Two-dimensional Crystallization of the Light-harvesting I

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J. Mol. Biol. (1997) 265, 107–111
COMMUNICATION
Two-dimensional Crystallization of the
Light-harvesting I–Reaction Centre Photounit
from Rhodospirillum rubrum
Thomas Walz1 and Robin Ghosh2*
1
Maurice-Müller Institute for
Microscopic Structural
Biology, Biozentrum der
Universität Basel
Klingelbergstr. 70, CH-4056
Basel, Switzerland
2
Laboratory for Bioenergetics
University of Geneva
Chemin des Embrouchis 10
CH-1254 Jussy-Lullier/GE
Switzerland
A stoichiometric unit of the light-harvesting complex I and the reaction
centre (LHI-RC complex) has been isolated from a carotenoid-less mutant
of the purple non-sulphur bacterium Rhodospirillum rubrum by mild
solubilization of photosynthetic membranes with the phospholipid
detergent diheptylphosphatidylcholine. Dialysis of the isolated LHI-RC
complexes in the presence of added dioleoyl-sn-phosphatidylcholine
produced ordered two-dimensional crystals. Digital image processing
revealed that the LHI-RC are packed together in a square lattice
(a = b = 16.3 nm). The dimensions of the LHI ring are essentially identical
with those determined from two-dimensional (2D) crystals of purified
carotenoid-containing light-harvesting I complexes after analysis by
cryo-electron microscopic techniques or from negatively stained 2D
crystals of purified LHI complexes from a carotenoid-less mutant. Each
LHI ring of the LHI-RC complex contains a central diffuse stain-excluding
region, which is assigned to the reaction centre. The analysis of the LHI-RC
2D crystals strongly suggests that the geometry and subunit stoichiometry
of the LHI ring is unaffected by the presence of a reaction centre that can
probably assume various orientations within the ring.
7 1997 Academic Press Limited
*Corresponding author
Keywords: light-harvesting complex; 2D crystallization; reaction centre;
Rhodospirillum rubrum; image processing, electron microscopy
Light-induced cyclic electron transport is the
central process for the utilization of light energy by
purple sulphur and non-sulphur bacteria. In this
process, light is captured by the reaction centre and
used to reduce a membrane-embedded quinone
molecule, which diffuses to the cytochrome bc1
complex to be oxidized. The capture of light is
mediated exclusively by the reaction centre and its
associated light-harvesting (LH) complexes, which
together form the minimal photounit. In general,
these minimal photounits are organized in large
arrays in the photosynthetic membrane (Miller,
Present addresses: T. Walz, Krebs Institute,
Department of Molecular Biology and Biotechnology,
University of Sheffield, Western Bank, Sheffield
S10 2HU, U.K. R. Ghosh, Department of Bioenergetics,
Biologisches Institut, Universität Stuttgart, D-70550
Stuttgart, Germany.
Abbreviations used: 2D, two-dimensional;
LH, light-harvesting; RC, reaction centre; DHPC,
diheptyl-sn-phosphatidylcholine; DOPC,
dioleoyl-sn-phosphatidylcholine.
0022–2836/97/020107–05 $25.00/0/mb960714
1982; Ueki et al., 1976). However, although the
functional relationships between photounits and
the cytochrome bc1 complex are well established,
the molecular details of the supermolecular
organization of the membrane are still controversial. Three classes of LH complexes are found, LHI
(B875, B880), LHII (B800-850), and LHIII (B800-820:
see Zuber, 1985). LHIII is a spectral variant of LHII.
In all cases the complex consists of two non-identical polypeptides, a and b, approximately 50 amino
acid residues in length. Functionally, kinetic studies
have shown that light energy proceeds from LHII
to LHI and from thence to the reaction centre (van
Grondelle, 1985). Recently, the structure of the LHII
complex from Rhodopseudomonas acidophila has been
solved at atomic resolution of 0.28 nm by X-ray
crystallography (McDermott et al., 1995). The
crystal structure revealed that the LHII complex is
comprised of nine ab heterodimers arranged in a
ring. The nine helical b-apoproteins form an inner
circle of radius 1.8 nm, while the nine a-apoprotein
helices are located on an outer circle of radius
3.4 nm. The three bacteriochlorophyll molecules
7 1997 Academic Press Limited
108
per ab dimer are sandwiched between these two
rings of membrane-spanning a-helices. A similar
arrangement of polypeptides and pigments has
been determined from the negative stain projection
map at 1.8 nm of 2D crystals of the LHII complex
from Rhodovulum sulfidophilum (Montoya et al.,
1995; Savage et al., 1996). However, the LHII from
Rhodospirillum molischianum is an octamer (Koepke
et al., 1996). A high-resolution projection map of the
LHI complex from Rhodospirillum rubrum, which
contains only a single LHI complex, has been
obtained at a resolution of 0.85 nm by cryo-electron
microscopic techniques and shows a ring of 16
subunits arranged in a ring-like structure, with an
overall diameter of 11.6 nm and an inner diameter
of 6.8 nm (Karrasch et al., 1995). The 11.6 nm LHI
particle analysed by cryo-electron microscopy has
been suggested to be the fundamental building
block of the photosynthetic membrane of R. rubrum
(Ghosh et al., 1993).
