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Applied and Environmental Microbiology, November 1999, p. 4781-4787, Vol. 65, No. 11
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Characterization of an Operon Encoding Two c-Type
Cytochromes, an aa3-Type Cytochrome
Oxidase, and Rusticyanin in Thiobacillus ferrooxidans
ATCC 33020
Corinne
Appia-Ayme,
Nicolas
Guiliani,
Jeanine
Ratouchniak, and
Violaine
Bonnefoy*
Laboratoire de Chimie Bactérienne,
Institut de Biologie Structurale et de Microbiologie, Centre
National de la Recherche Scientifique, 13402 Marseille Cedex 20, France
Received 22 April 1999/Accepted 17 August 1999
 |
ABSTRACT |
Despite the importance of Thiobacillus ferrooxidans in
bioremediation and bioleaching, little is known about the genes
encoding electron transfer proteins implicated in its energetic
metabolism. This paper reports the sequences of the four
cox genes encoding the subunits of an
aa3-type cytochrome c oxidase.
These genes are in a locus containing four other genes:
cyc2, which encodes a high-molecular-weight cytochrome
c; cyc1, which encodes a
c4-type cytochrome
(c552); open reading frame 1, which encodes a
putative periplasmic protein of unknown function; and rus,
which encodes rusticyanin. The results of Northern and reverse
transcription-PCR analyses indicated that these eight genes are
cotranscribed. Two transcriptional start sites were identified for this
operon. Upstream from each of the start sites was a
70-type promoter
recognized in Escherichia coli. While transcription in
sulfur-grown T. ferrooxidans cells was detected from the
two promoters, transcription in ferrous-iron-grown T. ferrooxidans cells was detected only from the downstream
promoter. The cotranscription of seven genes encoding redox proteins
suggests that all these proteins are involved in the same electron
transfer chain; a model taking into account the biochemistry and the
genetic data is discussed.
 |
INTRODUCTION |
The gram-negative eubacterium
Thiobacillus ferrooxidans is important for industry and
ecology because (i) this microorganism is able to solubilize metals
from ores, such as copper, uranium, and cobalt, and to decompose
recalcitrant gold-containing ores (39) and (ii) it is able
to remove heavy metals from contaminated industrial effluents or soils
and to desulfurize fossil fuels to avoid corrosion and atmospheric acid
depositions (7, 21, 22). In addition to its industrial
importance, T. ferrooxidans is of fundamental interest since
its way of life is one of the "most primitive extant"
(8): for growth, this microorganism requires only air, which
provides carbon from carbon dioxide, nitrogen, and oxygen, and ores
containing ferrous iron (Fe2+) or reduced sulfur compounds,
from which it derives its energy. Furthermore, it thrives at extremely
low pHs (between 4 and 1.5). T. ferrooxidans is one of the
most studied bioleaching microorganisms, but little is known about its
physiology and, more particularly, its energy metabolism. Because its
energy metabolism is responsible for its bioleaching and bioremediation
abilities, any attempt to improve these properties is dependent on an
understanding of the respiratory mechanisms. Although several redox
proteins have been identified (49), the electron pathways
from Fe2+ to oxygen (O2) and from reduced
sulfur compounds to O2 are not established. Several models
for the iron respiratory chain which differ with regard to the electron
carriers and the side of the cytoplasmic membrane on which oxygen
reduction takes place have been proposed (2, 5, 13, 17, 18,
50).
As an approach for elucidating the T. ferrooxidans
respiratory chains, we are studying the genes encoding electron
transfer proteins. We have previously cloned and sequenced the
rus, cyc1, and cyc2 genes, which
encode, respectively, the rusticyanin (4) and two
cytochromes c (2) from strain ATCC 33020. The
sequences of internal fragments of the rus genes from strain
ATCC 19859 (38) and from strain ATCC 23270 (15)
and the sequence of the iro gene from strain Fe-1
(26) have also been reported. We have also shown that in
strain ATCC 33020 the cyc1 and cyc2 genes are cotranscribed with at least two downstream open reading frames (ORFs)
(2) and that the rus gene is cotranscribed with
at least three upstream ORFs (4). In this paper, we
demonstrate that all these genes together with the genes encoding the
four subunits of a cytochrome c oxidase belong to the same operon.
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MATERIALS AND METHODS |
Strains, plasmids, growth conditions, and
-galactosidase
assays.
T. ferrooxidans ATCC 33020 was obtained from the
American Type Culture Collection. Escherichia coli MC4100
[araD139
(lacIPOZYA-argF)U169 rpsL
thi] was used when
-galactosidase activities had to be determined.
Phagemid Bluescript SK was purchased from Stratagene. Plasmid pGE593 is
an operon fusion vector containing the lacZ gene as the
reporter gene (10).
E. coli strains were grown in Luria-Bertani medium
(
31). Conditions for growth of
T. ferrooxidans on
iron or sulfur medium
have been described previously (
4).

-Galactosidase activities were determined according to the method of
Miller (
31) in whole cells grown on Luria-Bertani
medium
containing
ampicillin.
DNA manipulations.
General molecular biology techniques were
carried out by standard procedures (3) or as recommended by
the manufacturer. T. ferrooxidans genomic DNA preparation
has been described previously (4). Ultrapure plasmid DNA was
obtained with a Wizard plus Spin or vacuum minipreps DNA
purification system plasmid kit from Promega. Ligations were generally
carried out in the presence of the restriction enzyme used to cleave
the vector to prevent its recircularization.
