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(Received for publication, April 3,
1995; and in revised form, July 31, 1995) From the
Magnetospirillum sp. AMB-1 is a freshwater magnetic
bacterium which synthesizes intracellular particles of magnetite
(Fe
Biogenic magnetite (Fe The magnetic
particles of these spirilla are aligned in chains in the cells.
Furthermore, each particle is covered with a thin lipid layer (11) . Magnetic particles from strain AMB-1 are also covered by
organic membranes. In magnetic bacteria, a magnetic particle synthesis
system was proposed(12) , which involves (i) uptake of iron;
(ii) transport of iron to the cytoplasmic space and across the magnetic
particle membrane; (iii) precipitation of hydrated ferric oxide within
vesicles; and (iv) phase transformation of the amorphous iron phase to
magnetite, during both nucleation and surface-controlled growth.
Several aspects of the general system remain unclear, for example,
whether the ferric or ferrous ion is taken up and transported and which
proteins control the reactions in stages iii and iv. The proteins and
their genes have not yet been isolated or analyzed. We have
characterized iron uptake in Magnetospirillum sp.
AMB-1(13) . AMB-1 is nonselective in iron uptake. High affinity
iron(III) chelators, siderophores, are generally utilized for iron
uptake by
microorganisms(14, 15, 16, 17, 18) ,
but the iron transport system of AMB-1 does not include siderophore
production, secretion, and utilization, in contrast to M.
magnetotacticum MS-1(19) . In addition, the properties of
iron reduction which may be related to magnetite crystallization have
been described(20, 21) . However, no genes concerned
with the magnetite synthesis system have been described. Previously,
five nonmagnetic mutants were generated by introduction of transposon
Tn5 into the genome of Magnetospirillum sp.
AMB-1(10) . We present here genetic analysis of the 3-kilobase
pair genomic region interrupted in a nonmagnetic mutant, NM5. This work
represents the first report of the DNA sequence and putative product
information of a gene thought to be involved in the magnetite
biomineralization process.
Figure 2:
Nucleotide sequence of the mutagenized
genomic fragment of NM5. Boxed regions are TATA box-resembling
regions. Arrows indicate inverted repeats and hairpin
loops.
Figure 1:
Physical map of the Tn5 insertion site and open reading frames in the mutagenized region
of the nonmagnetic strain NM5. The ORFs are shown by boxed
lines. The putative promoter region is indicated by a triangle. Arrows show sequenced regions and the
direction of sequencing.
The
hypothetical protein encoded by the magA gene, MagA, consists
of 434 amino acids and has a predicted molecular mass of 46.8 kDa. MagA
was found to have high homology with the KefC protein from E.
coli(29) , with 25.4% similar amino acid residues. Fig. 3shows an alignment of MagA and KefC, which functions as a
potassium efflux protein for control of turgor. Moreover, the
Na
Figure 3:
Amino
acid sequence homology of MagA with KefC of E. coli. Identical
amino acids are indicated by bars. Equivalent amino acids are
shown as two or one dots. Two dots indicates
higher similarity than one dot. Total similarity index:
25.4%.
Figure 4:
Northern blot analysis of wild type AMB-1
and NM5. Lane 4 shows the band of hybridized mRNA
corresponding to 1.5 µg of the total RNA extracted from wild type
AMB-1 cells shown in lane 1. Lane 5 shows the hybridized mRNA
corresponding to 2.4 µg of total RNA from the wild type, shown in lane 2. Lane 6 shows the hybridized mRNA corresponding to 1.5
µg of total RNA from the mutant, NM5, shown in lane 3. Lane M shows 0.24-9.5-kb RNA ladder (Life Technologies, Inc.).
Preparation of total RNA from magnetic bacteria and hybridization
method is described under ``Experimental Procedures.'' Probes
were prepared by polymerase chain reaction using the primers shown in Fig. 2.
