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Journal of Bacteriology, November 2006, p. 7759-7764, Vol. 188, No. 22
0021-9193/06/$08.00+0 doi:10.1128/JB.00934-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Structural Investigations of the Membrane-Embedded Rotor Ring of the F-ATPase from Clostridium paradoxum
Thomas Meier,1*
Scott A. Ferguson,2
Gregory M. Cook,2
Peter Dimroth,1 and
Janet Vonck3
Institut für Mikrobiologie, ETH Zürich, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland,1
Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand,2
Max-Planck-Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany3
Received 28 June 2006/
Accepted 5 September 2006

ABSTRACT
The Na
+-translocating F-ATPase of the thermoalkaliphilic bacterium
Clostridium paradoxum harbors an oligomeric ring of c subunits
that resists dissociation by sodium dodecyl sulfate. The c ring
has been isolated and crystallized in two dimensions. From electron
microscopy of these c-ring crystals, a projection map was calculated
to 7 Å resolution. In the projection map, each c ring
consists of two concentric, slightly staggered, packed rings,
each composed of 11 densities representing the

-helices. On
the basis of these results, it was determined that the F-ATPase
from
C. paradoxum contains an undecameric c ring.

INTRODUCTION
The greatest challenge to alkaliphilic bacteria living at extreme
pH values (i.e., >pH 9) is the maintenance of their intracellular
pH near neutral in order to prevent cytoplasmic alkalinization.
These bacteria maintain a

pH of 1.5 to 2.5 units (acid inside),
which opposes the bioenergetics of ATP synthesis using a H
+-coupled
F
1F
o-ATP synthase. Due to the inverted pH gradient, the total
proton motive force (

µH
+) may drop to values well below
100 mV, which is not sufficient for ATP synthesis by
conventional mechanisms.
Clostridium paradoxum is an anaerobic
thermoalkaliphile that ferments glucose rapidly to acetate,
ethanol, and CO
2 and produces ATP by substrate phosphorylation
(
3,
10).
C. paradoxum has recently been reported to contain
a Na
+-translocating F
1F
o-ATPase, and several of the enzyme's
properties suggest that its primary operation is that of an
ATP-driven Na
+ ion pump rather than that of an ATP synthase
(
7). The net result of the pumping is the formation of an electrochemical
gradient of sodium ions (

µNa
+), which is purportedly used
to drive bioenergetic processes (e.g., transport and motility).
The Fo subcomplex of F1Fo-ATP synthases is involved in trafficking ions across the membrane. Either the electrochemical ion gradient across the membrane produces torque and drives ATP synthesis or ATP hydrolysis drives the active transport of the ions. An assembly of c subunits in the membrane forms an hourglass-shaped rotary cylinder, known as the c ring. As has been documented for the Na+-dependent ATP synthases of other bacteria (1, 9, 15), the ATP synthase of C. paradoxum contains an oligomeric c ring that is stable on sodium dodecyl sulfate (SDS)-polyacrylamide gels (7) and is therefore well-suited for structural analysis (12). Structural data on c-ring stoichiometries have been determined only for Na+-ATP synthases that operate under physiological conditions (e.g., during succinate or tartrate fermentation) in the ATP synthesis direction (6) and for a Na+-translocating V-ATPase that operates in the ATP hydrolysis direction (13). In this communication, we present the structural analysis of the c ring isolated from the ATP-hydrolyzing Na+-ATPase of C. paradoxum and show that the Fo rotor is assembled as an undecameric c ring.