Routine PCRs were performed with Boehringer Mannheim
Taq DNA
polymerase according to the manufacturer's recommendations in
a
Mini-cycler (MG Research). For cloning purposes, the
Pwo
polymerase
was preferred. Amplification of flanking sequences by
inverse
PCR was as described by Ochman et al. (
36). All
synthetic oligonucleotides
for PCR and sequencing were purchased from
Genset.
Sequences were determined with a Thermo Sequenase II dye terminator
cycle sequencing premix kit from Amersham. The DNA sequences
were
compiled and analyzed through the Worldwide Web Netscape
facilities.
The predicted proteins were compared with EMBL, GenBank,
and SwissProt
database entries by using the BLASTP program (
1)
with the
BLOSUM62 scoring matrix or, when specified, with the
BLOSUM30
matrix.
Plasmid constructions.
Different DNA fragments containing
the putative promoters of the cyc operon were amplified by
PCR with oligonucleotides d to h, f to h, d to k, or c to l (Table
1 and see Fig. 1A and 3A) from T. ferrooxidans genomic DNA and cloned into the SmaI site of pGE593 to yield plasmids 1, 2, 4, and 5, respectively. The
insert of plasmid 3 is the larger fragment obtained after digestion
with SspI of the PCR fragment obtained with oligonucleotides d to h.
Plasmid SK/
coxB was obtained by cloning the DNA PCR fragment
amplified between oligonucleotides a and p (Table
1; see Fig.
1A) into
the
EcoRV site of the Bluescript SK vector. Screening
was
performed by PCR with the oligonucleotides used to amplify
the DNA. In
all cases, the sequence of the cloned fragment was
checked.
RNA manipulations.
T. ferrooxidans total RNA was
prepared as described previously (14). RNA electrophoresis
was performed with agarose-formaldehyde gels (3). RNA was
transferred to a positively charged nylon membrane from Boehringer
Mannheim by capillary blotting. The digoxigenin (DIG)-labeled RNA probe
was obtained by in vitro transcription with T7 RNA polymerase from the
EcoRI-linearized SK/coxB plasmid described above
with DIG-UTP as the substrate according to the instructions of the
Boehringer Mannheim DIG RNA labeling kit. Prehybridization and
hybridization with a DIG-labeled probe were performed under stringent
conditions according to the recommendations of Boehringer Mannheim. RNA
was detected by a chemiluminescent reaction with
disodium 3-(4-methoxyspuro{1,2-dioxelane-3,2'-(5'-chloro)tricyclo [3.3.1.13.7] decan}-4-yl)
(CSPD) as recommended by Boehringer Mannheim.
Primer extension was performed with the Superscript II RNase
H

reverse transcriptase from Gibco BRL. The k, l, m, n,
and o primers
used (Table
1; see Fig.
3A) were labeled with
[

-
32P]ATP. Coupled reverse transcription and PCR
amplification (RT-PCR)
was performed with the Promega Access RT-PCR
system as described
previously (
14) with the a, b, c, d, e,
f, g, h, i, and j oligonucleotides
(Table
1; see Fig.
1A). For each
RT-PCR experiment, three control
experiments were performed: one
without template to detect any
contamination, one with genomic DNA as a
control for PCR amplification,
and one with RNA but without the reverse
transcriptase to ensure
that there were no DNA traces in the RNA
preparation.
Nucleotide sequence accession number.
The EMBL accession
number of the 8,007-bp DNA nucleotide sequence containing the
cyc2, cyc1, ORF1, coxB,
coxA, coxC, coxD, and rus
genes is AJ006456.
 |
RESULTS AND DISCUSSION |
Characterization of the cytochrome oxidase genes.
The
cyc2 and cyc1 genes encoding a
high-molecular-weight cytochrome c and a
c4-type cytochrome are cotranscribed with at
least one other gene (ORF1) encoding a putative periplasmic protein of
unknown function (2). We have determined the nucleotide sequence downstream from ORF1 by chromosome walking using PCR and
inverse-PCR approaches. Four putative open reading frames, each
preceded by a correctly positioned putative ribosome binding site, were
found on the same DNA strand between positions 3296 and 4060, 4417 and
6000, 6019 and 6570, and 6611 and 6805. The rus gene, which
we have already characterized (4), lies immediately downstream. Downstream from ORF1, the first and second ORFs encode proteins presenting significant similarities to subunits II and I,
respectively, of an aa3-type cytochrome
c oxidase and will be referred to herein as the
coxB and coxA genes. The two ORFs downstream from
the coxA gene are those found upstream from rus (ORF1 and ORF2 in reference 4) and will be referred
to herein as coxC and coxD (see below). Thus, the
gene order in this locus is
cyc2-cyc1-ORF1-coxB-coxA-coxC-coxD-rus.
Analysis of the coxB-encoded polypeptide.
The
coxB gene encodes a putative 254-amino-acid polypeptide
(CoxBTf) with a calculated molecular weight of 28,240. The
first 51 amino acids may constitute a long but standard signal
sequence. The mature protein has a higher similarity to subunit II of
aa3-type cytochrome c oxidases (and
more particularly to those of Synechococcus vulcanus,
Anabaena sp. strain PCC7120, and Synechocystis
sp. strain PCC6803) than to subunit II of quinol oxidases. Similar to
the cytochrome oxidases, the mature CoxBTf has two putative
N-transmembrane segments that serve as membrane anchors and a large
periplasmic carboxy-terminal domain (for extensive references, see
references 40 and 41). In the
periplasmic domain, the aromatic amino-acid-rich region
(145-WKWTFSY-151) involved in the electron transfer between subunits I
and II is present (20, 45). Furthermore, the residues binding the dinuclear copper center (CuA) (H181, C222, C226, H230, and
M233) (20, 25, 40), the residues stabilizing CuA (W145 and
D178), and three of the four highly conserved residues interacting with
cytochrome c (Q144, D178, and D193) (20, 27) are
also present, suggesting that CoxBTf belongs to a
c-type cytochrome oxidase.