Dot-blot Northern hybridization experiments showed that higher
levels of magA specific mRNA occurred in wild type AMB-1 cells
in iron-limited than in iron-sufficient medium (Fig. 5). This
suggests that transcription of the magA promoter is regulated
by environmental iron concentration. Moreover, RNA samples extracted
from mutant NM5 showed strong hybridization under iron-sufficient
growth conditions. This implies that hybridized RNA from NM5 was not
transcribed by the magA promoter and supports the hypothesis
of the transcription by the inherent promoter of Tn5 in NM5.
Regulation by iron is not very strict, as no significant difference
between pMKP transconjugant grown in iron-sufficient medium and in
iron-deficient medium was observed in the CAT promoter activity assay
(data not shown).
Figure 5:
Dot-blot Northern analysis of magA gene expression. Total RNA extracted from wild type AMB-1 cells
grown in iron-limited medium (a trace amount of iron) was loaded on dots 1-3; total RNA from wild type cells grown on
iron-sufficient medium (33 µM iron ion concentration) was
loaded on dots 4-6; total RNA from mutant NM5 cells
grown in iron-sufficient medium was loaded on dots 7-9.
Extracted total RNA was placed on the nylon membrane, with 5.8 ng on dots 1, 4, and 7; 58 ng on dots 2, 5, and 8; and 580 ng on dots 3, 6, and 9. The probe
used was the same as that in Fig. 5.
Figure 6:
Iron uptake by membrane vesicles.
Membrane vesicles were prepared as described under ``Experimental
Procedures'' and assayed in the TMSM buffer (25) at a
final protein concentration of 10 mg/ml supplemented with 330
µM iron and 5 mM ATP. The curves show change in
iron concentration due to vesicles from the pTrc99A transformant of E. coli DH5
The data presented above indicate that the ORF, magA, which was found in a mutagenized genomic fragment of
NM5, encodes a putative protein, MagA, highly homologous to proteins of E. coli. KefC consists of two domains, a hydrophobic membrane
binding domain and a strongly hydrophilic carboxyl terminus. The region
homologous with MagA corresponds to the hydrophobic domain, which is
thought to be a potassium-translocating channel(29) . The
sequence of hydrophobic amino acids could form eight to 10
transmembrane In E. coli, expression of iron
transport proteins is regulated by iron concentration via the Fur
repressor system in which a regulatory protein, Fur, binds ferrous ion
and represses transcription of the genes involved in iron
uptake(14, 32) . Fur-like regulation systems were
found in various bacteria, such as Yersinia
pestis(33) , Vibrio cholerae(34) , and Pseudomonas aeruginosa(35) , and low levels of
environmental iron induce high expression of the proteins involved in
iron uptake. Dot-blot analysis showed that magA expression
appears to be regulated in a similar way to iron uptake genes from E. coli. However, there is no domain similar to the
Fur-binding region near the magA promoter. One reasonable
hypothesis is that magnetic bacteria have a different system from the
Fur regulation and iron uptake systems. It is obvious from phylogenetic
analysis of 16 S rRNA that E. coli and AMB-1 are
evolutionarily different; E. coli belongs to the
Iron is an
essential element of the bacterial magnetic particle and must be
translocated across the cell and magnetic particle membranes. Thus,
iron transport has an important role in magnetic particle synthesis.
Homology data and iron regulation suggest that the magA gene
product is involved in iron transport. It has been confirmed by direct
iron uptake measurements in membrane vesicles that the magA gene product functions as an iron transporter in E. coli.
Moreover, this result verifies that the putative MagA protein is
located in the inner membrane in E. coli. The MagA protein may
function as an iron transport channel protein and be coupled with
ATPase. In E. coli, ferric iron uptake has been well studied,
and the transport of iron across the cytoplasmic membrane depends on
ATP hydrolysis(14) . As to the putative MagA, two hypotheses
may be put forward for the energy coupling. One is a direct driving of
iron transport by ATPase, with a protein encoded by the second ORF in
the cloned NcoI-BamHI restriction fragment
functioning as the ATPase or an ATPase derived from E. coli interacting with MagA. The other is an indirect ATPase coupling,
with MagA functioning as an
Fe The magA gene is
followed by a second ORF which overlaps magA by 25 bp.