MATERIALS AND METHODS
Bacterial strain and culture conditions.
Clostridium paradoxum DSM 7308 was maintained as a spore stock
preparation in sterile distilled water at 4°C. Spores were
germinated by heat shocking at 75°C for 2 min, followed
by rapid cooling on ice for 45 s.
C. paradoxum was grown anaerobically
at 56°C in YTG medium, which contained, per liter, 5.3 g
of Na
2CO
3, 0.36 g of Na
2HPO
4 · 2H
2O, 0.075 g of KCl,
5 g of yeast extract, 10 g of tryptone, 0.2 g of cysteine HCl,
0.2 g of Na
2S · 9H
2O, and 0.3% (wt/vol) glucose (
7).
The pH of the medium was adjusted to 10.5 at 25°C with 5
M NaOH. Bacterial growth was routinely monitored by following
the optical density of the culture at 600 nm. For large-scale
growth, 200 liters of
C. paradoxum cells was grown anaerobically
in a 300-liter fermentor. The fermentor was inoculated with
5 liters of a preculture, and after 6 h at 55°C, the bacteria
were harvested at a final optical density at 600 nm of 0.4 by
continuous centrifugation. The cells were frozen in liquid nitrogen
and stored at 80°C.
Purification of the c ring from C. paradoxum.
The F1Fo-ATPase of C. paradoxum was purified as previously described (7). The ATPase was mixed with 1% N-lauroylsarcosine and incubated for 10 min at 65°C. After the mixture was cooled to room temperature, ammonium sulfate was added to yield 67.5% saturation. After 20 min of incubation at 25°C, precipitated protein was removed by centrifugation (23,000 x g for 20 min). The supernatant, which contained the c ring, was filtered through a 0.22-µm polyvinylidene fluoride filter unit (Millipore) and dialyzed against 10 mM Tris-HCl buffer (pH 8.0) overnight at 25°C. The c ring was then adsorbed to 1/50 volume of hydroxyapatite in an Eppendorf tube (Bio-Gel HT; Bio-Rad, Richmond, CA), and after two washes with 10 ml of dialysis buffer containing 0.15% (wt/vol) Zwittergent 3-12, the c ring was eluted with 1 M potassium phosphate buffer (pH 8.0) containing 0.15% Zwittergent 3-12. To further concentrate the c ring and remove excess salt, the sample was loaded on an Amicon Ultra-4 tube (50,000-Da molecular mass cutoff). The sample was then washed three times with dialysis buffer containing 0.15% Zwittergent 3-12. The final concentration of the purified c ring was 4.7 mg/ml.
2D crystallization of the c ring.
For crystallization in two dimensions (2D), Zwittergent 3-12 (0.4% [wt/vol])-solubilized c ring (1 mg/ml) was mixed with 1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine (POPC; Avanti Polar Lipids Inc., Alabaster, AL) at lipid-to-protein ratios of 0.5, 1.0, and 1.5 (wt/wt). The mixture was dialyzed in 25-µl buttons (Hampton Research, Aliso Viejo, CA) against 250 ml of 10 mM Tris-HCl (pH 8.0), 200 mM NaCl, and 3 mM NaN3 buffer for 24 h at 25°C and another 24 h at 37°C. The two-dimensional crystals were stored at 4°C until further analysis.
Electron microscopy and image processing.
Two-dimensional crystal samples were prepared in 4.5% (wt/vol) trehalose on molybdenum grids (Pacific Grid-Tech, San Diego, CA) (19) by the back-injection method (8). Grids were examined in a JEOL 3000 SFF helium-cooled electron microscope at 4 K at an accelerating voltage of 300 kV. Images were recorded by a spot-scanning procedure, with 24 spots by 30 spots per image on Kodak SO-163 film at a magnification of x70,000 and with an electron dose of 20 to 30 electrons/Å2. The films were developed for 12 min in full-strength Kodak D-19 developer. Images selected by optical diffraction were digitized on a Zeiss SCAI scanner using a pixel size of 7 µm, corresponding to 1 Å on the specimen. Images were processed using the MRC (4) and CCP4 (2) program suites. Data were merged to a resolution of 7 Å.
Other methods.
SDS-polyacrylamide gel electrophoresis (SDS-PAGE) was performed as described previously (16), and gels were stained with silver (14). ATPase activity was determined by the coupled spectrophotometric assay as described previously (7). The protein concentration was determined according to the bicinchoninic acid method (17), with bovine serum albumin as the standard. To dissociate the c ring, c-ring samples (2 to 5 µg of protein) were treated with 5 volumes of 12% (wt/vol) trichloroacetic acid solution and incubated on ice for 5 min. The pellet was collected by centrifugation (11,000 x g for 5 min at 4°C) and dissolved in 1% (wt/vol) SDS-containing loading buffer. Prior to being loaded on an SDS-gel, the sample was neutralized by the addition of 1-µl aliquots of 0.5 M NaOH until the color of the bromphenol blue-stained loading buffer switched from yellow to blue.