An important question is: how do the LHI
complexes interact with the RC in purple bacterial photosynthetic membranes? For Rhodobacter
sphaeroides, a number of kinetic studies have
indicated that the LHI complexes probably form a
ring around the RC (Aargard & Sistrom, 1972;
Monger & Parson, 1977). However, although the
6.8 nm inner diameter observed from the 0.85 nm
projection of the R. rubrum LHI complex (Karrasch
et al., 1995) is sufficient to incorporate an RC
molecule (Allen et al., 1987; Deisenhofer et al., 1985),
the physical and stoichiometric association of the
two components has been largely based upon
electron microscopy and digital image processing
of natural 2D crystals obtained from Rhodopseudomonas viridis (Miller, 1982; Stark et al., 1984) and
Ectothiorhodospira halochloris (Engelhardt et al.,
1986). However, both structures were obtained only
at a relatively low resolution (approximately 2 nm).
In addition, the high level of organization of
photounits within these membranes is exceptional.
Single-particle analyses of LHI-RC particles suggests that the reaction centre is located within a ring
of LHI, although these data were obtained at an
even lower resolution than above (Boonstra et al.,
1994).
Here, we have employed a new purification
procedure (Kessi et al., 1996) to obtain highly
purified LHI-RC complexes lacking other components, and have crystallized these complexes in
two dimensions in the presence of the unsaturated
dioleolyl-sn-phosphatidylcholine (DOPC). Briefly,
the isolated chromatophore membranes obtained
from the carotenoid-less mutant R. rubrum ST2
(Wiggli et al., 1996) were suspended in 10 mM
sodium phosphate buffer (pH 7.5) containing
150 mM NaCl to A880 (1 cm) = 10 (calculated from a
diluted sample), and then solubilized with the
phospholipid detergent, diheptyl-sn-phosphatidylcholine (DHPC) to give a final concentration of
20 mM. After ultracentrifugation of the solubilisate
at 100,000 g for one hour, the crude LHI-RC
complexes were in the supernatant. The LHI-RC
LHI-RC 2D Crystallization
complexes were purified by DEAE-Sepharose
chromatography as described (Kessi et al., 1996)
and then used directly for 2D crystallization as
described for the wild-type LHI complexes (Ghosh
et al., 1993; Karrasch et al., 1995). At least 90% of the
protein in the LHI-RC preparations comprised
reaction centres and light-harvesting polypeptides
when analysed by SDS-PAGE. Photobleaching
experiments of the Qx band of the bacteriochlorophyll a comprising the ‘‘special pair’’ of the reaction
centre showed that the DHPC-solubilized LHI-RC
preparations retained high RC activity for weeks
when stored at 6°C.
Preparations containing 2D crystals were adsorbed to a carbon-coated collodion film that was
mounted on a 400-mesh copper grid. The grid was
washed twice with double-distilled water and
stained over two drops of 0.75 % (w/v) uranyl
formate (pH 4.2). Electron micrographs were taken
on Kodak SO-163 film with a Hitachi H-7000
transmission electron microscope operated at
100 kV and a nominal magnification of 50,000×.
The micrographs were screened with an optical
diffractometer (Aebi et al., 1973) and suitable areas
were digitized using an Eikonix 850 CCD imaging
camera equipped with a Zeiss S planar objective
lens. The pixel size corresponded to 00.64 nm in
the specimen plane. Digital image processing was
carried out as described previously (Walz et al.,
1994) using the SEMPER image processing system
for the calculation of correlation averages.