In spite of the acidic pH of the
T. ferrooxidans periplasm,
the periplasmic domain of CoxB
Tf is well conserved.
Acid-stable
proteins generally contain a relatively low number of
charged
residues (
29), but this is not the case in the
CoxB
Tf periplasmic
domain (11.6% R+H+K; 8% D+E). It is
noteworthy that two
T. ferrooxidans periplasmic redox
proteins, the high-potential iron sulfur protein
(HiPIP) encoded by
iro and rusticyanin, have already been noted
as exceptions
to this rule (
29). A possibility is that these
electron
transfer proteins are inaccessible to the periplasm medium
because they
are buried in a
supercomplex.
Analysis of the coxA-encoded polypeptide.
The
coxA gene encodes a putative 627-amino-acid polypeptide
(CoxATf) with a calculated molecular weight of 69,090. This
protein is related to subunit I of both quinol and cytochrome
c oxidases from archaea, eucarya, and bacteria but more
particularly to subunit I of the aa3-type
cytochrome c oxidase from Synechocystis sp. strain PCC6803, Synechococcus vulcanus, and
Anabaena sp. strain PCC7120. CoxATf contains the
12-transmembrane segment core common to all cytochrome oxidase subunits
I (41). In this core region are the residues binding and
stabilizing the low- and high-spin hemes (a and
a3) and the copper atom (CuB): H159, H333, H382, H383, H467, H469 (Cu and heme binding), W329, Y337 (CuB stabilization), W145, R529, and R530 (heme stabilization) (20, 40, 44). The
invariant phenylalanine residue (F468) involved in electron transfer
between the two hemes is also present (41). Based on the
predicted topology of CoxATf, all the residues binding
hemes and copper are within the membrane bilayer but near the
periplasm. This may explain why Kai et al. (23, 24) found
that the pH optimum for T. ferrooxidans cytochrome oxidase
was pH 3.5, a value corresponding to that of the periplasm. From the
crystal structure of the Paracoccus denitrificans cytochrome
c oxidase, two proton transfer pathways have been proposed:
the K and the D channels (16, 20, 37). Although not strictly
invariant, most of the residues involved in these channels are
conserved in the CoxATf subunit. Five of the seven residues
constituting the K channel and six of the nine residues constituting
the D channel are present. Altogether, these data strongly suggest that
the cox genes encode an aa3-type
cytochrome c oxidase.
In addition to the core region, CoxA
Tf contains an extended
N terminus with two hydrophobic regions that have no similarity
to
sequences in the protein data banks. Extra hydrophobic regions
have
been also described for the N termini of subunits I of the
cbb3-type cytochrome oxidases from
Bradyrhizobium japonicum and
Sinorhizobium
meliloti (
41).
The estimated molecular masses of subunits I of the
aa3-type cytochrome oxidases purified from the
T. ferrooxidans Fe-1, AP19-3,
and OK1-50 strains (53, 53 and
55 kDa, respectively) (
19,
24)
do not correspond with the
molecular mass deduced from the
coxA gene sequence reported
here (69 kDa). This discrepancy may be
due to an aberrant migration of
subunit I on sodium dodecyl sulfate
gels, as was previously observed
with other integral membrane
proteins. Another possibility is that the
cytochrome oxidase encoded
by the
coxBACD gene cluster
described in this paper is distinct
from the oxidases which have been
purified.
Analysis of the coxC- and coxD-encoded
polypeptides.
coxC and coxD genes encode putative
polypeptides of 183 and 64 amino acids with calculated molecular
weights of 20,202 and 7,211, respectively. These proteins are integral
membrane proteins, with five transmembrane helices for
CoxCTf and one for CoxDTf (4).
By specifying alternate scoring matrices, CoxC
Tf exhibits
some similarity with the
Mycobacterium tuberculosis,
Mycobacterium leprae,
Synechocystis sp. strain
PCC6803,
Synechococcus vulcanus,
and
Anabaena sp.
strain PCC7120 cytochrome
c oxidase subunits
III. Although
slight, this similarity is significant. Furthermore,
the
carboxy-terminal region is the best conserved, as has been
observed for
other cytochrome oxidase subunits III (
40).
As a general rule, subunit III is the second most conserved subunit in
the cytochrome oxidase family after subunit I. Surprisingly,
CoxC
Tf is less conserved than subunit II, suggesting that
it has
evolved more quickly because of an interaction with another
protein
partner(s) specific to
T. ferrooxidans.
Whatever the scoring matrices used, no similarity was detected for
CoxD
Tf. Because the bacterial cytochrome
c
oxidase structural
genes are always in the order
coxB-coxA-coxC-coxD if they are
clustered in the same locus
(
11,
46) and because cytochrome
c oxidase subunit
IV is generally a small protein which has one
transmembrane helix and a
sequence which is not always conserved
(
48), we have
inferred that the
coxD gene encodes cytochrome
oxidase
subunit
IV.
Interestingly, even though
T. ferrooxidans belongs to the
phylogenetic

subdivision of the
Proteobacteria,
CoxA
Tf, CoxB
Tf,
and CoxC
Tf amino
acid sequences are most closely related to those
of cyanobacteria
(
Synechococcus vulcanus,
Synechocystis sp., and
Anabaena sp). However, no significative similarities were
detected
at the nucleotide level, dismissing the hypothesis of a
lateral
gene transfer. On the other hand, the ancestors of the
cyanobacteria
were the first to introduce oxygen into an anaerobic
environment
and the
T. ferrooxidans way of life has been
described as one
of the "most primitive extant" by Cairns-Smith et
al. (
8),
arguing rather for a convergent
evolution.