RESULTS AND DISCUSSION
Purification of the native c ring from C. paradoxum F1Fo-ATPase.
Previous investigations have shown that c-ring assemblies of
Na
+-translocating F
1F
o-ATP synthases are of exceptional stability,
even sustaining being boiled in SDS (
1,
9,
15). This remarkable
stability is shared by the c ring of the Na
+-translocating F
1F
o-ATPase
from the thermoalkaliphilic bacterium
C. paradoxum (
7). A Na
+-binding
motif is also visible in the amino acid sequence of the c subunit
of this bacterium (Fig.
1). As a consequence, the oligomeric
c ring of
C. paradoxum could be isolated by a modification of
the protocol developed for the purification of the c ring from
the
Ilyobacter tartaricus ATP synthase (
11). The results of
an analysis of the purified c-ring sample of
C. paradoxum by
SDS-PAGE and mass spectrometry-matrix-assisted laser desorption/ionization
(MS-MALDI) are shown in Fig.
2. After SDS-PAGE, the c ring migrated
as a distinct band with an apparent molecular mass of 45 kDa
(Fig.
2A, lane 2). Another protein band migrating with an apparent
molecular mass of <6.5 kDa indicated a partial dissociation
of the c ring into its monomeric units. After acidification
of the sample with trichloroacetic acid, the c ring was completely
dissociated into monomeric c subunits (Fig.
2A, lane 3). The
mobility of the c ring from
C. paradoxum was slightly faster
than that of
I. tartaricus, and a corresponding difference in
the mobilities of the c monomers was also observed. The calculated
molecular mass of subunit c from
C. paradoxum was 8,257 Da (Fig.
2B), 538 Da smaller than that of the c ring from
I. tartaricus (8,795 Da), which could account for the different mobilities
of the c monomers and of the c rings if these contained the
same number of subunits (see below).
Structural investigations of the C. paradoxum c ring.
Two-dimensional crystals of the
C. paradoxum c ring were obtained
at a lipid-to-protein ratio of 0.5 to 1.0 with the lipid POPC.
Figure
3A shows an overview of a two-dimensional crystalline
C. paradoxum c-ring sample which consists of vesicles containing
crystalline areas with dimensions up to 0.5 µm. The 2D
crystals are of plane group p1 (Table
1). A unit cell has the
dimensions 99.2 ± 0.9 Å for
a, 98.5 ± 0.4
Å for
b, and 131.1 ± 0.3° for ß and
contains two c rings, each with a stoichiometry of 11. Each
ring is in contact with three neighboring c rings. Such a packing
was also observed in the 2D crystals of the
I. tartaricus (
18,
20) and
Propionigenium modestum (
11) c
11 rings. The projection
map, calculated to 7 Å resolution (Fig.
3B), shows that
each c ring contains two concentric, slightly staggered, packed
rings, each composed of 11 densities. Whereas the inner ring
of densities is tightly packed, the outer one is more loosely
arranged, and, by analogy with the
I. tartaricus c ring, the
densities correspond to the N- and C-terminal

