
counterpart of the bo3-type quinol
oxidase found in Escherichia coli (8, 35). The
ba3-type oxidase receives electrons
from ubiquinol, is expressed and increasingly active under conditions
that give rise to high reduction levels of the Q-pool, and apparently
serves to prevent that by rapidly transferring electrons from ubiquinol
to oxygen (27).
P. denitrificans is also able to synthesize four types of
N-oxide oxidoreductase, which catalyze the sequential reduction of
nitrate to dinitrogen gas via the intermediates nitrite, nitric oxide,
and nitrous oxide. This denitrification process takes place at nearly
anoxic conditions, during which nitrate substitutes for oxygen as a
terminal electron acceptor. Nitrate, nitrite, nitric oxide, and nitrous
oxide reductases are expressed when nitrate is present and oxygen is
virtually absent (2, 3, 14, 42).
Much of our knowledge on how electrons are transferred from the
dehydrogenases to the terminal oxidoreductases stems from the analyses
of mutants with mutations in genes encoding electron carriers that make
up the respiratory network (9, 11, 50, 51, 52, 53).
However, it has thus far been difficult to understand the exact role of
the different types of cytochrome c in situ since mutations
in their corresponding genes did not give clear phenotypes if at all.
Apparently, cytochromes c or other small redox carriers can
substitute for each other. The present study sought to elucidate the
roles of the cytochromes c550 and
c552 and the cytochrome
bc1 complex in electron transport in
P. denitrificans. The approach was to isolate P. denitrificans strains with mutations in the genes encoding these
three types of cytochrome c and in combinations of these
genes in order to study the resultant effects of these mutations on
their growth characteristics.
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MATERIALS AND METHODS |
Bacterial strains, plasmids, and growth conditions.
The
strains and plasmids used in this study are listed in Table
1. E. coli strains were
cultivated in yeast-tryptone medium at 37°C. P. denitrificans strains were grown at 34°C in batch cultures
either aerobically, i.e., in 2-liter flasks filled with 300 ml of
medium and shaken vigorously; semiaerobically, i.e., in 1-liter flasks
filled with 500 ml of medium and slowly shaken; or anaerobically, i.e.,
in flasks almost completely filled with medium and not shaken. The
P. denitrificans strains were grown on mineral batch medium
containing Lawford trace solution and methylamine (100 mM), succinate
(25 mM), or butyrate (25 mM) as carbon and free-energy sources at pH
7.0 (7, 24). Anaerobic cultures were supplemented with 100 mM potassium nitrate as an electron acceptor. Inhibition of the
cytochrome bc1 complex was achieved by
addition of 5 µM myxothiazol to the cultures (24). Cells
were harvested in the mid-exponential phase of growth when the
turbidity at 660 nm was ca. 1.0 cm
1. When
appropriate, antibiotics were added, i.e., rifampin (40 mg
liter
1), streptomycin (50 mg
liter
1), kanamycin (50 mg
liter
1), or ampicillin (100 mg
liter
1). Residual nitrite in denitrifying
cultures was determined by using nitrite strips from Boehringer.
Isolation of intact cells and membrane fractions.
Cells were
washed twice in 0.1 M of Tris (Tris hydroxymethyl aminomethaan)-HCl at
pH 7.5 at 4°C and then suspended in the same buffer to a turbidity of
50 at 660 nm. After the addition of MnCl2 to 10 mM and DNase I to 2 mg ml
1, cell extracts were
obtained by using a French pressure cell (American Instrument Company,
Silver Spring, Md.) at 10,000 lb/in2. Cell debris
was spun down for 5 min at 17,000 × g, and the
resulting supernatant was centrifuged at 438,000 × g
for 30 min at 4°C in order to separate the soluble and membrane
fractions. The pellet containing the membrane faction was resuspended
in 0.1 M Tris-HCl at pH 7.5. Protein concentrations were determined by
using the BCA Kit (Pierce) with bovine serum albumin as a standard.
Samples (at 10 mg of protein ml
1) were
routinely stored at
80°C.
PAGE and heme staining.
Sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was carried out
by using the Bio-Rad Mini-Protean II Gel System with 13% slab gels
(23). The samples (100 µg of protein each) were diluted
in sample buffer (60 mM Tris-HCl, pH 6.8; 25% glycerol [vol/vol];
2% SDS; 50 mM 2-mercaptoethanol; 50 mM dithiothreitol) and incubated
at room temperature for 10 min. The heme-binding proteins were detected
by using chemiluminescent substrate "Lumi-Light Plus" (Boehringer
Mannheim) on a high-performance chemiluminescence film (Amersham)
(29). The program NIH-Image/ppc 1.56b61 was used for
densitometric analyses.
Spectral analyses.
Spectra of dithionite (5 mg/ml) reduced
cell suspensions (turbidity at 660 nm of 50) were recorded in the
dual-wavelength mode of an automated Aminco/SLM DW-2 UV/Vis
spectrophotometer with the reference set at 578 nm. During kinetic
measurements, the reduction level of cytochromes c as a
function of time was recorded at 552 nm with the reference set at 578 nm. Cuvettes were thermostated at 20°C. Oxygen was released from 20 µl of 0.3% hydrogen peroxide by intracellular catalase activity.
Dithionite was added to a final concentration of 5 mg/ml.
Oxygen consumption.
Oxygen consumption rates of cells were
measured polarographically with a Clark-type oxygen electrode (Yellow
Springs, Ohio) in 1 ml of Tris-HCl (pH 7.5) at 25°C. Succinate (10 mM) was added as an electron donor. Where indicated, the electron flow
via cytochrome bc1 was inhibited by
adding antimycin A (6 µM) and myxothiazol (6 µM).
DNA manipulations.
Routine cloning procedures were performed
according to standard protocols (1). The construction of
marked and unmarked mutations in chromosomal genes is described in
Results and was performed as described earlier (52).
E. coli TG1 was used routinely for cloning procedures.
E. coli HB101(pRK2020) was used as the helper strain in the
conjugative transfer of plasmids via triparental mating.
Construction of cytochrome c single and multiple
mutant strains.
The following strains were constructed in an
earlier study (11): Pd21.21
(cycA::Kmr) with an
interrupted cytochrome c550 encoding
gene, Pd21.31 (
cycA) with an unmarked mutation in the
cytochrome c550 encoding gene, Pd24.21
(fbcC::Kmr) with an
interrupted cytochrome c1 encoding
gene, and the double mutant strain Pd92.06 (
cycA
fbcC::Kmr). In this study, an
internal part of the chromosomal fbcC gene that contained
the gene cartridge encoding kanamycin resistance (Kmr) in strains Pd24.21 and Pd92.06 was removed
in order to make the fbcC mutations in these strains
unmarked. For this, plasmid pBL250, which is a pBR322 derivative
containing the fbcC gene and flanking regions
(22), was cut with XhoI and SalI and
then religated. As a result, a 1,060-bp fragment within the
fbcC gene was removed. The fragment with the mutated gene
was then cloned in suicide vector pRVS1, yielding plasmid pRTd24.31.
This plasmid was used in the gene exchange technique described earlier
(52) in order to isolate strains Pd24.31
(
fbcC) and Pd92.07 (
cycA
fbcC), which have unmarked mutations in their chromosomal
fbcC genes. In this gene exchange technique, mutants with
unmarked mutations are selected by using the E. coli lacZ
gene as a suicide gene (52). Plasmid pAT8 harbors the
cytochrome c552 encoding cycM gene in which the gene cartridge encoding kanamycin
resistance was inserted in the internal StuI site
(43). A 4.6-kb NotI fragment of this plasmid,
which contains the mutated cycM gene, was cloned in suicide
vector pRVS2, yielding vector pRTd28.22. This plasmid was used in the
gene exchange technique described earlier (51) in order to
isolate strains Pd28.22
(cycM::Kmr), Pd92.26
(
cycA
cycM::Kmr), Pd92.28
(
fbcC cycM::Kmr), and
Pd93.14 (
cycA
fbcC
cycM::Kmr), which all have marked
mutations in their chromosomal cycM genes. The correctnesses
of the mutations were confirmed by Southern analyses of their
chromosomal DNA. As a result of these constructions, we had mutant
strains with mutations in one, two, or three of the genes encoding
cytochromes c550,
c552, and
c1.
 |
RESULTS |
Spectral analyses of the cytochrome c single and
multiple mutant strains.