However, no promoter-like region was found upstream of the start codon
of ORF2 at nucleotide 2162. ORF2 consists of a 606-bp section which
would encode a 21.6-kDa protein. The putative protein encoded by ORF2
was also analyzed. Strong homology (47.2% similarity) was exhibited
with E. coli RNase HII(36, 37) , which
specifically degrades the ribonucleotide moiety of RNA-DNA hybrid
molecules. Although the strong homology suggests that the protein
encoded by ORF2 has a similar function to RNase HII, it is not clear
whether an RNase HII function is involved in magnetic particle
synthesis or is concerned with the magA gene product, perhaps
as an ATPase. This is the first report on a gene and a protein
concerned with iron transport in a magnetic bacterium. Since
interruption of the magA gene prevents magnetite synthesis in
AMB-1, we suggest that the putative MagA protein may be localized in
the membrane covering the magnetic particles in AMB-1 and may transport
iron into the vesicles. In further work, biochemical analysis of the
putative MagA protein and the protein encoded by the second ORF will
help elucidate a part of the mechanism of magnetic particle synthesis
in this magnetic bacterium.
The nucleotide
sequence(s) reported in this paper has been submitted to the
GenBank(TM)/EMBL Data Bank with accession number(s)
D32253[GenBank].
Volume 270,
Number 47,
Issue of November 24, 1995 pp. 28392-28396
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
O
). A genomic DNA fragment required for
synthesis of magnetic particles was previously isolated from a
nonmagnetic transposon Tn5 mutant. We have determined the
complete nucleotide sequence of this fragment. The 2975-base pair
region contains two putative open reading frames. One open reading
frame, designated magA, encodes a polypeptide which is
homologous to the cation efflux proteins, the Escherichia coli potassium ion-translocating protein, KefC, and the putative
Na/H
-antiporter, NapA, from Enterococcus hirae. Northern hybridization demonstrated that
the magA mRNA transcript is 1.3 kilobases in size,
corresponding to the size of the magA gene. A functional
promoter was located upstream from the magA gene, and the
transcription in AMB-1 was regulated by environmental iron
concentration. Vesicles isolated from E. coli in which the
MagA protein was expressed exhibited iron accumulation ability. We
consider that the MagA protein is an iron transport involved in the
synthesis of magnetic particles in AMB-1.
O) was originally
identified as a strengthening mineral in the radula teeth of chitons (Mollusca and Polyplacophora spp.)(1) .
Magnetic particles have since been found in other higher animals, for
example migratory fish(2, 3) . The function and
mechanism of synthesis of these magnetic particles remains unclear.
Bacteria isolated from fresh water which synthesize intracellular
magnetic particles consisting of magnetite include Magnetospirillum
magnetotacticum MS-1(4) , Magnetospirillum sp.
MGT-1(5) , Magnetospirillum sp. AMB-1(6) , and Magnetospirillum gryphiswaldense(7) . Phylogenetic
analysis of 16 S rRNA sequences of Magnetospirillum spp. have
shown their close evolutionary relationships to some photosynthetic
bacteria(8, 9) . We are currently using AMB-1 as a
model system for the study of magnetite biomineralization at the
molecular genetic level(10) . The ecological significance of
bacterial magnetite remains unclear and the mechanism of magnetite
crystal formation has not yet been elucidated.