-helices of the
c ring, respectively. The inner and outer diameters of the rings,
measured at the density borders, are the same as in the
I. tartaricus c rings, approximately 17 Å and 50 Å.
Comparison of the crystal packing (I. tartaricus and C. paradoxum).
The packing of the 2D crystals of c rings from
C. paradoxum and
I. tartaricus ATPase appears to have the same unit cell
containing two rings, with each ring having three oppositely
oriented neighboring rings (Fig.
4). In both crystals, all three
crystal contacts in the unit cell are identical. However, the
two p1 unit cells differ significantly in their dimensions and
angles and also the packing of adjacent rings is different.
The crystal contacts in
I. tartaricus always involve two helices
from one of the rings and one helix from the other, in a staggered
arrangement, whereas in
C. paradoxum, two helices from each
ring are involved. The shape of the c ring resembles an hourglass,
and therefore, the amino acids at the ends of the helices are
responsible for the contact sites. In order to determine which
amino acids are involved, we have built the high-resolution
X-ray structure of the
I. tartaricus c ring (
12) into the electron
density obtained from the
I. tartaricus c-ring 2D crystals (
20).
According to this model, the crystal contacts consist on one
side of the membrane of the side chains between K50 and S55
(ring 1) and between P83 and G86 (ring 2). On the other side,
the contact sites are between Y80 and L87 (ring 1) and between
K50 and L59 (ring 2) (Fig.
1). Between the
I. tartaricus and
the
C. paradoxum c subunits, four amino acids differ in the
K50-L59 peptides and four amino acids differ in the Y80-L87
peptides. For clarity, we have marked in Fig.
1 the residues
in the crystal contact regions with colors. In a
C. paradoxum homology model that is based on the crystal structure of the
I. tartaricus c ring, several side chains that differ from those
in
I. tartaricus would cause several steric clashes, involving
K50 to Q, I54 to L, S55 to R, V58 to L, and G86 to N (
I. tartaricus numbering). To avoid these clashes, the rings are therefore
reoriented versus each other in the
C. paradoxum 2D crystal.
The Na+-binding site in the C. paradoxum c ring.
The Na
+-binding site in the c ring is the most notable feature
in the structure. The way a Na
+ ion is coordinated between two
subunits has profound consequences in the mechanism of ion translocation
and, hence, torque generation. Therefore, we have looked at
the binding site in the homology model (Fig.
5). Based on the
I. tartaricus model, the coordination site is located in the
middle of the membrane at the tightest part of the ring and
the entire ring is able to bind 11 sodium ions. The Na
+ ion
is bound at the interface of three helices: an N-terminal helix
and two C-terminal helices. A putative Na
+ coordination sphere
can be made up by the conserved side chains of Q28, E61, S62,
and the carbonyl oxygen of V59. Moreover, one could assume that
E61 acts not only as one of the four Na
+-binding ligands but
also as the recipient of hydrogen bonds, one hydrogen bond being
provided by Y66. In addition, the homology model shows that
all side chains in close proximity to the ion-binding site are
conserved as well. Almost all the differences between residues
from the
C. paradoxum and
I. tartaricus rings are located at
the termini or face towards the center of the ring. Based on
these observations, we propose that the sodium ion translocation
mechanisms are likely to be similar between the two c rings
(
6).
For an anaerobic bacterium like
C. paradoxum, the consequence
of having an 11-mer oligomeric c ring is that, for every three
ATP molecules hydrolyzed by the ATPase during glucose fermentation,
11 Na
+ ions are pumped across the membrane to generate the

µNa
+.
In the Na
+ F-type ATP synthases that operate primarily in the
synthesis direction during succinate or tartrate fermentation
(e.g., those in
P. modestum or
I. tartaricus, respectively),
the c ring also exists as an 11-mer. We conclude, therefore,
that an undecameric stoichiometry is suitable for both operational
modes in the F-ATP synthases.

ACKNOWLEDGMENTS
We thank Peter Tittmann and Heinz Gross (EMEZ, Electron Microscopy
Center of the ETH, Zürich, Switzerland) for the examination
of the 2D crystals and Deryck Mills for assistance with cryoelectron
microscopy. We also acknowledge Kay Diederichs (Structural Biology,
University of Konstanz, Germany) for help in the creation of
the homology model, Christoph von Ballmoos for MS-MALDI measurement,
and Stefanie Keis for critically reading the manuscript.
G.M.C. was supported by a Marsden grant from the Royal Society of New Zealand. S.A.F. was supported by an Otago postgraduate scholarship from the University of Otago.

FOOTNOTES
* Corresponding author. Mailing address: Max-Planck-Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany. Phone: 49-69-63033038. Fax: 49-69-63033002. E-mail:
thomas.meier{at}mpibp-frankfurt.mpg.de.

Published ahead of print on 15 September 2006. 

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Journal of Bacteriology, November 2006, p. 7759-7764, Vol. 188, No. 22
0021-9193/06/$08.00+0 doi:10.1128/JB.00934-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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