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Journal of Bacteriology, December 1999, p. 7394-7397, Vol. 181, No. 23
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Characterization of the Bradyrhizobium
japonicum ftsH Gene and Its Product
Franz
Narberhaus,*
Carmen
Urech, and
Hauke
Hennecke
Institut für Mikrobiologie,
Eidgenössische Technische Hochschule, CH-8092 Zürich,
Switzerland
Received 19 July 1999/Accepted 14 September 1999
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ABSTRACT |
The Bradyrhizobium japonicum ftsH gene was cloned by
using a set of widely applicable degenerated oligonucleotides. Western blot experiments indicated that the FtsH protein was produced under
standard growth conditions and that it was not heat inducible. Attempts
to delete the ftsH gene in B. japonicum failed,
suggesting a pivotal cellular function of this gene. The expression of
B. japonicum ftsH in an ftsH-negative
Escherichia coli strain significantly enhanced the fitness
of this mutant and reduced the steady-state level of
32.
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TEXT |
The Escherichia coli ftsH
(filamentation temperature-sensitive) gene encodes a 70-kDa
membrane-anchored ATP-dependent metalloprotease (24). FtsH
belongs to the AAA family (ATPases associated with diverse cellular
activities), members of which are found universally in prokaryotes and
in mitochondria and chloroplasts of eukaryotes. The presence of
ftsH even in the minimal genome of Mycoplasma genitalium (7) is indicative of its important cellular
function(s). A regulatory function of FtsH in E. coli is the
degradation of the heat shock sigma factor
32 under
normal growth conditions, in which only minute amounts of this
alternative sigma factor are required (10, 24). FtsH has
opposing effects on the stability or activity of
32 and
54. While the first is degraded by FtsH, the latter
gains functionality by the action of FtsH through an unknown mechanism
(6). Another task of FtsH, the capacity to degrade the
cII and cIII proteins, led to its alternative designation, HflB,
reflecting the high frequency of lysogeny phenotype of an
hflB mutant (11, 21). Up-regulated expression of
lipopolysaccharides due to stabilization of the committed deacetylase
in lipopolysaccharide biosynthesis is assumed to be the reason for the
lethality of an E. coli ftsH mutant (17). FtsH
also degrades integral membrane proteins such as SecY, a subunit of the
protein translocase, and subunit
of the
F1F0 ATPase complex (1, 2). Two
N-terminal transmembrane regions of FtsH mediate multimer formation of
the protein, resulting in the appearance of ring-shaped structures
(5, 21). There is accumulating evidence that FtsH serves
other functions in addition to being a protease. It participates in the
assembly of proteins into the membrane and in the translocation of
exported proteins (3, 4). The multifunctionality of FtsH is
manifested by its requirement in mRNA turnover. Its putative role in
mRNA decay has provoked yet another designation, namely, MrsC for mRNA
stability (8, 27).
Bradyrhizobium japonicum, the nitrogen-fixing root nodule
symbiont of soybean, is an interesting organism in this context because
it encodes three
32-type RpoH factors (14)
and two
54-type RpoN proteins (12) which
could be potential targets of FtsH. In order to determine whether
B. japonicum FtsH is involved in the regulation of responses
to heat shock and nitrogen limitation, we set out to characterize the
corresponding gene and its product.
Cloning of the B. japonicum ftsH gene.
FtsH-like
proteins from different bacteria display a number of conserved motifs
and domains (20), among them the highly conserved
ATP-binding Walker A and Walker B motifs. Degenerated oligonucleotides
based on these motifs and on an additional conserved sequence further
downstream were designed in accordance with the B. japonicum
codon frequency table (19) (Fig.