Transcription of the coxB, coxA,
coxC, and coxD genes in T. ferrooxidans.
If the genes encoding the different cytochrome
oxidase subunits are clustered in the same locus, they are always
cotranscribed (11, 46). To determine if the cox
genes of T. ferrooxidans ATCC 33020 are also organized in an
operon, we used the RT-PCR approach, which combines RNA RT and cDNA
amplification (PCR). An amplification product of the expected size was
obtained between oligonucleotides a and b, corresponding to the
coxB and coxA genes, respectively (Fig.
1A), indicating that these two genes are
cotranscribed (Fig. 1B). We have shown previously that (i)
coxB (ORF2 in reference 2) is
cotranscribed with cyc2, cyc1, and ORF1 and (ii)
coxA (ORFA in reference 4) is
cotranscribed with coxC, coxD (ORF1 and ORF2,
respectively, in reference 4), and rus,
the rus gene being the last gene of this operon. All these
results suggest that cyc2, cyc1, ORF1,
coxB, coxA, coxC, coxD, and
rus constitute an operon.

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FIG. 1.
RT-PCR on T. ferrooxidans total RNA. (A)
Localizations of the oligonucleotides used for RT-PCR experiments; (B)
RT-PCR experiments with oligonucleotides a and b on no template (lane
0), T. ferrooxidans genomic DNA (lane D), total RNA from
T. ferrooxidans cells (lane R), total RNA from T. ferrooxidans but without reverse transcriptase (lane ); (C)
RT-PCR experiments with oligonucleotides c and i, d and i, and f and i
on RNA extracted from sulfur-grown cells (lanes R and ); (D) RT-PCR
experiments with oligonucleotides e and i, f and i, and g and j on RNA
extracted from ferrous-iron-grown cells (lanes R and ). Lanes M, 1-kb
molecular weight ladder from Boehringer Mannheim.
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To confirm this hypothesis, the transcription of the
cox
genes was studied by Northern hybridization with total RNAs from
ferrous-iron-grown cells. The RNA probe was chosen to hybridize
to the
coxB transcript. As predicted, one major transcript of
approximately 7.4 kb was detected (Fig.
2). The size of this transcript
is in
agreement with
cyc2-cyc1-ORF1-
coxB-coxA-coxC-coxD-rus
cotranscription.
Larger minor transcripts were also observed. These
minor transcripts
can be due either to mRNA processing, to
transcription initiation
from several promoters (see below), or to the
presence of more
than one cytochrome
c oxidase in
T. ferrooxidans. The last hypothesis
is supported by the facts that
(i) different cytochrome oxidases
have been detected in several
T. ferrooxidans strains (
9,
17,
28) and (ii)
cytochrome
c oxidases, in which subunit I has a
lower
apparent molecular weight than that predicted for CoxA
Tf,
have been previously purified in
T. ferrooxidans (
19,
24).

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FIG. 2.
Northern blot of total RNA from ferrous-iron-grown
T. ferrooxidans cells (1.1 µg) probed with DIG-UTP-labeled
coxB RNA. The positions and the sizes of the RNA ladder from
Gibco BRL are indicated on the left.
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Characterization of the operon promoter(s).
Because no ORF has
been detected in the 450 bp upstream from cyc2
(2), this gene is likely the first cistron of the operon. To
determine approximately where the transcription of this operon is
initiated, RT-PCR experiments were performed with a set of oligonucleotides hybridizing in the 5' untranslated region of cyc2 (c, d, e, and f) and convergent oligonucleotides
hybridizing at the beginning of cyc2 (h and i) (Fig. 1A) on
total RNA extracted from sulfur- or Fe2+-grown cells. With
RNAs extracted from sulfur-grown cells, cDNAs of the expected sizes
were obtained between all the different pairs of oligonucleotides
except with oligonucleotide c (Fig. 1C), suggesting that the mRNA
starts between oligonucleotides c and d, which are between positions 1 and 75. With RNA extracted from Fe2+-grown cells, however,
no amplification product was obtained with the different pairs of
oligonucleotides except a faint band with oligonucleotide f (Fig. 1D),
suggesting that under Fe2+ growth conditions, the mRNA
starts in the region where oligonucleotide f hybridizes. Because an
amplification product was obtained with two cyc2 internal
oligonucleotides, g and j (Fig. 1D), the inhibition of avian
myeloblastosis virus reverse transcriptase or Tfl polymerase in RNA preparation from Fe2+-grown cells is excluded. From
these RT-PCR experiments, we conclude that cyc2 is the first
gene of the operon and that this operon is transcribed from at least
two promoters, the upstream promoter being nonfunctional under
Fe2+ growth conditions. According to these results, the
eight genes of the operon are transcribed in sulfur- as well as in
ferrous-iron-grown ATCC 33020 cells, confirming that rusticyanin is
synthesized when thiosulfate, sulfur, or ferrous iron is present in the
growth medium (4) and suggesting that the proteins encoded
by the operon play a role not only in ferrous-iron- but also in
sulfur-grown cells.
The 5' ends of these transcripts were determined more precisely by
primer extension analysis with RNA samples prepared from
T. ferrooxidans cells grown with ferrous iron or sulfur as the
energy
source. No signal was obtained with oligonucleotide o (data
not
shown), indicating that the transcription of the
cyc operon
initiates downstream from this oligonucleotide (position 22).
A band
was obtained with oligonucleotides k and l (Fig.
3) from
sulfur- but not from
Fe
2+-grown cells. This signal corresponds to a G (position
51) located
398 bp upstream from the translational initiation site of
cyc2.