Strains and Growth Conditions
Escherichia
coli DH5
was used for cloning of genes, chloramphenicol
acetyltransferase (CAT) (
)assay experiments, and preparation
of vesicles. E. coli S17-1 was utilized to transfer
conjugative plasmids to Magnetospirillum sp. AMB-1 (10) . E. coli was cultured in Luria broth at 37
°C after adding appropriate antibiotics. Wild type and mutant Magnetospirillum sp. AMB-1 were cultured in MSGM medium (4) at 25 °C as described previously(6) .Nucleotide Sequence Analysis
Samples for
sequencing were prepared from plasmid pCN5(10) , which contains
the EcoRI fragment including Tn5, from NM5. The
Tn5 flanking regions were cloned separately, and deletion
series for sequencing were constructed. DNA sequencing was carried out
by the dideoxy method (22) on plasmid templates, using the
AmpliTaq cycle sequencing kit, and fluorescein isothiocyanate-labeled
primers (Takara Shuzo, Shiga, Japan) or primers synthesized on the
basis of sequence information using a DNA synthesizer (ABI, Carson
City, CA). An automatic DNA sequencing machine, DSQ-1 (Shimadzu, Kyoto,
Japan), was used for running samples, detection of fluorescence, and
determination of nucleotide sequence. All sequencing reactions were
performed three times at least and on both strands. The computer
software packages, DNASIS (Hitachi Software Engineering Co., Ltd.,
Kanagawa, Japan) and LASERGENE (DNASTAR Ltd., London, United Kingdom),
were used for analysis of DNA and protein sequences.Cloning of Uninterrupted Wild Type Genomic
Fragment
The wild type genomic EcoRI fragment of AMB-1
was isolated from a ZAP gene bank and subcloned for sequencing. A
334-bp downstream of EcoRI fragment, which was isolated from BamHI genomic DNA bank of NM5 containing a kanamycin-resistant
gene derived from Tn5, was also sequenced.
Detection of Promoter Activity
A promoter probe
vector, pXCAT, was constructed for the detection of promoter activity.
pXCAT is derived from pXCA601, which was a kind gift from J. T.
Beatty(23) . In pXCAT, the CAT gene was inserted in place of
the lacZ reporter of pXCA601. Transcription of a fragment
cloned into pXCAT can be detected as CAT activity of cell extracts
obtained by lysing cells with acetone. Measurement of CAT activity was
performed using the FluoReporter FAST CAT gene fusion detection kit
(Molecular Probes, Pitchford City, OR), and high pressure liquid
chromatography was used for the measurement of acetylated fluorescent
chloramphenicol substrate. This method was reported previously. (
)CAT activity was calculated from the proportion of
chloramphenicol acetylated. One unit of CAT activity acetylates 1 nmol
of chloramphenicol/min.Northern Hybridization Analysis
Northern blot
hybridization of total RNA extracted from AMB-1 and NM5 cells using the magA fragment as a probe was carried out. Total RNA extracted
from cells grown up to late log phase using the RNaid PLUS KIT (BIO
101, Inc., Vista City, CA). DIG luminescent kit (Boehringer Mannheim
GmbH Biochemica, Mannheim, Germany) was employed for hybridization, and
the probe was prepared by polymerase chain reaction using primers,
Primer1 and Primer2, designed within the magA ORF (shown in Fig. 2). Furthermore, dot-blot hybridization was performed in
order to measure the amount of mRNA transcribed from the magA gene using the same polymerase chain reaction probe as for
detection. RNA samples were extracted from magnetic bacterial cells
grown on iron-sufficient MSGM, containing 33 µM iron, and
iron-limited MSGM, containing a trace amount of iron.
Preparation of Vesicles
pTrc99A (24) was
employed for expression of a protein in E. coli DH5.
DH5 transformant cells were utilized for preparation of vesicles
following the protocol of Waser et al.(25) .Iron Uptake
Vesicles were suspended in TMSM buffer (25) to a final protein concentration of 10 mg/ml and
supplemented with 330 µM ferrous ammonium sulfate
(FeSO(NH)SO
6HO;
Mohr's salt) as an iron source and 5 mM ATP. At various
times, 0.8-ml aliquots were removed and centrifuged at 15,000 
g for 15 min to remove vesicles. The iron concentration of the
buffer was measured using ferrozine, a spectrophotometric reagent for
iron(26) . Fifty µl of 60% hydroxylamine hydrochloride was
added to 100 µl of the samples as a reductant, and argon gas was
sealed into sample tubes and incubated for 24 h. Finally, 100 µl of
glacial acetic acid-sodium acetate buffer (pH 6.0) and 200 µl of 1%
ferrozine were added, and the absorbance of sample solutions at 526 nm
was measured spectrophotometrically.