1). Internal ftsH fragments
were amplified by touchdown PCR. The annealing temperature was
gradually lowered by 2°C from 50 to 42°C every second cycle. Amplification was completed after 30 cycles at an annealing temperature of 48°C. Amplification with total DNA of B. japonicum and
the primers Sig148 and Sig150 resulted in the expected 280-bp fragment (PCR product 1; Fig. 2A and
3). Furthermore, a 190-bp fragment was
amplified with Sig148 and Sig149b (PCR product 2). This short product
was also obtained when the isolated 280-bp fragment served as the
template for a nested PCR with Sig148 and Sig149b (PCR product N). The
amplification products were cloned into pUC18, and sequencing of the
inserts clearly revealed the internal sequence of an
ftsH-like gene. The 280-bp ftsH fragment was then
used as a hybridization probe to isolate the complete ftsH
gene region of B. japonicum (Fig. 3). The presence of only a
single band per digest in a Southern hybridization experiment suggested
that the B. japonicum genome contains only a single copy of
the ftsH gene (data not shown). Two fragments, a 2.1-kbp
PstI fragment and a 6.9-kbp BamHI fragment, were
cloned into pUC18 and designated pRJ5175 and pRJ5176, respectively
(Fig. 3). Sequencing confirmed that the inserts carried large and
overlapping portions of the B. japonicum ftsH gene. In order
to obtain the complete ftsH gene on a single plasmid,
pRJ5184 was constructed (Fig. 3) by ligating a 2.4-kbp EcoRI
fragment from pRJ5175 into a 4.8-kbp EcoRI fragment of
pRJ5177, a subclone of pRJ5176.

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FIG. 1.
Alignment of the deduced amino acid sequences of an
internal region of several AAA-type proteins. Only the amino acids
corresponding to E. coli FtsH from position 179 to position
428 are shown. FtsH proteins from E. coli (Eco)
(25), B. subtilis (Bsu)
(16), M. genitalium (Mge)
(7), and A. thaliana (Ath)
(13) are listed and compared with B. japonicum
(Bja) FtsH (this work). The conserved Walker motifs and the
putative Zn2+ binding site comprising two conserved
histidines are indicated. Residues that are identical in all five
proteins are defined by capital letters in the consensus (Con) sequence
line. Amino acids present in four of the five proteins are indicated by
lowercase letters. The sequences of degenerated oligonucleotides used
to amplify internal ftsH fragments are listed above the
corresponding amino acid sequence. The code for mixed nucleotides is as
follows: S is C or G, R is G or A, Y is C or T, and I is inosine. The
true nucleotide sequence obtained by sequencing of the B. japonicum ftsH gene is provided in italic letters above the
oligonucleotides.
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FIG. 2.
PCR amplification of internal ftsH fragments
from various bacteria. Total DNAs of B. japonicum (A); the
gram-negative bacteria E. coli (Eco), S. meliloti (Sme), A. tumefaciens
(Atu), and P. putida (Ppu) (B); and
the gram-positive bacteria B. subtilis (Bsu) and
S. aureus (Sau) (C) were subjected to touchdown
PCR. An aliquot of the PCR mixture was separated on 1.5% (wt/vol)
agarose gels. Amplification products obtained with the primer pair
Sig148-Sig150 are in lanes 1, and products obtained with Sig148-Sig149b
by using either total DNA or isolated product 1 as the template are in
lanes 2 or N, respectively. Fragments corresponding to the expected
sizes are boxed. The lengths (in base pairs) of representative bands
from the 100-bp ladder (lanes M) are indicated on the left.
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FIG. 3.
Physical map of the B. japonicum ftsH gene
region. Numbers indicate the nucleotide positions of open reading
frames and recognition sites of restriction enzymes as follows:
B, BamHI; EI, EcoRI;
EV, EcoRV; E47III,
Eco47III; P, PstI; S,
SalI; X, XhoI. The positions of PCR
products 1, 2, and N with respect to the ftsH gene are
indicated. The inserts of relevant plasmids harboring the
ftsH gene region are given with their corresponding plasmid
designations. Plasmids pRJ5175, pRJ5176, and pRJ5184 contain pUC18
(15) as a vector. The inserts of pRJ5180 and pRJ5181 were
cloned into pSUP202pol3, a derivative of pSUP202 (22).
Plasmid pRJ5188 is based on pBAD18-Cm (9).
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Analysis of the ftsH gene region.
The deduced
ftsH gene product displays significant overall sequence
similarity to other known proteases of the AAA family. B. japonicum FtsH shares 57.7, 50.6, and 53.4% positionally
identical amino acids with its homologs from E. coli,
Bacillus subtilis, and Arabidopsis thaliana,
respectively. Two putative transmembrane regions (residues 7 to 25 and
102 to 125) can be predicted as a potential membrane anchor. A
particularly high degree of conservation is evident in the regions that
had served for the design of degenerated oligonucleotides (Fig. 1).
This finding prompted us to test whether the primers would also yield
specific amplification products with chromosomal DNAs from other
bacteria. Total DNAs from a variety of prokaryotes were subjected to
PCR amplifications using the Sig148-Sig149b and Sig148-Sig150 primer
pairs and to the nested PCR as described for B. japonicum.
