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From the
Received for publication, October 17, 2001, and in revised form, November 12, 2001
The Escherichia coli H-NS protein is
a nucleoid-associated protein involved in both transcription regulation
and DNA compaction. Each of these processes involves H-NS-mediated
bridge formation between adjacent DNA helices. With respect to
transcription regulation, preferential binding sites in the promoter
regions of different genes have been reported, and generally these
regions are curved. Often H-NS binding sites overlap with promoter core
regions or with binding sites of other regulatory factors. Not in all
cases, however, transcriptional repression is the result of
preferential binding by H-NS to promoter regions leading to occlusion
of the RNA polymerase. In the case of the rrnB
P1, H-NS actually stimulates open complex formation by
forming a ternary RNAP·H-NS·DNA complex, while
simultaneously stabilizing it to such an extent that promoter clearance
cannot occur. To define the mechanism by which H-NS interferes at this
step in the initiation pathway, the architecture of the
RNAP·H-NS·DNA complex was analyzed by scanning force microscopy (SFM). The SFM images show that the DNA flanking the RNA polymerase in
open initiation complexes is bridged by H-NS. On the basis of these
data, we present a model for the specific repression of transcription
initation at the rrnB P1 by H-NS.
The Escherichia coli nucleoid-associated protein H-NS,
originally identified as a heat stable transcription factor (1), is one
of the major components of the bacterial nucleoid (2, 3). It was
therefore proposed to be involved in the structural organization of the
E. coli chromosome. Overproduction of H-NS leads to extreme
nucleoid condensation and is lethal (4). The absence of H-NS in an
hns deletion mutant results in an increased degree of
negative supercoiling of both plasmid and chromosomal DNA (5). In
vitro, effects of H-NS on DNA topology and condensation have also
been shown (6-8).
Mutations in H-NS not only affect nucleoid structure (9), but also the
expression of a wide variety of genes (10), illustrating the second
important role of H-NS as a pleiotropic regulator of transcription.
Around 5% of the genes in E. coli are affected at the level
of transcription by changes in the intracellular levels of H-NS (11).
Although other nucleoid-associated proteins that also function as
transcription factors, such as IHF and Fis, recognize more or less
specific sequences (for a recent review, see Ref. 12), H-NS binding
does not occur with any obvious sequence specificity. Nevertheless, the
protein is involved in specific regulation of transcription of a large
number of genes such as proU, hns,
virF, fimB, rrnB, bgl, and
the genes involved in the early development of bacteriophage Mu
(13-19).
To explain the role of H-NS in transcription regulation, two
mechanisms, which are not necessarily mutually exclusive, have been
proposed. First, H-NS might indirectly regulate initiation from
supercoiling-sensitive promoters as a consequence of the in
vivo effects of H-NS on DNA supercoiling (5, 20). Second, H-NS can
also, as a classic prototype inhibitor (21), directly inhibit
transcription by preferential binding to the promoter region. In
vitro evidence for such preferential binding of H-NS to the
promoter regions of proU, hns, virF,
clyA, and rrnB has been obtained by footprinting
experiments (13-15, 22, 23). In addition, indications that H-NS has a
binding preference to these regions as well as the promoter region of
fimB have come from competitive gel retardation studies (14,
16, 17, 23-25). However, the difference in affinity between a
preferred H-NS binding site and a nonspecific site is not as large as
for classical transcription regulators (often less than an order of magnitude).
Mutational studies have revealed the domain organization of H-NS. The
protein (136 residues) consists of an oligomerization domain (residue
15-64) and a DNA binding domain (residue 90-121), connected by a
flexible linker region (26). Whereas H-NS has long been thought to
exist as a dimer or tetramer in solution (9, 27), recent studies point
to the formation of a wide range of higher oligomeric forms dependent
upon its concentration (28). The integrity of the oligomerization
domain of H-NS has been shown to be essential both for preferential
binding and DNA condensation (9).