Nucleotide Sequence Analysis
A portion of the
genomic DNA fragment from the Tn5 flanking region of NM5 was
sequenced. A physical map of this region is shown in Fig. 1. The
transposon insertion site is also shown. An open reading frame with a
putative ribosomal binding site which resembles an SD sequence (27) was found. In Fig. 1, the black line represents one of the open reading frames, ORF1, termed magA, which is interrupted by the Tn5 insertion. We
focused on analysis of the magA gene, and Fig. 2shows
the nucleotide sequence of the genomic fragment containing magA. Within magA, there is a Tn5 target
sequence, TTCTGACC, at nucleotide 1524, which was duplicated by Tn5 integration in the mutagenized genome of NM5. The magA gene is 1305 bp in length, and a putative promoter region is
located 75 bp upstream of the start codon of magA at
nucleotide 883. Two TATA box-resembling domains are shown as boxed
regions, and inverted repeats near the TATA box-resembling domains
are indicated by arrows in Fig. 2. Furthermore, there
is a region of dyad symmetry at nucleotide 2227, downstream of the stop
codon of magA, which resembles a Rho-independent
terminator(28) . These gene structures suggest that the magA gene is a gene encoding an actual protein.
/H
-antiporter, NapA of Enterococcus hirae(25) , is homologous to MagA, with
24.1% similarity. The similarity between KefC and NapA has been
described (30) , and these proteins form a group of cation
efflux antiporters.
Detection of Promoter Activity
The transcriptional
function of the promoter-like region which was found upstream of magA was investigated. A 547-bp KpnI-PstI
fragment containing the promoter-like region was cloned upstream from
the CAT reporter gene of the promoter probe vector, pXCAT, in the
orientation in which the putative promoter transcribes the CAT gene,
and this plasmid was designated pMKP. pXCAT and pMKP were transferred
into wild type AMB-1 cells by conjugation(10, 31) ,
and CAT activities were measured with cell growth, and the average CAT
activities of AMB-1 transconjugants containing either pXCAT or pMKP in
log-phase were calculated. The pXCAT transconjugant did not show any
CAT activity. In contrast, high CAT activity, 1.9 10 units/mg of protein, was measured for the pMKP transconjugant.
This result suggests that the 547-bp fragment cloned from upstream of
the magA gene contains an active promoter which is functional
in AMB-1 cells. E. coli transformants containing pXCAT and
pMKP were also analyzed for magA promoter activity. Both
transformants exhibited little CAT activity, less than 10 units/mg
protein, indicating that the magA promoter does not function
in E. coli.Effect of Iron on the magA Transcription
A 1.3-kb
mRNA was detected in total RNA extracted from wild type AMB-1 (Fig. 4). This corresponds to the size of the magA gene
and suggests that magA is transcribed independently of other
unidentified ORFs. Furthermore, a 1.3-kb band was not detected in
mutant NM5, but a much larger band hybridized to the probe. Thus,
Tn5 insertion interrupts transcription of magA, and
the large transcript is probably transcribed by a Tn5 promoter, such as the promoter of the kanamycin resistance gene.
Iron Transport in Membrane Vesicles
A 2094-bp
fragment from NcoI-BamHI digestion was connected to
the multicloning site of pTrc99A to express the magA gene in E. coli. This plasmid, designated pTMG5, was transferred into E. coli DH5, and the transformed cells were utilized to
prepare membrane vesicles. Iron transport by the magA gene
product was verified by direct measurements of iron in membrane
vesicles. When ATP was added to transformant vesicles, iron uptake
could be observed (Fig. 6). However, when ATP was omitted, iron
uptake was not observed (data not shown). This result shows that the magA gene product functions as an iron transporter in the
cytoplasmic membrane in E. coli and that the energy of
transport is directly or indirectly coupled with ATP hydrolysis.
() and the pTMG5 transformant
(
).
-helices.-proteobacteria and AMB-1 to the
-proteobacteria(8) .
Thus, this evolutionary difference probably is reflected by differences
in metabolic systems between E. coli and AMB-1./H
-antiporter driven by the proton
motive force of F
F
-ATPase, like the KefC
protein of E. coli and the NapA protein of E.
hirae(25, 29) .
))
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
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