From Fe
2+- as well as from sulfur-grown
cells, a weak band was obtained
with oligonucleotide m (Fig.
3, lanes S
and F). This signal corresponds
to a G (position 289) located 161 bp
upstream from the
cyc2 translational
initiation site. This
signal was confirmed with oligonucleotide
n, even though other bands of
unknown origin were observed with
this oligonucleotide without any
template (Fig.
3B, lanes 0).
Correctly positioned upstream from the
operon transcriptional
initiation sites identified are two
E. coli 
70-type promoters:
TTGGAC(17 bp)TATAAT
for the upstream promoter and TTGCAA(17 bp)TAAATA
for the downstream promoter.

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FIG. 3.
Primer extension experiments. (A) Localizations of the
oligonucleotides used. (B) RT experiments with the k, l, m, and n
oligonucleotides on no template (lanes 0); E. coli carrying
plasmid 1, 2, or 3 (lanes 1 to 3, respectively); total RNA from
ferrous-iron (lanes F)- or sulfur (lanes S)-grown T. ferrooxidans (T.f) cells. Lanes M,
[ -32P]ATP-labeled X174 HinfI markers
(from Promega).
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To determine if these promoters are functional in
E. coli,
different regions of the 5' untranslated region of the operon have
been
cloned in the operon fusion vector pGE593 (see Materials
and Methods).

-Galactosidase activities of strain MC4100 (
lac)
carrying the resulting plasmids were determined. The results
unambiguously
show that a sequence functioning as a promoter in
E. coli is present
between the
SspI site and
oligonucleotide k (positions 159 and
290) and that there is a second
such sequence between oligonucleotides
c and l (positions 1 to 190)
(data not shown). Primer extension
experiments with RNA samples
prepared from
E. coli MC4100 carrying
plasmids 1, 2, and 3 (Fig.
3B, oligonucleotides m and n) and plasmid
5 (data not shown) have
confirmed these results and have shown
that the same transcriptional
start sites are used in both
T. ferrooxidans and
E. coli.
The transcription of the genes of the operon appears to be complex
because at least three promoters have been characterized:
two upstream
from
cyc2 (this paper) and one between
coxD and
rus (
4). The function of the internal promoter
may be to uncouple
expression of the
rus gene from that of
the other genes of the
operon under certain growth conditions. Two of
these promoters
are active only under sulfur growth conditions: the
most upstream
promoter from
cyc2 (this paper) and the
internal promoter (
4).
The requirement for multiple
promoters suggests that the expression
of the different genes of the
operon must be tightly regulated
depending on the growth conditions to
allow the cells to adapt
quickly to the environmental changes. Further
work will focus
on (i) looking for environmental signals involved in
the transcriptional
regulation of this operon and (ii) determining how
these signals
are transmitted to the transcriptional
machinery.
Electron transfer pathway between ferrous iron and molecular oxygen
in T. ferrooxidans ATCC 33020.
In most cases, the
cytochrome oxidase subunits are encoded within an operon with the order
coxB-coxA-coxC-coxD (11, 46). In some cases,
other genes required in the biogenesis of the oxidase (biosynthesis of
heme A or heme O) (11, 46) or encoding other redox proteins
belong to this operon. This is the case for
cbb3-type cytochrome c oxidases
(46) and for Sulfolobus acidocaldarius terminal
oxidase complexes (41, 42). The cytochrome oxidase subunit I
gene of the cbb3-type oxidases is cotranscribed
with the genes encoding a mono- and a bihemic membrane-bound cytochrome c and a small membrane protein of unknown function
(46). In Sulfolobus acidocaldarius, the genes
encoding subunits I and II of one cytochrome oxidase are cotranscribed
with the genes encoding an a-type cytochrome and a small
hydrophobic subunit (41, 42). In a second cytochrome
oxidase, the gene encoding subunit II and the gene encoding a subunit
I-subunit III fusion protein are cotranscribed with the genes encoding
sulfocyanin, an iron-sulfur protein, and a cytochrome b
(41, 42). In these three cases, the redox proteins encoded
by the operon constitute a respiratory chain organized as a
supercomplex. Because the T. ferrooxidans
aa3-type cytochrome c oxidase genes
are cotranscribed with the genes encoding two cytochromes c
(cyc2 and cyc1) and rusticyanin (rus),
we infer that all these proteins belong to the same electron transfer
chain and constitute a respiratory supercomplex. We have previously proposed the following electron pathway (1):
Fe2+
X
rusticyanin
cytochrome
c4
cytochrome oxidase
O2, in
which the carrier which transfers electrons from ferrous iron to
rusticyanin (X) is unknown. The HiPIP encoded by the iro
gene has been proposed to receive the electrons from ferrous iron and thus to be the first electron carrier in the respiratory chain (13, 50). However, several observations appear to disagree with this hypothesis: (i) HiPIPs are generally found in photosynthetic bacteria, where they are assumed to transfer electrons between two
integral transmembrane complexes, from the bc1
complex to the photosynthetic reaction center or to the terminal
oxidase (6, 30); (ii) no HiPIP protein has been detected in
the Tf-3 and F424 T. ferrooxidans strains (9, 17,
28); and (iii) the iro gene is monocistronic in strain
Fe-1 (26), which suggests that the HiPIP is not synthesized
concomitantly with the electron carriers encoded by the
cyc2, cyc1, coxBACD, and
rus genes. The HiPIP would rather be a nonobligatory carrier
in ferrous-iron oxidation or an intermediate carrier between the
bc1 complex and the terminal oxidase. We propose
that the high-molecular-weight cytochrome would be a better candidate
for the role of the first electron acceptor because (i) the
cyc2 gene encoding this cytochrome is the first gene of the
operon, (ii) this cytochrome is indeed translocated to the periplasm
because it has a signal sequence that is cleaved (1), (iii)
this cytochrome is likely to be acid stable because it has a low number
of charged amino acids, and (iv) from its amino-acid sequence, the
Psort program (35) predicts that this cytochrome
c is an outer membrane protein. Some organisms, such as
Desulfovibrio gigas (47), Geobacter sulfurreducens (12, 43), and Shewanella
putrefaciens (32-34), have outer membrane cytochromes
c. Interestingly, Geobacter sulfurreducens and
Shewanella putrefaciens are able to reduce ferric iron and this ferric iron reductase activity is associated with an outer membrane cytochrome c which makes direct contact with the
solid substrate.