Many of the preferred binding sites contain an A/T-rich region,
suggesting that a sequence-induced curvature is causing the preferential binding. It has been shown in vitro that indeed
H-NS binds with a higher affinity to strongly curved DNA when compared with noncurved or moderately curved DNA, independent of the base composition (29, 30). Footprints of H-NS on the most strongly curved
DNA fragment examined show specific protection of the curved region
(31). Scanning force microscopy has shown that preferential binding to
this curved DNA fragment occurs as a result of the DNA around the curve
being bridged by H-NS, which leads to the formation of a hairpin-like
structure at the position of the curve (32).
Although evidence for promoter occlusion by specific binding of H-NS
has been found in some cases, in other cases alternative mechanisms are
likely to be involved. It has recently been demonstrated that
repression of transcription initiation at the rrnB P1 (33) is not due to occlusion of the RNA polymerase from its promoter region,
even though preferential binding to this region in the absence of RNA
polymerase had been shown (17). Instead, binding of RNAP together with
H-NS occurs in a cooperative fashion. A ternary open initiation complex
is formed, which is stabilized so strongly that it interferes with
promoter clearance. Only short abortive transcripts are produced. To
identify the molecular mechanism underlying this novel kind of
H-NS-mediated repression, we have analyzed RNAP·H-NS·DNA complexes
by SFM.1
Substrate for Scanning Force Microscopy--
The plasmid pGP1451
was constructed by inserting the 260-bp
EcoRI/BamHI fragment of pUC18-1 (containing the
complete rrnB P1 promoter region, including the upstream
activating sequence (34)) in between the respective sites of
pBR322. To obtain a plasmid on which no other promoters are present
close to the rrnB P1, a DNA fragment had to be placed
between the ampicillin gene and the rrnB P1 fragment.
Insertion of the 1282-bp EcoRI fragment from pUC4KAPA
(Amersham Biosciences, Inc.) in between the EcoRI sites of pGP1451 gave rise to pGP1452. The orientation of the insert
was checked by restriction analysis. The DNA substrate for SFM was
subsequently generated by PCR from pGP1452. One of the oligonucleotides
was chosen within the pUC4KAPA insert, the second one on pBR322. Thus a
fragment was obtained with a length of 1192 bp containing position +1
of the rrnB P1 close to its center (arms are 544 and 649 bp). One of the oligonucleotides used was biotinylated and also led to
the introduction of a SmaI site in the PCR product. This
allowed for purification of the DNA fragment using paramagnetic beads
as described previously (32).
Protein Purification--
RNA polymerase was purified as
described previously (35, 36). The activity of the RNA
polymerase was assessed by a quantitative assay (37). H-NS was purified
from the overproducing strain KA1764 (38) as described previously
(8).
Scanning Force Microscopy--
The ~1200-bp DNA fragment (27 fmol/µl) and To study the structural basis of H-NS-mediated stabilization of
RNA polymerase in the open initiation complex at the rrnB P1
promoter, we constructed a linear DNA fragment of around 1200 bp
containing the transcription start site (+1) close to its center (see
"Materials and Methods"). Incubation of this DNA fragment with RNA
polymerase in the presence of the initiating nucleotides ATP and CTP,
which have been shown to be essential for stable open complex formation
at the rrnB P1 (39), followed by a challenge with heparin
allows visualization of specific RNAP·DNA complexes (Fig.
1A). Nonspecific binding of
RNA polymerase mostly occurs at the DNA ends, whereas nonspecific
binding to internal positions on the fragment is negligible (not
shown). In the observed specific open complexes an RNAP molecule is
bound close to the center of the DNA molecule, and induces a strong
"kink" in the DNA at that position. Quantitative analysis in the
form of contour length measurements (see Table
I) of these complexes reveals that
around 50% of the RNAP·DNA complexes is considerably
shortened when compared with naked DNA. The other complexes show no
significant change in length. This is in agreement with a recent SFM
study, which showed that the apparent DNA contour length in open
RNAP·DNA complexes is reduced as a result of the DNA being wrapped
around the RNAP (40). The kink formed upon RNAP binding is a
direct consequence of this DNA wrapping. The observed reduction in
length (~30 nm) is in close agreement with the reduction observed by
Rivetti et al. (40) and also with the size (around 80 bp) of
the RNA polymerase footprint at the rrnB P1 (39). The other
complexes show no significant change in length and probably correspond
to a closed complex form, in which the DNA is not wrapped.
