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J Bacteriol, January 1998, p. 416-421, Vol. 180, No. 2
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
The ATP Synthase atpHAGDC
(F1) Operon from Rhodobacter capsulatus
Roberto
Borghese,
Massimo
Crimi,
Luca
Fava, and
Bruno Andrea
Melandri*
Laboratory of Biochemistry and Biophysics,
Department of Biology, University of Bologna, 40126 Bologna, Italy
Received 2 September 1997/Accepted 6 November 1997
 |
ABSTRACT |
The atpHAGDC operon of Rhodobacter
capsulatus, containing the five genes coding for the
F1 sector of the ATP synthase, has been cloned and
sequenced. The promoter region has been defined by primer extension
analysis. It was not possible to obtain viable cells carrying
atp deletions in the R. capsulatus chromosome, indicating that genes coding for ATP synthase are essential, at least
under the growth conditions tested. We were able to circumvent this
problem by combining gene transfer agent transduction with conjugation.
This method represents an easy way to construct strains carrying
mutations in indispensable genes.
 |
TEXT |
ATP synthase is a multisubunit
enzyme that catalyzes the respiratory or photosynthetic synthesis of
ATP coupled to the exoergonic flux of protons across the inner membrane
of mitochondria, the thylakoid membranes of chloroplasts, or the plasma
membrane of bacteria. The enzyme can also promote the active
translocation of protons driven by ATP hydrolysis (8, 9,
25). The ATP synthase consists of two parts, an extrinsic sector
(F1) formed by five different subunits (
,
,
,
,
and
) with a stoichiometry of
3
3

and connected through a thin
stalk to the second part, an intrinsic membrane sector (F0)
formed by a minimum of three proteins (a, b, and c) with a
stoichiometry of ab2c8-12. In photosynthetic
membranes, F0 is consistently formed by four different
subunits in all cases studied to date (7, 11, 28), the
fourth subunit, b', being a duplication of b. The extrinsic F1 sector contains three sites in which the synthesis or
hydrolysis of ATP is catalyzed and three noncatalytic nucleotide
binding sites, whose role is still not understood. The catalytic
reaction is coupled to the transmembrane proton flow through the
F0 sector presumably by means of long-range conformational
changes propagated along the stalk structure. A rotational catalytic
mechanism has been proposed; according to this mechanism, the
interaction of the single-copy subunits confers, cyclically in time,
different affinities for ATP, ADP, and phosphate to the catalytic site
in each 
pair (reviewed in reference 2). This
model has received decisive support from the atomic structure of
F1 from bovine heart mitochondria, recently resolved at 2.8 Å by X-ray crystallography (1). The rotational catalytic
model is also in agreement with recent functional experiments with
isolated F1 (5, 21, 22).
The gene structure of the ATP synthases has been studied for a great
number of organisms. For the enzymes from photosynthetic organisms,
sequences have been elucidated, for at least some subunits of
F1, for about 16 higher plants and 6 algae. Of 23 complete sequences of genes coding for eubacterial F0F1
ATPase found in the databases, 16 show a unique atp operon
with the F0 genes preceding the genes for F1.
The seven remaining species, all photosynthetic, have the
atp genes split into two operons (three in
Synechococcus sp. strain 6716 [28]). The
cyanobacteria Synechococcus sp. strain 6301 (4),
Anabaena strain PCC 7120 (18), and
Synechocystis strain PCC 6803 (14) and probably
the green sulfur bacterium Chlorobium limicola
(34) possess one operon comprising the F0 genes
together with the first three F1 genes and a second operon with the genes for F1
and
subunits. In the
Rhodospirillaceae family members Rhodospirillum
rubrum (6, 7) and, probably, Rhodopseudomonas
blastica, for which only the F1 sequence is known (27), the structural genes of F0 and
F1 are organized into two separate operons. Surprisingly,
the gene organization and sequences for the ATP synthase of the two
species of Rhodospirillaceae most intensively studied from
biochemical and genetic standpoints (i.e., Rhodobacter
sphaeroides and Rhodobacter capsulatus) are still unknown.
In this paper, we present the complete gene sequence of the
F1 operon (atpHAGDC) of Rhodobacter
capsulatus B100. We also describe a procedure that makes possible
the introduction of chromosomal deletions in essential genes followed
by complementation with a new copy of the same genes. This method will
allow us to perform easy site-directed mutagenesis studies on
Rhodobacter capsulatus F0F1 ATPase.
Cloning and sequence analysis of the atpHAGDC
operon.
The probe to be used for library screening was made by
amplification of a portion of the gene coding for the
subunit
(atpA). The primers used for PCR (5'
GACCGTCAGACCGGCAAGACCGC 3' and 5' AGTCTACAGCGACGACGACGCGG
3') were designed based on the sequence of the close relative
Rhodospirillum rubrum and chosen in highly conserved regions
in the middle of the
subunit. The screening of 550 colonies gave
six positive clones, one of which was chosen for further study. The
sequencing of 8 kb carrying the atp operon was completed by
use of the dideoxynucleotide chain termination method (23).
The genes coding for the five subunits of the ATPase F1
component were identified by their homology to corresponding
atp genes from both prokaryotes and eukaryotes. The order of
the genes in the operon is atpHAGDC, corresponding to
subunits
,
,
,
, and
, respectively. In
Rhodobacter capsulatus, no genes coding for F0
were found upstream of the atpHAGDC operon, like the
situation found in Rhodopseudomonas blastica and
Rhodospirillum rubrum (6, 27). This organization
seems to be unique to the Rhodospirillaceae.
All of the reading frames corresponding to the
atp genes are
preceded by a canonical Shine-Dalgarno sequence. The first codon
is ATG
in four genes,
atpA, -
G, -
D, and
-
C, but is a GTG in the
first gene of the operon,
atpH. Interestingly, the same feature,
specific for the