Electron micrographs of reconstituted membranes revealed large arrays of well-ordered
LHI-RC complexes packed within a square lattice
(a = b = 16.3 (20.2) nm; n = 16: Figure 1A). The best
2D crystals were obtained at a DOPC/LHI ab molar
ratio of 1.0. Calculated power spectra (see Figure 1A, inset) show sharp diffraction spots up to
the reciprocal lattice order (5,1), suggesting that the
crystals are well ordered. Figure 1C shows the
optically filtered image from the area shown in
Figure 1B. A contrast difference in the projection
structures of neighbouring LHI-RC complexes is
distinct. This is due to slightly different staining of
the adjacent complexes, which originates from the
opposite orientations of the complexes within the
membrane. Upon closer inspection of the optically
filtered image, the LHI ring contains a central body
that may be assigned to the reaction centre. This
stain-excluding domain has often an elongated
shape and is located slightly off-centre in the LHI
ring. However, upon correlation averaging of the
crystalline areas (Figure 1D and E), the reaction
centre is visualized as a diffuse, circular object in
the centre of the LHI ring whose inner and outer
radii are approximately 6 nm and 12 nm, respectively. The loss of fine structure and a defined shape
is probably due to the averaging of many unit cells,
which are defined by the regularly arranged LHI
rings, but in which the reaction centres are oriented
differently, as suggested by Stark et al. (1984).
However, in the unsymmetrized correlation average, there are four faint stain-excluding domains
LHI-RC 2D Crystallization
Figure 1. A, An electron micrograph of negatively
stained 2D arrays of the LHI-RC complex crystallized in
the presence of DOPC (the scale bar represents 150 nm).
The inset shows the power spectrum calculated from the
marked area. Strong diffraction spots are visible up to the
reciprocal lattice order (5,1), indicating a resolution of
3.2 nm (the scale bar represents (5 nm)−1 ). The raw data
(B) are very noisy due to the low recording dose
employed. However, after Fourier peak filtration (C)
most of the noise is eliminated and the single LHI-RC
complexes forming the 2D lattice become distinct (the
scale bar represents 50 nm). The unsymmetrized correlation average in continuous (D) and contour (E)
representations are shown, with stain-excluding mass
regions appearing bright, and the surrounding stainfilled areas appearing dark. The square unit cell
(a = b = 16.3 nm) is outlined, and is comprised of two
LHI-RC complexes that are incorporated into the
membrane in opposite orientations. While the LHI rings
reveal some fine structure, the RCs appear as featureless
round areas. The three ‘‘empty’’ LHI rings shown within
the V-shaped bracket have been superimposed from a
correlation average obtained from 2D crystals from the
purified carotenoid-less LHI complex (unpublished
results) in the presence of added DOPC, to illustrate the
identical packing of the two types of crystals.
that connect the RC to the LHI ring. This conclusion
is supported by time-resolved phosphorescence
anisotropy data of reaction centres in native
chromatophore membranes, which showed the
reaction centre to be immobilized on the millisecond time-scale (Mar et al., 1981). In addition,
109
LHI-RC complexes are extracted quantitatively by
DHPC under optimal conditions and empty rings
are rarely, if ever, observed. The latter implies a
strong protein-protein interaction and not merely a
protein-phospholipid interaction, as DHPC has
been shown to be very efficient in extracting
phospholipids and thus solubilizing proteins (Kessi
et al., 1994). At present, we cannot definitively
ascertain whether the RC has a single locus of
interaction within the LHI ring or whether it can
take up a variety of fixed orientations (radial
disorder) within the ring. Further studies to answer
this question are in progress.
The packing of the LHI rings was identical with
that observed for highly purified carotenoid-less
LHI complexes crystallized in two dimensions in
the presence of DOPC (see the V-shaped brackets in
Figure 1D and E; and unpublished results). The
latter 2D crystals show that despite the fact that LHI
rings lacking carotenoid crystallize in a different
lattice (square) from those preferentially formed
from the wild-type containing carotenoid (tetragonal lattice; Karrasch et al., 1995), the dimensions
of the rings are identical.
The organization of the LHI complexes around
the RC of purple photosynthetic bacteria is
controversial at present. On the one hand,
ultrastructural data from electron microscopy have
indicated for membranes from R. viridis or E.
thiorhodospira containing natural 2D crystals of
LHI-RC complexes that a single RC is completely
surrounded by a continuous ring of LHI complexes
(Engelhardt et al., 1986; Miller, 1982). These data
have been supported by negatively stained images
of purified LHI-RC complexes from R. viridis (Jay
et al., 1984), and R. molischianum (Boonstra et al.,
1994). For the LHI-RC complex of R. molischianum,
a single-particle analysis was performed, which
also indicated a closed ring of LHI units around the
RC (Boonstra et al., 1994). A difficulty of the
single-particle analyses of these complexes so far is
that the resolution of the images obtained is quite
low (4 to 5 nm) necessitating symmetrization
according to a preconceived model.