The structural mechanism underlying H-NS-mediated trapping of RNA
polymerase in the open initiation complex (33) was investigated by
simultaneous addition of H-NS and heparin to preformed RNAP·DNA complexes. The presence of heparin as a competitor is required both for
specific binding of H-NS (41) and for limiting the amount of
nonspecific RNAP·DNA complexes (39). Under these conditions we
observe ternary complexes in which the DNA on both sides of the RNA
polymerase is bridged by H-NS and held together over a large but
variable part of the DNA molecule (Fig. 1B and Table II). Next to this, complexes are observed
without bridging, which are similar to the open initiation complexes
formed when no H-NS is present (Fig. 1A). The frequency with
which complexes with specifically bound RNA polymerase are observed is
around 10% (Table II). In close to 50% of these complexes the DNA
aside of the bound RNAP is bridged. The binding of H-NS is evident from
the increase in height relative to DNA alone in the bridged regions as
can be seen in the tilt views of some typical ternary complexes (Fig. 1C). The increase in height in the DNA tracts bridged by
H-NS is much larger than in the case of random DNA contacts, and is of
the same order as observed in previous experiments, in which H-NS was
shown to form bridges between two DNA helices on plasmid DNA (8) and
around the apex of a curved sequence (32). The formation of such
bridges is favored when two DNA helices are spatially close and is a
consequence of the oligomeric nature of H-NS, which leads to the
simultaneous availability of two or more DNA binding domains. Our
observations indicate that RNAP can be trapped within a bridged
H-NS-DNA complex, after an open complex has been formed. The wrapping
of the DNA around RNAP apparently changes the conformation of the DNA
in such a way that a "preferential binding site" is created on
which a stable H-NS·DNA complex can be formed. Control reactions
lacking RNAP (with or without heparin) did not show any specific
H-NS·DNA structures in the region of the rrnB P1. Probably
this kind of stable binding of H-NS encompassing the bound RNAP
provides a physical barrier to promoter clearance. This would explain
the H-NS-induced abortive initiation described previously (33).
The ternary RNAP·H-NS·DNA complexes that are observed by SFM
strongly resemble the complexes formed with curved DNA (32), in which
H-NS causes the DNA to fold back onto itself in a hairpin-like structure with the apex at the position of the curved sequence. It has
been proposed that preferential binding to curved sequences stems from
the fact that there is a higher probability of forming oligomers
between DNA-bound H-NS proteins (32). The binding of H-NS to RNAP·DNA
complexes is likely based on the same principle (Fig.
2). In the open initiation complex DNA is
wrapped around the RNA polymerase (see "Results" and Refs. 40 and
42). Thus, after open complex formation the DNA upstream and downstream
of the bound RNA polymerase is brought in close vicinity. In this situation H-NS-mediated bridging between these DNA regions will be
favored, and the RNA polymerase becomes physically trapped (Fig.
2A). The parallel between preferential binding to curved DNA, which could lead to promoter occlusion when involving the promoter
region, and RNA polymerase trapping is illustrated by the structural
similarity schematized in Fig. 2.
Structural Basis for H-NS-mediated Trapping of RNA Polymerase in
the Open Initiation Complex at the rrnB P1*
,
Laboratory of Molecular Genetics, Gorlaeus
Laboratories, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands, the § Department
of Cell Biology and Genetics, Erasmus University, P. O. Box 1738, 3000 DR Rotterdam, The Netherlands, and the ¶ Institut für
Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstrasse 1, D-40225
Düsseldorf, Germany
ABSTRACT
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ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
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INTRODUCTION
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ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
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MATERIALS AND METHODS
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DISCUSSION
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70-saturated RNA polymerase (47.5 fmol/µl) were incubated at 37 °C for 15 min in incubation buffer
(50 mM HEPES (pH 8.0), 60 mM KCl, 15 mM NaCl, 1.5 mM MgCl2, 1 mM ATP, and 0.1 mM CTP), to allow stable open initiation complex formation. After open complex formation the mixture
was further incubated at 24 °C for 10 min upon addition of an
H-NS/heparin mixture (final concentration of 5.6 pmol/µl and 12.5 ng/µl, respectively). Samples were deposited on mica as described (8)
after 20-fold dilution into dilution buffer (2.5 mM HEPES
(pH 8.0), 8 mM MgCl2, 1 mM ATP, and
0.1 mM CTP) and subsequently imaged by SFM. The control
samples without H-NS were prepared similarly, by adding only heparin
after open complex formation.