Based on genetic and biochemical evidence, we propose the pathway shown
in Fig.
4 for electron transfer between
ferrous iron
and oxygen in
T. ferrooxidans ATCC 33020; the
high-molecular-weight
cytochrome
c encoded by the
cyc2 gene transfers electrons from
ferrous iron to
rusticyanin, which passes them to the cytochrome
c4 and from there to the cytochrome oxidase. To
confirm this model,
subcellular localization of the
high-molecular-weight cytochrome
c will be determined and
the interaction between the cytochrome
c4 and
the cytochrome oxidase subunit II will be studied.

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|
FIG. 4.
Proposed electron transfer pathway between ferrous iron
and oxygen in T. ferrooxidans ATCC 33020. OM, outer
membrane; IM, inner membrane; Cyt c4, cytochrome
c4; Hmc, high-molecular-weight cytochrome
c.
|
|
 |
ACKNOWLEDGMENTS |
We owe special thanks to L. Thöny-Meyer and Y. Quentin for
helpful discussions. We thank M. Chippaux and more particularly J. DeMoss for critical readings of the manuscript. We are grateful to the
Centre de Séquençage d'ADN (I.B.S.M., Marseille, France). We thank Patrice Brucella for skillful technical assistance.
This work was supported by grants from the CNRS, the Agence de
l'Environnement et de la Maîtrise de l'Energie (A.D.E.M.E.), the Bureau de Recherche Géologique et Minière, and the
Compagnie Générale des Matériaux (CO.GE.MA). N.G.
acknowledges the support of a graduate scholarship from A.D.E.M.E., and
C.A.-A. acknowledges support from M.E.S.R.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Laboratoire de
Chimie Bactérienne, Institut de Biologie Structurale et de
Microbiologie, Centre National de la Recherche Scientifique, 31 chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France. Phone: (33) 491 164 146. Fax: (33) 491 718 914. E-mail:
bonnefoy{at}ibsm.cnrs-mrs.fr.
 |
REFERENCES |
| 1.
|
Altschul, S. F., and W. Gish.
1996.
Local alignment statistics.
Methods Enzymol.
266:460-480[Medline].
|
| 2.
|
Appia-Ayme, C.,
A. Bengrine,
C. Cavazza,
M.-T. Giudici-Orticoni,
M. Bruschi,
M. Chippaux, and V. Bonnefoy.
1998.
Characterization and expression of the cotranscribed cyc1 and cyc2 genes encoding the cytochrome c4 (c552) and a high molecular weight cytochrome c from Thiobacillus ferrooxidans ATCC33020.
FEMS Microbiol. Lett.
167:171-177[Medline].
|
| 3.
|
Ausubel, F. M.,
R. Brent,
R. E. Kingston,
D. D. Moore,
J. G. Seidman,
J. A. Smith, and K. Struhl.
1992.
Current protocols in molecular biology.
Greene Publishing, New York, N.Y
|
| 4.
|
Bengrine, A.,
N. Guiliani,
C. Appia-Ayme,
E. Jedlicki,
D. S. Holmes,
M. Chippaux, and V. Bonnefoy.
1998.
Sequence and expression of the rusticyanin structural gene from Thiobacillus ferrooxidans ATCC33020 strain.
Biochim. Biophys. Acta
1443:99-112[Medline].
|
| 5.
|
Blake, R. C., II, and E. A. Shute.
1994.
Respiratory enzymes of Thiobacillus ferrooxidans. Kinetic properties of an acid-stable iron:rusticyanin oxidoreductase.
Biochemistry
33:9220-9228[Medline].
|
| 6.
|
Bonora, P.,
I. Principi,
B. Monti,
S. Ciurli,
D. Zannoni, and A. Hochkoeppler.
1999.
On the role of high-potential iron-sulfur proteins and cytochromes in the respiratory chain of two facultative phototrophs.
Biochim. Biophys. Acta
1410:51-60[Medline].
|
| 7.
|
Bos, P., and G. Kuenen.
1990.
Microbial treatment of coal, p. 343-377.
In
H. L. Ehrlich, and C. L. Brierley (ed.), Microbial mineral recovery. McGraw-Hill Publishing Company, New York, N.Y
|
| 8.
|
Cairns-Smith, A. G.,
A. J. Hall, and M. J. Russell.
1992.
Mineral theories of the origin of life and an iron sulfide example, p. 161-180.
In
Origins of life and evolution of the biosphere. Kluwer Academic Publishers, Dordrecht, The Netherlands
|
| 9.
|
Cobley, J. G., and B. A. Haddock.
1975.
The respiratory chain of Thiobacillus ferrooxidans: the reduction of cytochromes by Fe2+ and the preliminary characterization of rusticyanin, a novel "blue" copper protein.
FEBS Lett.
60:29-33[Medline].
|
| 10.
|
Eraso, J.-M., and G. M. Weinstock.
1992.
Anaerobic control of colicin E1 production.