Recently, a high-resolution 0.85 nm projection
map of a highly purified LHI complex from R.
rubrum assembled in 2D arrays has indicated that
the LHI complex consists of a closed ring of 16 ab
units containing sufficient space to accommodate
the reaction centre. A criticism of this work has
been that the LHI complexes were dissociated to ab
dimers prior to crystallization and that the closed
ring structure might be an artifact of the
crystallization process. Here, however, we have
isolated the LHI-RC complex using a mild
phospholipid detergent that, under optimal solubilization conditions, does not cause dissociation of
the LHI complex. This is indicated by the absence
of the characteristic absorption maxima of the
dissociated forms at 820 nm and 775 nm, the
different elution behaviour on DEAE-Sepharose,
and the different migration in sucrose gradients.
Nevertheless, the resulting 2D crystals reveal that
110
the dimensions of the LHI rings are essentially
identical in the presence or absence of reaction
centres. We conclude, therefore, that in R. rubrum
the RC is surrounded by the closed ring-like LHI
structure with the same subunit composition as
determined by Karrasch et al. (1995).
The closed ring structure of the LHI complex
around the RC is at variance with the well
established dogma that electron transfer between
the RC and the cytochrome bc1 complex is mediated
by free diffusion of a membrane-bound quinone
molecule between them. This apparent contradiction might be resolved by several possibilities. (1)
The LHI structure might allow the close approach
of quinone molecules from both sides of the ring
structure to allow electron transfer between them.
(2) ‘‘Breathing motions’’ of the a-helices might
allow direct diffusion of the planar quinone
molecules across the ring structure. (3) An
additional gene product may be present that
participates in the 16-fold symmetric ring structure
of the LHI complex, thereby forming a ‘‘quinone
channel’’. In the case of R. sphaeroides and
Rhodobacter capsulatus, an additional protein PufX is
coexpressed with the RC (Bauer et al., 1988;
Farchaus & Oesterhelt, 1989; Lee et al., 1989) and
recent evidence suggests that PufX may be
involved in the supramolecular organization of the
LHI-RC complexes, perhaps by interrupting the
ring of LHI subunits and thus providing a channel
to the cytochrome bc1 complex (Barz et al., 1995a,b).
For R. sphaeroides, kinetic evidence indicates that
two RCs may form a supercomplex with the
cytochrome bc1 complex (Joliot et al., 1990),
although this has been disputed (FernàndezVelasco & Crofts, 1991). Yet, the characteristics of a
supercomplex could not be found for R. rubrum,
and no gene (or gene product) homologous to pufX
has been found in this organism (Bélanger et al.,
1988; unpublished results). However, one candidate for this function is the V-polypeptide, a small
4 kDa hydrophobic polypeptide that copurifies
with the LHI ab dimer in a stoichiometry of about
1 to 10 (Ghosh et al., 1994). As neither the amino
acid sequence nor the corresponding gene have yet
been determined, it is still not known whether the
V-polypeptide functionally interacts with the LHI
complex.
The introduction of a local asymmetry by an
additional protein component, to yield a pseudo16-fold symmetric LHI ring is an attractive
possibility, as it may help to explain the still
unresolved question of how excitons are persuaded
to leave the LHI complex and be transferred to
either its unoccupied RC or to an adjacent LHI ring
for long-range energy transfer. Unfortunately, this
possibility must remain speculative, as the resolution of 0.85 nm obtained by Karrasch et al. (1995)
is not sufficient to differentiate between a real or
pseudo-16-fold symmetry.
In summary, the ultrastructural data presented
here suggest that: (1) the packing of the LHI-RC
complexes is determined exclusively by interaction
LHI-RC 2D Crystallization
between neighbouring LHI rings; (2) a single
reaction centre is surrounded by a single LHI ring;
(3) the dimensions of the LHI ring in the LHI-RC
complex are identical with those obtained from the
high-resolution projection map of purified LHI
complexes crystallized in the presence of DOPC; (4)
no indication of a ‘‘quinone channel’’ in the LHI
ring can be detected at the present resolution.
Acknowledgements
We thank Professors A. Engel, J. P. Rosenbusch and
R. J. Strasser for encouragement and support, and Marlis
Zoller for the photographic work. R.G. also acknowledges the Swiss Priority Program for Biotechnology
(grant nos 5002-41801 and 5002-39816) for generous
financial support. T.W. acknowledges the Swiss National
Science Foundation for the receipt of a post-doctoral
fellowship.
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Edited by R. Huber
(Received 23 May 1996; received in revised form 30 September 1996; accepted 30 September 1996)
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