RESULTS
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ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES
View larger version (148K):
[in a new window]
Fig. 1.
A, SFM images of representative
open complexes formed between RNAP and the rrnB P1.
RNAP·DNA complexes are specifically formed at the position of the
transcription start site (+1) of the rrnB P1 (at one half of
the DNA fragment length) only. B, SFM images of
representative ternary complexes formed when H-NS binds to open
initiation complexes between RNAP and the rrnB P1.
C, SFM images, presented as tilt views to emphasize
topography, of representative ternary complexes formed when H-NS binds
to open initiation complexes between RNAP and the rrnB P1.
These images illustrate the considerable thickening caused by the
H-NS-mediated DNA bridging. All images show a 300 × 300 nm
surface area. Color represents height ranging from 0.0 to 1.5 nm (from
dark to bright).
Contour length of free DNA molecules and RNAP·DNA complexes
Length of bridged tracts of RNAP·H-NS·DNA complexes
DISCUSSION
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View larger version (14K):
[in a new window]
Fig. 2.
A, model for H-NS-mediated trapping of
RNA polymerase in the open initiation complex. When the DNA strands are
close enough (as is the case for the regions flanking the RNA
polymerase upon wrapping of the DNA), the bound protein can form
intramolecular bridges. Split oval represents an H-NS oligomer exposing
at least two binding domains. B, model for preferential
binding of H-NS to curved DNA, which can lead to promoter occlusion
when the promoter region is close to or part of the region of
preferential binding (32). This figure illustrates the mechanistic
parallel between preferential binding of H-NS to curved DNA and
trapping of RNA polymerase in an open initiation complex.
The binding of H-NS does not have apparent boundaries (i.e. the length of the DNA tracts involved in the bridging events is variable, see Table II), which agrees with a model in which bridge formation results from an increased probability of oligomerization. Upon formation of the first bridges at a nucleation point, which is likely to be close to the RNA polymerase, lateral extension will occur in a cooperative fashion (8). Similarly, also on curved DNA bridge formation by H-NS is often not limited to the curved region only (32).
The process of transcription initiation is a multistep process.
Regulation of transcription initiation (either activation or
repression) by transcription factors can occur at any of the steps in
the initiation process. In general, the step affected is the
rate-limiting step for factor-independent transcription initiation on a
specific promoter (21). The mechanism of H-NS-mediated repression as
described here exhibits a structural parallel with repression by loop
formation, e.g. as occurs in the case of the AraC protein
(44). There is to our knowledge, however, no evidence that, in any of
the systems for which regulation by loop formation has been described,
trapping of RNAP causes repression. A mechanistic parallel exists with
several other transcription factors, which have been shown to cause
repression of transcription initiation by stabilization of either the
closed complex (GalR at P1 in the gal operon (45, 46)) or
the open complex (p4 at the 
29 A2C promoter (47)). The observed
stabilization in those cases, however, is due to specific contacts
between the repressor and the 
-CTD of RNA polymerase. The mechanism
of H-NS-mediated repression as proposed here differs from these
previously described mechanisms as it does not necessarily involve
specific H-NS·RNAP contacts. Such contacts cannot be excluded on the
basis of the data presented here. However, the binding of H-NS will be
different from binding of GalR or p4, which interact with a more
specific DNA target site as defined dimers or tetramers, respectively,
and direct interaction of H-NS with the -CTD has not been shown. An
obvious advantage of mechanisms in which RNA polymerase is trapped on the promoter is that it needs not be recruited from "solution" once
repression is relieved, which allows a rapid response to changes in
environmental conditions.