J. Bacteriol.
174:5101-5109[Abstract/Free Full Text].
|
| 11.
|
García-Horsman, J. A.,
B. Barquera,
J. Rumbley,
J. Ma, and R. B. Gennis.
1994.
The super-family of heme-copper respiratory oxidases.
J. Bacteriol.
176:5587-5600[Free Full Text].
|
| 12.
|
Gaspard, S.,
F. Vazquez, and C. Holliger.
1998.
Localization and solubilization of the iron(III) reductase of Geobacter sulfurreducens.
Appl. Environ. Microbiol.
64:3188-3194[Abstract/Free Full Text].
|
| 13.
|
Giudici-Orticoni, M.-T.,
W. Nitschke,
C. Cavazza, and M. Bruschi.
1997.
Characterization and functional role of a cytochrome c4 involved in the iron respiratory electron transport chain of Thiobacillus ferrooxidans, p. PB4.1-PB4.10.
In
A.I.M. Ritchie, and D. Pollard (ed.), Biomine. The Australian Mineral Foundation, Glenside, Australia
|
| 14.
|
Guiliani, N.,
A. Bengrine,
F. Borne,
M. Chippaux, and V. Bonnefoy.
1997.
Alanyl tRNA synthetase gene of the extreme acidophilic chemolithotrophic Thiobacillus ferrooxidans is highly homologous to alaS from all living kingdoms but cannot be transcribed from its promoter in Escherichia coli.
Microbiology
143:2179-2187[Abstract/Free Full Text].
|
| 15.
|
Hall, J. F.,
S. S. Hasnain, and W. J. Ingledew.
1996.
The structural gene for rusticyanin from Thiobacillus ferrooxidans: cloning and sequencing of the rusticyanin gene.
FEMS Microbiol. Lett.
137:85-89[Medline].
|
| 16.
|
Hofacker, I., and K. Schulten.
1998.
Oxygen and proton pathways in cytochrome c oxidase.
Proteins
30:100-107[Medline].
|
| 17.
|
Ingledew, W. J., and J. G. Cobley.
1980.
A potentiometric and kinetic study on the respiratory chain of ferrous iron grown Thiobacillus ferrooxidans.
Biochim. Biophys. Acta
590:141-158[Medline].
|
| 18.
|
Ingledew, W. J.,
J. C. Cox, and P. J. Halling.
1977.
A proposed mechanism for energy conservation during Fe2+ oxidation by Thiobacillus ferrooxidans; chemiosmotic coupling to net H+ influx.
FEMS Microbiol. Lett.
2:193-197.
|
| 19.
|
Iwahori, K.,
K. Kamimura, and T. Sugio.
1998.
Isolation and some properties of cytochrome c oxidase purified from a bisulfite ion resistant Thiobacillus ferrooxidans strain, OK1-50.
Biosci. Biotechnol. Biochem.
62:1081-1086[Medline].
|
| 20.
|
Iwata, S.,
C. Ostermeier,
B. Ludwig, and H. Michel.
1995.
Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans.
Nature
376:660-668[Medline].
|
| 21.
|
Jensen, A. B., and C. Webb.
1995.
Treatment of H2S-containing gases: a review of microbiological alternatives.
Enzyme Microb. Technol.
17:2-10.
|
| 22.
|
Juszczak, A.,
F. Domka,
M. Kolowski, and H. Wachowska.
1995.
Microbial desulfurization of coal with Thiobacillus ferrooxidans bacteria.
Fuel
74:725-728.
|
| 23.
|
Kai, M.,
T. Yano,
Y. Fukumori, and T. Yamanaka.
1989.
Cytochrome oxidase of an acidophilic iron-oxidizing bacterium, Thiobacillus ferrooxidans, functions at pH 3.5.
Biochem. Biophys. Res. Commun.
2:839-843.
|
| 24.
|
Kai, M.,
T. Yano,
H. Tamegai,
Y. Fukumori, and T. Yamanaka.
1992.
Thiobacillus ferrooxidans cytochrome c oxidase: purification, and molecular and enzymatic features.
J. Biochem.
112:816-821[Abstract/Free Full Text].
|
| 25.
|
Kelly, M.,
P. Lappalainen,
G. Talbo,
T. Haltia,
J. van der Oost, and M. Saraste.
1993.
Two cysteines, two histidines, and one methionine are ligands of a binuclear purple copper center.
J. Biol. Chem.
268:16781-16787[Abstract/Free Full Text].
|
| 26.
|
Kusano, T.,
T. Takeshima,
K. Sugawara,
C. Inoue,
T. Shiratori,
T. Yano,
Y. Fukumori, and T. Yamanaka.
1992.
Molecular cloning of the gene encoding Thiobacillus ferrooxidans Fe(II) oxidase.
J. Biol. Chem.
267:11242-11247[Abstract/Free Full Text].
|
| 27.
|
Lappalainen, P.,
N. J. Watmough,
C. Greenwood, and M. Saraste.
1995.
Electron transfer between cytochrome c and the isolated CuA domain: identification of substrate binding residues in cytochrome c oxidase.
Biochemistry
34:5824-5830[Medline].
|
| 28.
|
Mansch, R., and W. Sand.
1992.
Acid-stable cytochromes in ferrous ion oxidizing cell-free preparations from Thiobacillus ferrooxidans.
FEMS Microbiol. Lett.
92:83-88.
|
| 29.
|
Matzke, J.,
B. Schwermann, and E. P. Bakker.
1997.
Acidostable and acidophilic proteins: the example of the -amylase from Alicyclobacillus acidocaldarius.
Comp. Biochem. Physiol.