subunit, has been found in the close relatives
Rhodospirillum
rubrum and
Rhodopseudomonas blastica (
6,
27)
but not in any other prokaryote checked; in these other prokaryotes,
atpH begins with a more typical ATG.
The transcription initiation site was determined by primer extension
(
3). The 5' end of the message was mapped at an adenine
residue, 108 nucleotides upstream of the GTG start codon of the

subunit (Fig.
1A). A possible promoter
sequence was recognized
around the

10 and

35 regions. Similar
elements have been found
in
Rhodobacter capsulatus in a
number of other operons, particularly
operons involved in
bacteriochlorophyll and carotenoid biosynthesis,
in which
identification of the putative promoter elements has
been substantiated
by mutagenesis analysis (
15). In particular,
the TTG stretch
in the

35 element is completely conserved (Fig.
1B).

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FIG. 1.
(A) Determination of transcription initiation. The
sequencing ladder, to the left of the lane containing the primer
extension product, shows the actual sequence of the template strand;
for the sake of clarity, however, the letters at the top of the lanes
have been changed to correspond to the sense strand, and the sequence
should be read from top to bottom. The corresponding sequence, on the
right, should also be read from top to bottom, as indicated by the
arrow. The boldface A corresponds to the 5' end of the mRNA. (B) For
the promoter region, the sequence includes 40 bases upstream of the
start of transcription, which is marked by +1. The 10 and 35
elements are identified by their distance from the +1 position. For the
terminator, the TGA at the 5' of the sequence corresponds to the stop
codon of the last gene of the operon (atpC).
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|
A terminator sequence is clearly recognizable 23 bp downstream of the
atpC stop codon (Fig.
1B). This sequence shows the
characteristics
of a typical rho-independent terminator, including a
stem-loop
structure, a GC-rich region at the base of the stem, and a
stretch
of five T's at the end of the structure.
The amino acid sequence derived from the gene structure is confirmed by
the amino-terminal sequence of the peptides published
by Gabellini et
al. (
10). The latter study has indicated, however,
that all
amino-terminal
N-formylmethionines have been removed
in the
mature peptides. This holds also for the terminal amino
acid of the

subunit corresponding to the code of valine (probably
also an
N-formylmethionine). With this fact taken into account,
the
relative molecular weights of the five subunits should be
54,670, 50,097, 31,076, 18,760, and 13,357 for

,

,

,

, and

,
respectively, corresponding to an overall molecular mass of
377,494 Da.
Four other open reading frames (ORFs) were found upstream and
downstream of the
atpHAGDC sequence (see Fig.
3A). All of
these
ORFs have a high degree of sequence similarity with ORFs found
around the
atp operon of the other photosynthetic bacterium,
Rhodopseudomonas blastica (
27). The overall
organization is identical in the
two species, except that
Rhodopseudomonas blastica has two extra
ORFs. One, ORF5, is
found immediately upstream of
atpH and is
apparently
transcribed in the opposite direction; the second,
ORF6, is placed
between
atpG and
atpD. Rhodobacter capsulatus ORF1, which we have sequenced for only 443 bases, corresponds
to ORF2
in
Rhodopseudomonas blastica with 89% identity. ORF1 also
has 50% sequence identity with
Escherichia coli clpA.
Rhodobacter capsulatus ORF2, ORF3, and ORF4 correspond to
Rhodopseudomonas blastica ORF3, ORF4, and ORF7 with
identities of 56, 65, and 62%,
respectively. Apparently there is no
correspondence with sequences
upstream of the
atpHAGDC
operon of
Rhodospirillum rubrum, the
other closely related
photosynthetic bacterium (
6).
We show in Fig.
2 the
sequence alignments of