Appropriate amplification products of the expected sizes were obtained
with DNAs from the gram-negative bacteria E. coli,
Sinorhizobium meliloti, Agrobacterium
tumefaciens, and Pseudomonas putida (Fig. 2B) and from
the gram-positive bacteria B. subtilis and
Staphylococcus aureus (Fig. 2C). In all cases, additional
PCR products longer than the putative ftsH fragments were
observed, most likely because the primers Sig148 and Sig149b were
designed against the Walker motifs. These highly conserved sequences
occur not only in FtsH but in many other nucleotide-binding proteins
(26).
An open reading frame coding for a protein with an unknown function
similar to
E. coli YaeN (MesJ) (
18) is located
upstream
of
B. japonicum ftsH (Fig.
3). The gene is oriented
in the same
direction as
ftsH, and the two genes might form
an operon (see
below).
Expression of the B. japonicum ftsH gene.
Western
blot analysis of B. japonicum extracts with antiserum raised
against E. coli FtsH revealed a protein band of
approximately 70 kDa. Consistent with its calculated molecular mass of
69.9 kDa, the B. japonicum protein migrated slightly faster
than the 70.7-kDa E. coli FtsH protein (Fig.
4A). In contrast to E. coli FtsH, which is a
32-dependent heat shock protein
(10), B. japonicum FtsH appeared to be
constitutively expressed at 30°C without being heat inducible. A
refined kinetic evaluation showed that the cellular level of B. japonicum FtsH did not change significantly over a period of 1 h after a temperature upshift from 30 to 43°C (Fig. 4B). This is unprecedented, as in all of the bacteria tested so far,
ftsH expression was induced by a temperature upshift and by
other stress conditions (20). Immunodetection of B. japonicum FtsH produced from plasmid pRJ5188 in
ftsH-negative E. coli AR3291 served as a control
to demonstrate that the antiserum used indeed recognizes the rhizobial
protein (Fig. 4C).

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FIG. 4.
Immunodetection of FtsH protein in E. coli
and B. japonicum extracts. E. coli C600 or
B. japonicum 110spc4 cells were grown to
mid-exponential phase at 30°C. After a reference sample had been
taken, the culture was shifted to 43°C and samples were collected at
the indicated time points after heat shock (HS). Crude cell extracts
were prepared, separated on a sodium dodecyl sulfate-12%
polyacrylamide gel, and subjected to Western blot analysis using
anti-E. coli FtsH serum (U. Jenal, Basel, Switzerland;
original source, P. Bouloc, Paris, France; 1,000-fold dilution). Only
the area around 70 kDa is shown. Panels A and B represent two
independent experiments with different sampling periods. A
10-fold-diluted E. coli extract was loaded in panel A in
order to avoid a strong signal due to the use of a homologous
antiserum. For the experiments shown in panels C and D, E. coli AR3291/pBAD18-Cm and AR3291/pRJ5188 were grown at 30°C in
LB medium with arabinose (0.1% [wt/vol]) to mid-exponential phase
and samples were subjected to Western blot analyses. The absence ( )
or presence (+) of B. japonicum (Bja) FtsH
expressed from pRJ5188 is indicated. Bands representing B. japonicum FtsH in panel C and E. coli 32
in panel D are labeled. The sigma factor was detected by the use of
anti-E. coli 32 serum (B. Bukau, Freiburg,
Germany; 3,000-fold dilution). The molecular masses of marker proteins
are indicated in kilodaltons on the left.
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The relative abundance of FtsH in
B. japonicum under normal
growth conditions suggested an important cellular function of
this
protein. In line with this assumption is the fact that repeated
attempts to delete a large internal fragment of the
ftsH
gene
by marker replacement mutagenesis using plasmids pRJ5180 and
pRJ5181
(Fig.
3) failed. The occurrence of kanamycin- and
tetracycline-resistant
colonies demonstrated that the constructs
containing a mutated
ftsH gene had been mobilized and
cointegrated into
B. japonicum.
However,
tetracycline-sensitive colonies resulting from double
homologous
recombination could not be
recovered.