The repression of transcription initation at the rrnB P1 can
be alleviated by Fis (17, 43), which has three binding sites (
70,
100, and 140) in the upstream region of this promoter. These
binding sites are located within the region where bridging of the DNA
by H-NS occurs. Sequence-specific binding of Fis may interfere with
H-NS binding and thus with bridging.
The conditions under which the in vitro experiments (both the SFM and the structural and functional analyses of Schröder and Wagner (33)) were conducted basically reflect the physiological situation bacterial cells encounter when growth ceases or during stationary phase. Under those conditions rRNA synthesis is effectively shut off mainly as a result of specific inhibition of rRNA P1 promoters. Although several additional mechanisms are responsible for this rapid shut down (e.g. the global effector ppGpp) the transcriptional activator FIS and the repressor protein H-NS contribute to a great extent to this down-regulation. FIS and H-NS act as antagonists, and their regulatory effects on rRNA transcription have been demonstrated both in in vitro and in vivo (43, 48). The antagonistic properties of both regulators largely correlate with their cellular concentrations, which at stationary growth are significant for H-NS (about 20,000 copies per cell) and negligible for FIS (<100 copies per cell). Both factors bind to overlapping sites upstream of all seven rRNA P1 promoters (49),2 and mechanistic models for their antagonism based on binding competition studies have been proposed (22). The RNA polymerase-trapping mechanism, which has been documented biochemically (33) and for which the SFM images provide strong structural support, not only explains the physiological situation at rRNA synthesis shut off, but also gives an immediate explanation for the rapid increase in rRNA synthesis after nutritional upshift when growth resumes. The cellular FIS concentration shows a strong transient increase (50), relieving H-NS-mediated repression. Transcription can then be resumed from promoters at which RNAP has been trapped immediately without the requirement of de novo initiation after the balance between the transcription factors has been changed in favor of FIS. This may be of special importance under conditions in which the cellular RNA polymerase concentration is low, and rRNA promoters, which have a low affinity are not saturated.
It is very likely that the mechanism we propose here for
transcriptional repression by H-NS at the rrnB P1 is also
responsible for H-NS-mediated repression of other genes. The fact that
DNA wrapping by RNA polymerase in the open complex seems to be a
general phenomenon (42) does, however, pose a number of new questions as to how this type of repression may affect only some genes in an
in vivo situation. Partly this may be explained by
differences in the extent of DNA wrapping around RNAP or by differences
in the spatial orientation of the "arms," leaving the RNAP in the open initiation complex. In the case of the rrnB P1, the
upstream UP element, which is involved in the extended RNAP-DNA
interactions (51), could play a role in changing the extent of wrapping
and thus the relative orientation of the DNA arms in the open complex. Furthermore, a preferential binding of H-NS within the upstream activating sequence, close to the RNAP initiation site, could constitute a "nucleation site" for H-NS and thereby contribute significantly to directing the bridging events. Finally, trapping of
RNA polymerase by H-NS is expected to be affected by the rate with
which the transition occurs from the open complex into the phase of
productive elongation. This rate differs for different promoters and is
determined by the ease with which RNAP·DNA contacts can be broken.
Especially if the rate-limiting step of transcription initiation is
promoter clearance, a gene may be more susceptible to repression by
H-NS. A favorable combination of the factors mentioned above will
determine whether a promoter is regulated by H-NS through the described
trapping mechanism. Identification of the promoter-specific factors
that are involved in providing susceptibility for the H-NS-mediated
regulation described in this paper will require further systematic study.
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FOOTNOTES |
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* This work was supported by the Chemical Council of the Netherlands Organization for Scientific Research (NWO-CW) and the Deutsche Forschungsgemeinsschaft.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
To whom correspondence should be addressed: Laboratory of
Molecular Genetics, Gorlaeus Laboratories, Leiden Inst. of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The
Netherlands. Tel.: 31-71-5274773; Fax: 31-71-5274537; E-mail:
N.Goosen@chem.Leidenuniv.nl.
Published, JBC Papers in Press, November 19, 2001, DOI 10.1074/jbc.C100603200
2 A. Hillebrand and R. Wagner, unpublished data.
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ABBREVIATIONS |
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The abbreviation used is: SFM, scanning force microscopy.
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