,

, and

subunits from
Rhodobacter capsulatus,
E. coli (
30),
and bovine
mitochondria (
29), together with structural
information, where
available. The amino acid sequences of the

and

subunits confirm
that they are the most conserved ones in the whole
ATP synthase
complex. The identities with sequences of other
photosynthetic
bacteria are striking (79 and 89% with
Rhodospirillum rubrum and
Rhodopseudomonas
blastica 
subunits, respectively; 74 and 86%
with
Rhodospirillum rubrum and
Rhodopseudomonas
blastica 
subunits,
respectively (
6,
27); the
sequence homology with nonphotosynthetic
eubacterial ATP synthases is
also very extensive (e.g., 69 and
55% identities with
E. coli 
and

subunits, respectively) (
30).
The
homology is also quite strong with the ATP synthase from eukaryotic
organisms (78 and 68% identities with

and

subunits,
respectively,
in bovine mitochondria) (
29). In Fig.
2A, the
alignment of
subunit sequences indicates that identity is
particularly marked
in several key sectors, including the catalytic
site (
1), where
all the amino acid residues are entirely
conserved in the three
sequences. Subunit

, only partially resolved
by X-ray crystallography
of bovine heart mitochondria F
1
(
1), constitutes the central
axis of the complex in the form
of a coiled-coil helical stem
in the middle of the


hexamer. In
ATP synthases of higher-plant
chloroplasts, the

subunit is some 40 residues longer and carries
a short 8 amino acid sequence, containing
two conserved cysteines,
involved in the activation of the catalytic
activity of the enzyme
by thiol-reducing agents (
20). This
sequence should be present
immediately downstream of the blandly
conserved segment of the

subunit sequence at positions 180 to 200 but is absent in
Rhodobacter capsulatus (Fig.
2B), in
agreement with previous observations
for other
Rhodospirillaceae (
6,
27) and cyanobacteria
(
4,
14,
18,
28).

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FIG. 2.
Alignment of the amino acid sequences of (A), (B), and (C) subunits of Rhodobacter capsulatus (rc),
E. coli (ec), and bovine heart mitochondria (bt). Asterisks
indicate identical residues, dots indicate conservative substitutions,
E's and double underlines indicate strands, and H's and black
boxes indicate helices. The secondary structures of and subunits have been obtained from the atomic coordinates of bovine heart
mitochondria F1 (1), and the secondary
structural elements of the subunit have been obtained from nuclear
magnetic resonance models of E. coli (33).
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Construction of a deletion mutant.
Gene transfer agent (GTA)
particles produced by Rhodobacter capsulatus cells pack,
randomly, pieces of DNA about 4.6 kb long, either from the chromosome
or from resident plasmids, and transfer them to acceptor cells, where
they are integrated into the chromosome by homologous recombination
(17). This results in an exchange between the incoming DNA
and the corresponding chromosomal DNA which is lost in the process. The
genetic characteristics of transfer using GTA particles make it a
method of choice for the introduction of gene deletions into the
chromosome. To this end, two plasmids, pRCA107 and pRCA108 (Fig.
3A), were constructed upon cloning in the
broad-host-range plasmid pRK415 (13). pRCA107 carries a complete deletion of the atpHAGDC operon, which is replaced
by a Kmr cassette; pRCA108 has the cassette inserted at the
EcoRV site downstream of the operon. In both cases, the
resistance cassette is flanked by portions of Rhodobacter
capsulatus DNA to allow for easy homologous recombination.