P. denitrificans wild-type and
mutants with single and multiple mutations in the cycA,
cycM, and fbcC genes were cultured aerobically in
mineral medium containing succinate as the sole carbon and free-energy
source. Cell suspensions from these cultures exhibited composite
-bands of ca. 555 nm at which cytochromes b (at ca. 560 nm) and c (at ca. 550 nm) have their maximum absorbance (Fig. 1). It should be noted that the
absorbance at that wavelength reflects not only all three cytochromes
c that are important here, i.e., cytochromes
c550,
c552, and
c1, but also further contributions from other cytochromes c as well. Both the shape and the
height of that composite band differed between the strains. Only the cytochrome c552-deficient mutant
displayed a spectrum very similar to that of the wild-type strain.
Paradoxically, strains Pd24.31 (c1 deficient)
and Pd92.28 (c552/c1
deficient) had a higher cytochrome c peak than the wild-type
strain, whereas that peak is lower in strains Pd21.31 and Pd92.26,
which are cytochrome c550 and
cytochrome c550/c552-deficient
mutants, respectively. A sharp decrease in the height of that band is
observed in the spectra of strains Pd92.07 and Pd93.14, which are
cytochrome
c550/c1- and
cytochrome c550/c552/c1-deficient
mutants. Another remarkable observation is that the peak at ca. 605 nm
where hemes a of cytochrome
aa3 have their maximum absorbance is
decreased to ca. 20% of the wild-type signal in the spectra of strains
Pd21.31 (cytochrome c550 deficient), Pd92.26 (cytochrome
c550/c552
deficient), and Pd93.14 (cytochrome c550/c552/c1
deficient).

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FIG. 1.
Dithionite-reduced absorption spectra at room
temperature of cell suspensions from the wild-type strain (Pd1222
[C]) and from mutant strains deficient in cytochrome
c1 (Pd24.31 [A]), cytochromes
c552/c1 (Pd92.28
[B]), cytochrome c552 (Pd28.22 [D]),
cytochromes
c550/c1 (Pd92.07
[E]), cytochrome c550 (Pd21.31 [F]),
cytochromes
c550/c552
(Pd92.26 [G]), or cytochromes
c550/c552/c1
(Pd93.14 [H]). The cells had been grown aerobically to their
mid-exponential phase of growth (optical density at 660 nm
[OD660] = ~1.0 cm 1) in batch
cultures with succinate as the carbon and free-energy source.
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In order to study the effect of the oxygen concentration on the
spectral properties of the mutant cells, the spectra of cells
grown
semiaerobically were also recorded (results not shown).
These spectra
show that the cytochrome
c peak of strain Pd24.31
(cytochrome
c1 deficient) is ca. four
to five times higher than
that of the wild-type strain and that the
cytochrome
b peak is
also slightly increased. The cytochrome
c550/c1-deficient
double-mutant
strain, in contrast, showed a decrease in both the
cytochrome
c and cytochrome
b absorption bands.
Apparently, the cytochrome
c mutations, as well as the
oxygen concentration, affect the concentrations
of cytochromes
c other than the ones that were mutated. The consequences
of
oxygen deprivation, as well as of the cytochrome
c
mutations,
include reduced electron flow through the respiratory
system,
resulting in reduction of its constituent components. Perhaps
P. denitrificans possesses a signal transduction mechanism
that
governs the expression of cytochrome
c genes in
response to that
altered redox state. In order to test that hypothesis,
P. denitrificans wild-type cells were cultured aerobically
under different conditions,
between which we expected the reduction
levels of the redox enzymes
to differ. In one approach,
P. denitrificans wild-type cells were
grown aerobically in mineral
medium with either succinate or butyrate
as the sole carbon and energy
source. Since butyrate is a more
reduced substrate than succinate, one
would expect a rise in the
electron-input rates and thus higher
reduction states of the redox
enzymes in butyrate-grown cells compared
to succinate-grown cells.