Primer extension experiments performed to identify a promoter in the
intergenic region between
yaeN and
ftsH or
upstream of
yaeN were unsuccessful, indicating that
ftsH might be part of
an extended operon. This proposition
is supported by two additional
observations: (i) the presence of a
putative rho-independent transcription
terminator downstream of
ftsH (nucleotides 3410 to 3438) but not
between
yaeN and
ftsH or in the sequenced region upstream
of
yaeN and (ii) the strict arabinose dependence of FtsH
production from
pRJ5188 in our complementation experiments (see
below).
Functional expression of B. japonicum ftsH in an
E. coli
ftsH mutant.
Since the
ftsH gene could not be eliminated in B. japonicum, we started an initial characterization of the gene and
its product in an E. coli ftsH mutant strain.
ftsH
E. coli AR3291 is a viable ftsH null mutant with a
suppressor mutation in sfhC (fabZ) that allows
cells to survive (17, 23). The mutant was transformed with
either pBAD18-Cm or pRJ5188 bearing B. japonicum ftsH on the
same replicon (Fig. 3). The lack of FtsH in the strain containing the
pBAD vector without an insert resulted in a concomitant, high level of
32 protein (Fig. 4C and D). More importantly, the
presence of B. japonicum FtsH in E. coli
AR3291/pRJ5188 was paralleled by a significantly reduced level of the
sigma factor. This result suggests that B. japonicum FtsH
has the inherent capacity to degrade
32 protein.
When
E. coli AR3291/pBAD18-Cm and AR3291/pRJ5188 were grown
at 37°C in the absence of the inducer arabinose, they showed a
clear
growth defect (Fig.
5). The growth curves
of the two strains
were almost indistinguishable in Luria-Bertani (LB)
medium or
in LB medium with glucose. Growth was significantly improved
when
expression of
B. japonicum ftsH was induced by the
addition of
arabinose (closed circles in Fig.
5). We conclude from
these growth
experiments that
B. japonicum ftsH is able to
confer a general
growth advantage upon the
E. coli ftsH
mutant, indicating that
the heterologous protein can compensate for the
loss of at least
some of the important FtsH functions in
E. coli AR3291. One of
these functions might be to balance the
cellular level of
32. We also tested whether
B. japonicum FtsH would be able to promote
growth of the
E. coli ftsH mutant under conditions that require
active
54. The expression of
B. japonicum ftsH did
not alleviate the growth
defect of the mutant under nitrogen-limiting
conditions (data
not shown). Moreover,
B. japonicum FtsH was
unable to assist in
54-dependent transcription of a
pspA-lacZ fusion in
E. coli (data
not shown).
Modulation of
54 has only been demonstrated for the
E. coli AAA protease (
6).
Apparently, many
features of the multifunctional FtsH protein
are not understood and
remain to be explored.

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FIG. 5.
Growth complementation of an E. coli ftsH
mutant by B. japonicum ftsH. E. coli AR3291
transformed with pBAD18-Cm (open symbols) or with pRJ5188 carrying
B. japonicum ftsH (closed symbols) was grown at 37°C in
either LB medium (triangles), LB medium with glucose (0.02%
[wt/vol]; squares), or LB medium with arabinose (0.1% [wt/vol];
circles). OD600, optical density at 600 nm.
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Nucleotide sequence accession number.
The nucleotide sequence
of the B. japonicum ftsH gene region between the
SalI sites at positions 1 and 3710 in Fig. 3 has been
deposited in the EMBL, GenBank, and DDBJ databases under accession no.
AJ243808.
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ACKNOWLEDGMENTS |
We are grateful to Amos Oppenheim for providing strains, Urs Jenal
and Bernd Bukau for antisera, Hans-Martin Fischer for plasmid pSUP202pol3, Manuel Carmona for the pspA-lacZ fusion on
plasmid pJD31, and Michael Kertesz and Ines Kullik for chromosomal DNA samples. Dino Bertani is acknowledged for performing the PCRs shown in
Fig. 2.
This work was supported by grants from the Federal Institute of
Technology, Zürich, Switzerland, and the Swiss National
Foundation for Scientific Research.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Institut
für Mikrobiologie, Eidgenössische Technische Hochschule,
Schmelzbergstrasse 7, CH-8092 Zürich, Switzerland. Phone:
41-1-632-2586. Fax: 41-1-632-1148. E-mail:
fnarber{at}micro.biol.ethz.ch.
 |
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Journal of Bacteriology, December 1999, p. 7394-7397, Vol. 181, No. 23
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
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69: 2512-2520
[Abstract]
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