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FIG. 3.
(A) Restriction maps of plasmids pRCA51, pRCA107, and
pRCA108. Thick lines represent Rhodobacter capsulatus DNA.
Gray bars indicate atp genes, and open bars represent ORFs.
Solid bars in pRCA107 and pRCA108 are kanamycin resistance cassettes
inserted at the positions shown. Restriction site abbreviations: B,
BamHI; X, XhoI; N, NotI; E,
EcoRI; Bg, BglII; EV, EcoRV. Vectors
are not shown. (B) Hybridization pattern of Rhodobacter
capsulatus total DNA digested with EcoRI. Lanes: 1 and
4, wild-type B100; 2 and 5, strain RCAK1; 3 and 6, deletion mutant
RCAK4. Hybridization was done with a -subunit probe (lanes 1 to 3)
and then with a kanamycin resistance probe (lanes 4 to 6). The two
panels are pictures of the same filter hybridized with the first probe,
stripped, and rehybridized with the second probe.
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Transfer experiments using GTA particles were carried out as described
previously (
35) with rifampin-resistant strain J1
(
31) plasmid-containing cells as the donors and wild-type
B100
(
12) cells as the acceptors. In each of a number of
trials,
no
atpHAGDC deletion mutants were detected despite
extensive efforts.
In a typical experiment, slow-growing colonies
resistant to kanamycin,
putative
atp mutants, started to
appear on RFD2 minimal plates
(standard RCV medium
[
32] modified with fructose as the carbon
source and
dimethyl sulfoxide [DMSO] as the final electron acceptor
and
supplemented with 0.05% yeast extract) after 8 to 14 days
under
aerobic, photosynthetic, or anaerobic growth conditions.
Control
colonies, with the Km
r cassette insertion downstream of the
operon, grew in 2 to 9 days
under corresponding conditions. No growth
was detected under pure
fermentative conditions (
24), on
RFD2 medium supplemented with
sodium bicarbonate but lacking DMSO, even
after prolonged incubation.
The putative mutants were checked for
aerobic growth on RCV standard
minimal medium, with malate as the
carbon source. Under these
conditions, cells missing the ATP synthase
complex are not expected
to grow. All of the kanamycin-resistant
putative
atp mutants grew
on RCV medium, indicating that a
functional ATP synthase was still
present. In addition, genomic DNA was
isolated from five putative
mutants and from strain RCAK1 carrying the
Km
r cassette inserted downstream of the operon. Total DNA
digestions
were probed with the

-subunit gene and with the
Km
r gene. All of the putative mutants had conserved the
atpHAGDC operon and showed no Km
r cassette
insertion (data not shown), indicating that the resistance
trait was
due to spontaneous mutations, whereas the RCAK1 control
strain
hybridized to both probes, showing that the Km
r cassette
had been inserted into the chromosome. The impossibility
to isolate
atp deletion mutants represents a good indication that
Rhodobacter capsulatus cannot grow without a functional ATP
synthase
under all growth conditions tested.
The problem of introducing a genomic deletion in the
atpHAGDC operon or, more generally, in an
indispensable gene, was addressed
in a different way by combining
transfer using GTA particles and
conjugation procedures. We reasoned
that it would be possible,
in principle, to insert a genomic deletion
via GTA particles followed
by complementation with a wild-type copy of
the operon present
on a plasmid introduced by conjugation. Given the
efficiency of
transfer using GTA particles for a gene present on a
plasmid and
the efficiency of conjugation, measured in control
experiments,
it was calculated that approximately 4 × 10
9 cells were required for one positive event. The
GTA-conjugation
experiment was started with 3.5 ml of a
Rhodobacter capsulatus B100 full-grown culture (~7 × 10
9 cells) and 3.5 ml of GTA containing filtrate from a J1
donor
strain culture. This mixture was then centrifuged, resuspended
in
3.5 ml of RCV minimal medium, and incubated at 30°C for 1 h.
Conjugation of plasmid pRCA51 (pRK415 carrying the
atpHAGDC
operon)
(Fig.
3A) was carried out by adding to the
Rhodobacter
capsulatus cell suspension 750 µl each of the two
E. coli strains used in
triparental matings, and the mixture was
plated as described previously
(
26), on RCV minimal medium
plus kanamycin. Under these conditions,
three colonies that were then
found to be resistant to both kanamycin
and tetracycline (marker
carried by pRCA51) appeared, suggesting
the presence of both the
Km
r cassette and the complementing plasmid. These colonies
were grown
as liquid cultures on RCV minimal medium with kanamycin but
in
the absence of tetracycline. Under these growth conditions, the
selective pressure for plasmid maintenance is considered to be
the
presence of a functional ATP synthase rather than the antibiotic
resistance. After repeated subculturing, all of the colonies derived
from these cultures tested positive for resistance to both kanamycin
and tetracycline. Under the same conditions and without antibiotic
selection, the vector, pRK415, was lost in up to 40 to 50% of
the
cells. Plasmid preparations confirmed that the complementing
plasmid
was still present. For direct evidence of the genomic
insertion of the
Km
r cassette, genomic DNA was isolated from wild-type
strain B100,
strain RCAK1, and one of the strains with double
resistance, RCAK4.
Total DNA
EcoRI digestions were checked
by hybridization with
the