The cytochrome
c peak of
butyrate-grown cells was almost five
times higher than that of the
succinate-grown cells (results not
shown). In another approach,
P. denitrificans wild-type cells
were cultured aerobically
in mineral medium with succinate as
the sole carbon and free-energy
source and in the presence of
increasing concentrations of myxothiazol,
which is an inhibitor
of the cytochrome
bc1 complex. The growth rates of these
cultures
did not differ significantly from one another, indicating that
the myxothiazol-treated cells had sufficiently adapted their mode
of
respiration in response to the presence of the inhibitor. Spectral
analyses of these cultures showed an increase in the cytochrome
c peak with increasing concentrations of myxothiazol
ultimately
resulting in a more than fivefold increase of the cytochrome
c peak at a concentration of 5 µM myxothiazol (results not
shown).
PAGE and heme staining of cytochrome c single and
multiple mutant strains.
In order to study the cytochrome
c composition of the mutants in more detail, cells from
cultures grown aerobically on succinate were broken and centrifuged to
yield soluble and membrane fractions. For each fraction, the proteins
were separated by PAGE, after which the cytochromes c were
visualized by a heme staining approach. Two important conclusions can
be drawn from the results (Fig. 2).
First, they confirm that the mutations in the cycA,
cycM, and fbcC genes of the mutants had resulted
in the inability to express the corresponding cytochromes c
as judged by the absence of heme-stained proteins of 14 kDa (cytochrome
c550) in the periplasmic fractions
(Fig. 2A) and of 22 kDa (cytochrome
c552) and ca. 60 kDa (cytochrome
c1) in the membrane fractions (Fig.
2B) of the corresponding mutants. The faint band at ca. 14 kDa observed
in the lane of the cytochrome
c550/c552-deficient
double mutant in Fig. 2A probably originates from a cytochrome
c different from cytochrome
c550 and which is specifically
expressed in this mutant. This band is not present in the lane of its
parent strain Pd21.31 (Fig. 2A, lane 2). We monitored the staining of
the cytochromes c present in that part of the gel over time
(Fig. 3) and noticed that cytochrome
c550 stained much faster than the
unknown one (maximally stained after 1 min and after 15 min,
respectively). The second conclusion is that the knockout of
cytochromes c550, c552, and
bc1 singly and in various combinations
had resulted in the increased expression of other types of cytochrome
c. The periplasmic fractions of the wild-type strain and the
cytochrome c552-deficient strain
contained moderate levels of cytochrome c550, but its concentration was more
than 10-fold increased in the cytochrome
c1- and cytochrome
c552/c1-deficient
mutant strains. In addition, all of the strains that lacked the
cytochrome bc1 complex induced high
levels of cytochrome c peroxidase (45 kDa), as well as two
cytochromes c of ca. 25 and 35 kDa. The 35-kDa cytochrome
c was abundant in the cytochrome
c550/c552-deficient mutant strain. Since this abundance correlated with the appearance of
the unknown cytochrome c of 14 kDa, the latter might be a
heme containing breakdown product of the former. In contrast
to the cytochrome bc1 mutants, the
cytochrome
c550/c552-deficient
mutant strain did not show a significantly increased induction
of cytochrome c peroxidase nor of the 25-kDa cytochrome
c. This correlation could indicate that the 25-kDa
cytochrome c was a heme-containing breakdown product of
cytochrome c peroxidase. Inspection of the cytochromes
c in the membrane fraction indicated that the concentrations of the cytochrome bc1 complex and of
cytochrome c552 in the mutants still
able to express them were not significantly different from those of the
wild-type strain. In contrast, the intensities of the bands containing
the cytochrome c containing subunits of the cbb3-type oxidase, CcoO and, to a lesser
extent, CcoP, were up to five times higher in the cytochrome
bc1 mutants compared to the wild-type
strain.

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FIG. 2.
SDS-PAGE and subsequent heme staining of cytochromes
c in the soluble fractions (A) and membrane fractions
(B) of P. denitrificans wild-type (lanes 1) and mutant
strains deficient in cytochrome c550 (lanes
2), cytochrome c552 (lanes 3), cytochrome
c1 (lanes 4), cytochromes
c550/c1 (lanes
5), cytochromes
c550/c552 (lanes
6), cytochromes
c552/c1 (lanes
7), and cytochromes
c550/c552/c1
(lanes 8). Growth and harvesting conditions were as shown in the legend
of Fig. 1. The fractions, containing 100 µg of protein each, were
obtained from one set of experiments and analyzed in parallel. The
relative concentrations of heme c-containing proteins
within each gel were determined by densitometric analyses. The
c-type cytochromes indicated are cytochromes
c550 and c552
(CycA and CycM), cytochrome c peroxidase (Ccp), subunits
of the cbb3-type oxidase (CcoO and CcoP),
and cytochrome c1 (FbcC). Sizes of the
molecular mass markers are indicated on the right of the gels in
kilodaltons.