118:475-479.
|
| 30.
|
Menin, L.,
J. Gaillard,
P. Parot,
B. Schoepp,
W. Nitschke, and A. Vermeglio.
1998.
Role of HiPIP as electron donor to the RC-bound cytochrome in photosynthetic purple bacteria.
Photosynth. Res.
55:343-348.
|
| 31.
|
Miller, J. H.
1972.
A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria.
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
|
| 32.
|
Myers, C. R., and J. M. Myers.
1992.
Localization of cytochromes to the outer membrane of anaerobically grown Shewanella putrefaciens MR-1.
J. Bacteriol.
174:3429-3438[Abstract/Free Full Text].
|
| 33.
|
Myers, C. R., and J. M. Myers.
1997.
Outer membrane cytochromes of Shewanella putrefaciens MR-1: spectral analysis, and purification of the 83-kDa c-type cytochrome.
Biochim. Biophys. Acta
1326:307-318[Medline].
|
| 34.
|
Myers, J. M., and C. R. Myers.
1998.
Isolation and sequence of omcA, a gene encoding a decaheme outer membrane cytochrome c of Shewanella putrefaciens MR-1, and detection of omcA homologs in other strains of S. putrefaciens.
Biochim. Biophys. Acta
1373:237-251[Medline].
|
| 35.
|
Nakai, K., and M. Kanehisa.
1991.
Expert system for predicting protein localization sites in Gram-negative bacteria.
Proteins Struct. Funct. Genet.
11:95-110.
[Medline] |
| 36.
|
Ochman, H.,
M. M. Medhora,
D. Garza, and D. L. Hartl.
1990.
Amplification of flanking sequences by inverse PCR, p. 219-227.
In
M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White (ed.), PCR protocols, a guide to methods and applications. Academic Press, Inc., Harcourt Brace Jovanovich, Publishers, San Diego, Calif
|
| 37.
|
Ostermeier, C.,
S. Iwata, and H. Michel.
1996.
Cytochrome c oxidase.
Curr. Opin. Struct. Biol.
6:460-466[Medline].
|
| 38.
|
Pulgar, V.,
L. Nunez,
F. Moreno,
O. Orellana, and E. Jedlicki.
1993.
Expression of rusticyanin gene is regulated by growth condition in Thiobacillus ferrooxidans, p. 541-548.
In
A. E. Torma, M. L. Apel, and C. L. Brierley (ed.), Biohydrometallurgical technologies, vol. II. The Minerals, Metals and Material Society, Warrendale, Pa
|
| 39.
|
Rawlings, D. E., and S. Silver.
1995.
Mining with microbes.
Bio/Technology
13:773-778.
|
| 40.
|
Saraste, M.
1990.
Structural features of cytochrome oxidase.
Q. Rev. Biophys.
23:331-366[Medline].
|
| 41.
|
Saraste, M.,
J. Castresana,
D. Higgins,
M. Lübben, and M. Wilmanns.
1994.
Evolution of cytochrome oxidase, p. 255-289.
In
H. Baltscheffsky (ed.), Origin and evolution of biological energy conversion. VCH, New York, N.Y
|
| 42.
|
Schäfer, G.
1996.
Bioenergetics of the archaebacterium Sulfolobus.
Biochim. Biophys. Acta
1277:163-200[Medline].
|
| 43.
|
Seeliger, S.,
R. Cord-Ruwisch, and B. Schink.
1998.
A periplasmic and extracellular c-type cytochrome of Geobacter sulfurreducens acts as a ferric iron reductase and as an electron carrier to other acceptors or to partner bacteria.
J. Bacteriol.
180:3686-3691[Abstract/Free Full Text].
|
| 44.
|
Shapleigh, J. P.,
J. P. Hosler,
M. M. J. Tecklenburg,
Y. Kim,
G. T. Babcock,
R. B. Gennis, and S. Ferguson-Miller.
1992.
Definition of the catalytic site of cytochrome c oxidase: specific ligands of heme a and the heme a3-CuB center.
Proc. Natl. Acad. Sci. USA
89:4786-4790[Abstract/Free Full Text].
|
| 45.
|
Steffens, G. J., and G. Buse.
1979.
Studies on cytochrome c oxidase, IV. Primary structure and function of subunit II.
Hoppe-Seyler's Z. Physiol. Chem.
360:613-619[Medline].
|
| 46.
|
Thöny-Meyer, L.
1997.
Biogenesis of respiratory cytochromes in bacteria.
Microbiol. Mol. Biol. Rev.
61:337-376[Abstract].
|
| 47.
|
Van Ommen Kloeke, F.,
R. D. Bryant, and E. J. Laishley.
1995.
Localization of cytochromes in the outer membrane of Desulfovibrio vulgaris (Hildenborough) and their role in anaerobic corrosion.
Anaerobe
1:351-358.
|
| 48.
|
Witt, H., and B. Ludwig.
1997.
Isolation, analysis, and deletion of the gene coding for subunit IV of cytochrome c oxidase in Paracoccus denitrificans.
J. Biol. Chem.
272:5514-5517[Abstract/Free Full Text].
|
| 49.
|
Yamanaka, T., and Y. Fukumori.
1995.
Molecular aspects of the electron transfer system which participates in the oxidation of ferrous ion by Thiobacillus ferrooxidans.
FEMS Microbiol. Rev.
17:401-413[Medline].
|
| 50.
|
Yamanaka, T.,
T. Yano,
M. Kai,
H. Tamegai,
A. Sato, and Y. Fukumori.
1991.
The electron transfer system in an acidophilic iron-oxidizing bacterium, p. 223-246.
In
Y. Mukohata (ed.), New era of bioenergetics. Academic Press, Tokyo, Japan
|
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