-subunit gene (
atpG) and the
Km
r gene. The hybridization results are shown in Fig.
3B.
Wild-type
strain B100 hybridizes to the

-subunit probe, showing a
5.3-kb
restriction fragment (Fig.
3B, lane 1), but not to the
Km
r gene (lane 4). Strain RCAK1 (lanes 2 and 5) shows the
same hybridization
band with both probes (see pRCA108 restriction map
in Fig.
3A).
These 6.9-kb signals correspond to the 5.3-kb
EcoRI restriction
fragment of the wild type plus the 1.6-kb
Km
r gene inserted at the end of the operon. Strain RCAK4
probed with
the

-subunit gene (lane 3) shows a signal corresponding
to a
fragment of 18.5 kb, which is exactly the size of the plasmid
pRCA51 linearized with
EcoRI. In lane 3, there is no trace
of
the 5.3-kb hybridization band that represents the wild-type
chromosomal
copy of
atpHAGDC, indicating that the operon has
been deleted
from the chromosome. In lane 6, hybridization of the same
RCAK4
DNA with the Km
r gene indicates that the resistance
cassette has been inserted
into the chromosome in place of the
atpHAGDC operon. The size
of this fragment does not
correspond to the 6.9 kb of the hybridization
band in lane 5 minus the
5.1 kb of the
atp operon because the
EcoRI site
present inside the operon has been lost in the process
of deletion.
From the experiment just described derives the possibility
of testing
the effect of site-directed mutations in essential
genes in
Rhodobacter capsulatus simply by substituting in the
wild-type copy, on the incoming plasmid, a mutated version of
the gene
under study.
Conclusions.
We have cloned and sequenced the
atpHAGDC operon coding for ATP synthase
from Rhodobacter capsulatus. The operon contains only
the five genes of the extrinsic sector (F1), while the
genes of the transmembrane subunits (F0) are in a different
region of the chromosome, resembling the situation found in the close
relatives Rhodospirillum rubrum and Rhodopseudomonas
blastica. Cloning and sequencing of the F0 operon are
in progress.
Rhodobacter capsulatus was reported to grow quite poorly
under pure fermentative conditions, with fructose as the carbon source
(
24). Substantial growth was observed when DMSO or
trimethylamine-
N-oxide
was used as an exogenous electron
sink (
16). We tried to isolate
F
1 deletion
mutants under both growth conditions. Cells were incubated
either
anaerobically in the dark or in the light (as additional
energy source)
or aerobically with the respiratory chain used
as an electron sink. No
such deletion mutants were obtained under
any of these growth
conditions. It was possible, however, to isolate
strains with a
chromosomal deletion in the
atpHAGDC operon after
conjugation with an F
1-containing plasmid. Our data can be
considered
in the light of previous conflicting results on the
requirement
of oxidative phosphorylation for growth under conditions of
anaerobic
respiration with DMSO or trimethylamine-
N-oxide
(
16,
19,
24).
Regarding the question of whether anaerobic
electron flow is required
just to dissipate the reducing power
generated during fermentation
or is necessarily associated with
oxidative phosphorylation, our
results clearly favor the second
hypothesis.
This work represents the first step in the genetic characterization of
the ATP synthase system in this photosynthetic bacterium.
The
well-developed genetics of this species and the good biochemical
characterization of its energy-producing components make it a
preferred
system for genetic and structural analysis of photosynthetic
ATP
synthesis in prokaryotes. We have described here a genetic
procedure
that will make possible the easy introduction of mutated
copies of the
atpHAGDC operon for site-directed functional and
structural analyses.
Nucleotide sequence accession number.
The DNA sequence
presented has been assigned the EMBL accession no. X99599.
 |
ACKNOWLEDGMENTS |
This work was supported by the European Community under contract
BIO2-CT93 0078.
We are grateful to A. G. W. Leslie and J. E. Walker, MRC
Laboratory, Cambridge, United Kingdom, who allowed access to the atomic
coordinates of bovine heart mitochondrial F1. We also thank Paola Turina for helpful discussions and for preparation of Fig. 3. The
work of our students, Daniela Costa, Andrea Romano, and Luigi Altomare,
is also acknowledged.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Università
di Bologna, Dipartimento di Biologia, via Irnerio 42, 40162 Bologna,
Italy. Phone: 39-51-351293. Fax: 39-51-242576. E-mail:
melandri{at}alma.unibo.it.
Present address: Istituto Policattedra, Facoltà di Scienze,
Università di Verona, 37134 Verona, Italy.
 |
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J Bacteriol, January 1998, p. 416-421, Vol. 180, No. 2
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
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