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FIG. 3.
Time-dependent staining of soluble cytochromes
c run into the gel to the position of the 14-kDa marker.
Lane 1, the cytochrome
c550/c552-deficient
mutant; lane 2, the cytochrome c1-deficient
mutant. The exposure times of the film are indicated at the left in
minutes.
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Growth characteristics of the cytochrome c mutants.
P.
denitrificans wild-type strain and the cytochrome
c550,
c552, and
bc1 single and multiple mutants were
grown in mineral medium under three different growth conditions. The
increase in cell density with time was determined, as well as their
final turbidity at 660 nm. The growth conditions were (i) aerobic with succinate as the sole electron donor, (ii) aerobic with methylamine as
the sole electron donor, and (iii) anaerobic with succinate as the
electron donor and nitrate as the electron acceptor. The data were used
to estimate the maximum specific growth rates and the maximum cell
numbers (as determined from turbidity measurements) of the strains.
These values are presented in Table 2.
The maximum specific growth rates of succinate-grown cells did not
differ significantly between the strains. The final turbidities
of the
mutant cultures, however, were all ca. 10% less compared
to that of
the wild type. The only exception was the cytochrome
c552-deficient mutant, which had
wild-type growth
characteristics.
More-drastic differences between the strains were observed when they
were cultured in medium with methylamine as the sole
free-energy
source. Except for the cytochrome
c552-deficient mutant,
all of the
strains had decreased maximum specific growth rates
and final
turbidities compared to the wild-type strain. The most
profound
decrease in growth rate was observed for the cytochrome
c1-, cytochrome
c550/c1-, and
cytochrome
c550/c552-deficient
mutant
strains, which grew up to 50% more slowly than the wild-type
cells.
The cytochrome
c550/c552/c1-deficient
triple mutant was unable
to grow on methylamine. Apparently, a possible
electron transfer
route from amicyanin, the dedicated electron acceptor
of methylamine
dehydrogenase (
53), to any of the
cytochrome
c oxidases cannot
support growth of the mutant
strain under this condition. Since
all of the cytochrome
c
double mutants (cytochrome
c550/c552-,
cytochrome
c550/c1-, and
cytochrome
c552/c1-deficient
mutant strains)
were able to grow on methylamine, cytochrome
c550, cytochrome
c552, or the cytochrome
bc1 complex all suffice for electron
flow
from amicyanin to
oxygen.
Electrons that are passed on via amicyanin to the cytochrome
bc1 complex may either be directed to
oxygen via the Q-pool and
the
ba3-type
quinol oxidase in a reversed electron flow mechanism
(
45)
or via cytochrome
c1 to any of the
cytochrome
c oxidases.
In order to study the fate of
electrons in a cytochrome
c550/c552-deficient
mutant, this strain was grown with methylamine as an electron
donor in
the presence of 10 µM antimycin A and myxothiazol in
order to
inactivate the heme
b-containing subunit of cytochrome
bc1. As a control, we also cultured
strain Pd93.11, a strain that
lacks the
cbb3- and
aa3-type oxidases. This strain has
been shown
to be able to grow on methylamine by redirecting the
electrons
from cytochromes
c via the cytochrome
bc1 complex and the Q-pool
to the
ba3-type quinol oxidase
(
45). Both the wild-type strain
and the cytochrome
c550/c552-deficient
mutant were still able
to grow under this condition, indicating that
the inhibition of
the heme
b-containing subunit of the
cytochrome
bc1 complex did
not prevent
electron transport in these strains. The double cytochrome
c
oxidase mutant, however, was unable to grow under this condition,
indicating that the reversed electron transfer route from methylamine
to oxygen in this strain was completely blocked. The experiments
described above imply that, in the absence of cytochromes
c550 and
c552, electrons can flow from the
cytochrome
bc1 complex directly
to one
or both of the cytochrome
c oxidases, most probably to
the
cbb3-type oxidase since the
aa3-type oxidase is hardly present
in
the cytochrome
c550/c552-deficient
mutant. In order to test
this hypothesis, we constructed a
triple-mutant strain, which
lacks cytochromes
c550 and
c552, as well as the
aa3-type oxidase.
This strain grew as
fast on methylamine as the cytochrome
c550/c552-deficient
strain, indicating that electrons from the cytochrome
bc1 complex
can indeed be directly
transferred to the
cbb3-type
oxidase.
All mutant strains were also able to grow on plates supplemented with
methanol as the sole source of free energy, except for
the triple
mutant lacking cytochromes
c550 and
c552 and the cytochrome
bc1 complex. Quantitative data are not
included since the cells
grew poorly in batch cultures with methanol as
sole source of
carbon and free
energy.
In the course of our studies on the role of the cytochromes
c in electron transport under denitrifying conditions, we
noticed
that cytochrome
c550-deficient
mutants that were cultured in brain
heart infusion (BHI) broth were
unable to reduce nitrite and grew
to low turbidities. This may well
have been due to the cytotoxicity
of nitrite, which accumulated in
these cultures. Earlier studies
with that mutant, however, had
indicated that its growth characteristics
during denitrification were
similar to those of the wild-type
strain when they were raised in
mineral medium supplemented with
succinate and nitrate
(
51). Apparently, a component essential
for denitrifying
growth in the latter medium was absent from the
BHI broth. We therefore
added the individual ingredients of the
mineral medium to BHI broth and
studied the resultant effects
on denitrifying growth. We found that the
cultures of the cytochrome
c550-deficient mutant that had copper
added to it were able to
denitrify again. In order to study the
importance of that metal
on the denitrifying growth of the mutant
strains, we determined
their characteristics of growth in media with or
without added
copper. The results presented in Table
2 show that the
cytochrome
bc1 mutant strains had
disturbed growth, accumulated nitrite,
and reached final turbidities of
ca. 25% of the wild-type value.
All other mutants showed
characteristics comparable to those of
the wild-type when they were
cultured in medium that contained
copper. In the absence of copper,
however, both the cytochrome
c550 and
cytochrome
c550/c552-deficient
mutant strains displayed
characteristics similar to those of the
cytochrome
bc1 mutants.
They showed
disturbed growth as a consequence of nitrite accumulation
and did not
produce gas in the culture medium, which would be
diagnostic for the
operation of a fully competent denitrification
pathway. Apparently,
electron transfer to at least the nitrite
reductase requires a
copper-containing component, which compensates
for the loss of
cytochrome
c550. We also noticed that
the supernatants
of the cytochrome
c550 and cytochrome
c550/c552-deficient
mutants,
which were raised under denitrifying growth conditions in
mineral
medium without copper, were yellow, whereas the supernatants of
the other strains were not. The component responsible for this
yellow
color could not be precipitated with trichloroacetic acid,
indicating
that it was not a protein. The spectrum of the yellow
component
displayed an absorption band with a maximum at ca. 360
nm.
Kinetics of electron transport in cytochrome c
mutants.
P. denitrificans wild-type strain and
cytochrome c mutants were grown under aerobic conditions
with succinate as the sole carbon and free-energy source. Cells grown
to their mid-exponential phase of growth were harvested, washed, and
resuspended. The oxygen consumption rates of these suspensions were
determined with succinate as the electron donor (Table
3). The data show that the oxygen consumption rates of the strains that still had the potential to
synthesize the cytochrome bc1 complex
were comparable. Those that lacked the complex had rates ca. 15%
higher than that of the wild-type strain. In the presence of antimycin
A and myxothiazol, inhibitors of the cytochrome
bc1 complex, the oxygen consumption rates of the wild-type and cytochrome
c552-deficient mutant were almost
halved compared to the uninhibited condition, whereas they were ca.
25% decreased in cytochrome c550- and
cytochrome
c550/c552-deficient mutants. The respiratory inhibitor hardly if at all affected the oxygen
consumption rates of the cytochrome
c1-deficient strains.
We also studied the kinetics of oxidation and reduction of cytochromes
c present in the wild-type and the cytochrome
c1-deficient
mutant strains. The
suspensions were incubated with succinate
as reductant to the
cytochromes, the reduction level of which
was recorded
spectrophotometrically in time (results not shown).
Oxygen was supplied
to these suspensions at a concentration of
1 mM by adding hydrogen
peroxide, which is rapidly converted into
oxygen and water by
intracellular catalase activity (
12). The
traces show that
the cytochromes
c became more oxidized upon the
addition of
oxygen and became reduced again after oxygen had been
fully consumed.
The wild-type strain consumed the supplied oxygen
at a rate of ca. 130 nmol of oxygen min
1 mg of
protein
1 (results not shown). Cytochrome
bc1-deficient strains did so
between
10 to 15% faster. The subsequent reduction of the cytochromes
c in the latter strains occurred at an at least
40-fold-lower
rate than that of the wild-type strain (results not
shown).
 |
DISCUSSION |
The studies presented in this study have shed more light on the
roles of cytochromes c550,
c552, and
c1 in controlling the rates of
electron transfer in P. denitrificans grown at various growth conditions. The data also indicate that cytochrome c
deficiencies by the mutations are in many cases accompanied by changed
levels of expression of other respiratory enzymes.
Much of our knowledge on the makeup and function of the P. denitrificans respiratory system at various growth conditions has been described in earlier studies (reviewed in references 2, 3, and 46). The roles of cytochromes
c550,
c552, and
c1 in that electron transport have now
been defined by careful examination of the growth characteristics of
mutant strains lacking one or more of these types of cytochrome. A
scheme of the flexible respiratory network of methylamine grown cells
as based on these studies is presented in Fig.
4. It shows that cytochrome
c550 is a potential electron donor to
any of the cytochrome c oxidases. Cytochrome c552 is a dedicated donor to only the
aa3-type oxidase, in agreement with
the observation that cytochrome c552
made part of a purified supercomplex containing the cytochrome
bc1-complex and the
aa3-type oxidase, which was functional
in electron transport (4). Our results further show that
cytochrome c552 is not a donor to the cbb3-type oxidase in agreement with an
earlier observation that a mutant strain lacking cytochromes
c1 and
c550, as well as the aa3-type oxidase, was unable to grow
with methylamine as the sole free-energy source, whereas it could still
express cytochrome c552 and the
cbb3-type oxidase (11).

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|
FIG. 4.
Scheme of the respiratory network of P.
denitrificans during growth with methylamine as sole source of
free energy. The sequential oxidation of methylamine to carbon dioxide
(dashed arrows) is mediated by methylamine dehydrogenase (MADH),
formaldehyde dehydrogenase (FyDH), and formate dehydrogenase (FDH).
Physiologically important electron transfer routes (straight arrows)
from NADH dehydrogenase (NADHDH) and MADH to the terminal oxidases were
deduced from the studies in this study. amic, amicyanin.
|
|
The studies described here present a qualitative view on all possible
electron transfer pathways during methylamine oxidation as they operate
in the various mutant strains. Our observation do not prove that all of
these pathways operate to the same extent in the wild-type cells as
they do in these mutants. The deletions of cytochromes
c1 and
c550 resulted in decreased maximum
specific growth rates of the mutant strains by 40 and 20%,
respectively. These cytochromes are apparently essential for optimal
performance of the methylamine oxidizing pathways since they have
multiple tasks in connecting quinol and amicyanin oxidation to
cytochrome c reduction. However, it is not possible to
deduce from these numbers the relative electron fluxes through the
parallel electron transfer pathways in the wild-type cells. This is
because every mutation in these mutants gives rise to changes in the
kinetics of the remaining electron transfer reactions as a consequence of (i) changes in the expression levels of the respiratory components (28) and (ii) changes in the reduction levels of them
(27).
The respiratory network of methanol-grown cells is quite similar to
that of methylamine-grown cells. The difference is that methylamine
dehydrogenase and its dedicated electron acceptor amicyanin (19,
53) are replaced by a methanol dehydrogenase and its dedicated
electron acceptor cytochrome c551i
(18, 50). Just like amicyanin, this cytochrome requires
another cytochrome c as electron acceptor and is unable to
donate to any of the cytochrome c oxidases.
When the cytochrome c-deficient strains were grown with
succinate as the carbon and free-energy source, their maximum specific growth rates were quite comparable to that of the wild-type strain, indicating that these mutant cells adapt completely in that respect to
compensate for the loss of any of these cytochromes c. That adaptation involves higher electron transfer fluxes through the ba3-type quinol oxidases since these
mutants display lower maximum cell numbers (since this pathway is less
efficient with respect to free-energy transduction) and higher maximum
oxygen uptake activity via the
ba3-type oxidase. This result is in
agreement with earlier studies on cytochrome
bc1-deficient mutants
(27).
The analyses of the mutants grown under denitrifying conditions
indicated that cytochrome c1 is
essential for the reduction of nitrite to dinitrogen gass. This result
is in agreement with the view that the cytochrome
bc1 complex is a compulsory
intermediate in electron transfer from the Q-pool to the nitrite,
nitric oxide, and nitrous oxide reductases (reviewed in reference
34). At least up to and including nitrite reductase, the
pathway also involves cytochrome c550,
which appeared to be an essential electron donor to this enzyme during
copper limitation. In the presence of copper, however, the mutation in
the gene encoding cytochrome c550 had
hardly any effect on the denitrifying potential of that mutant strain,
indicating that a copper-dependent electron carrier substituted for
cytochrome c550 (51). A
likely candidate is pseudoazurin, which is a type I blue copper protein
and able to mediate electron transfer between the cytochrome
bc1 complex and the nitrite, nitric
oxide, and nitrous oxide reductases in vitro (21, 25, 26).
Indeed, it has been shown that a mutant strain deficient in cytochrome
c550 and pseudoazurin failed to reduce nitrite (30; Stuart Ferguson, unpublished data).
Cytochrome c552 is apparently
redundant in the denitrifying pathways since we observed virtually no
effect of its absence on the denitrifying potential of the mutant cells
and since it was unable to compensate for the loss of cytochrome
c550 under copper limitation.
In the course of our studies, we noticed that the expression levels of
certain types of cytochrome c was increased in aerobically grown mutant strains, especially in those that lacked the cytochrome bc1 complex. Apparently, the mutations
in the cytochrome c-deficient mutants cause metabolic
changes that result in changes in transcription activation of the genes
encoding these cytochromes c. One of these metabolic changes
affects the activity of the FnrP protein, which is a transcription
activator regulating the expression of genes in response to oxygen
limitation (47). This conclusion is based on the
observation that the concentrations of the cytochrome
c-containing subunits of the
cbb3-type oxidase and cytochrome
c peroxidase, the genes of which are regulated by FnrP
(47), are increased in the mutant strains. Some of the
mutants, i.e., the cytochrome c550
single mutant, the cytochrome
c550/c552
double mutant, and the cytochrome
c550/c552/c1
triple mutant, also displayed lower levels of the
aa3-type oxidase as judged by
spectroscopic analyses. That phenomenon has been described earlier for
the cytochrome c550-deficient mutant
(51). The reason for the observed decrease is not clear at
present but cannot be merely ascribed to the cycA mutation
alone since the cytochrome
c550/c1-deficient
double mutant has wild-type levels of the
aa3-type oxidase.
Taken together, these observations indicate that the performance of the
respiratory network is continuously monitored and that its makeup
adapted in response to changes in that performance apparently in order
to maintain an optimal electron flux at each given growth condition.
 |
ACKNOWLEDGMENTS |
This work was supported by the Chemical Sciences Foundation (CW),
with additonal financial aid from The Netherlands Organization for
Scientific Research (NWO).
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Molecular Cell Physiology, Faculty of Biology, Free University, De
Boelelaan 1087, 1081 HV Amsterdam, The Netherlands. Phone:
31-20-4447179. Fax: 31-20-4447229. E-mail:
spanning{at}bio.vu.nl.
 |
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275:217-220[CrossRef][Medline].
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Journal of Bacteriology, December 2001, p. 7017-7026, Vol. 183, No. 24
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.24.7017-7026.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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