1. Structural Biology and Molecular Biophysics
  2. Chromosomes and Gene Expression
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Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity

  1. Ramon A van der Valk
  2. Jocelyne Vreede
  3. Liang Qin
  4. Geri F Moolenaar
  5. Andreas Hofmann
  6. Nora Goosen
  7. Remus T Dame  Is a corresponding author
  1. Leiden University, Netherlands
  2. Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Netherlands
  3. University of Heidelberg, Germany
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Cite this article as: eLife 2017;6:e27369 doi: 10.7554/eLife.27369

Abstract

Bacteria frequently need to adapt to altered environmental conditions. Adaptation requires changes in gene expression, often mediated by global regulators of transcription. The nucleoid-associated protein H-NS is a key global regulator in Gram-negative bacteria and is believed to be a crucial player in bacterial chromatin organization via its DNA-bridging activity. H-NS activity in vivo is modulated by physico-chemical factors (osmolarity, pH, temperature) and interaction partners. Mechanistically, it is unclear how functional modulation of H-NS by such factors is achieved. Here, we show that a diverse spectrum of H-NS modulators alter the DNA-bridging activity of H-NS. Changes in monovalent and divalent ion concentrations drive an abrupt switch between a bridging and non-bridging DNA-binding mode. Similarly, synergistic and antagonistic co-regulators modulate the DNA-bridging efficiency. Structural studies suggest a conserved mechanism: H-NS switches between a ‘closed’ and an ‘open’, bridging competent, conformation driven by environmental cues and interaction partners.

https://doi.org/10.7554/eLife.27369.001

eLife digest

The genetic information every cell needs to work properly is encoded in molecules of DNA that are much longer than the cell itself. A key challenge in biology is to understand how DNA is organized to fit inside each cell, whilst still providing access to the information that it contains. Since the way DNA is organized can influence which genes are active, rearranging DNA plays an important role in controlling how cells behave.

In Escherichia coli and many other bacteria, a protein called H-NS contributes to DNA reorganization by forming or rupturing loops in the DNA in response to changes in temperature, the levels of salt and other aspects of the cell’s surroundings. In controlling loop formation, it dictates whether specific genes are switched on or off. However, it remains unclear how H-NS detects the environmental changes.

To address this question, van der Valk et al. used biochemical techniques to study the activity of H-NS from E. coli under different environmental conditions. The experiments show that changes in the environment cause structural changes to H-NS, altering its ability to form DNA loops. A previously unnoticed region of the protein acts as a switch to control these structural changes, and ultimately affects which genes are active in the cell.

These findings shed new light on how bacteria organize their DNA and the strategies they have developed to adapt to different environments. The new protein region identified in H-NS may also be present in similar proteins found in other organisms. In the future, this knowledge may ultimately help to develop new antibiotic drugs that target H-NS proteins in bacteria.

https://doi.org/10.7554/eLife.27369.002

Introduction

Although the bacterial genome is compacted by a vast variety of factors, including DNA supercoiling, and macromolecular crowding, it owes much of its organization to nucleoid-associated proteins (Dame, 2005; Dame et al., 2011; Dillon and Dorman, 2010; Dorman, 2013; Rimsky and Travers, 2011; Travers and Muskhelishvili, 2005; Luijsterburg et al., 2008; Dame and Tark-Dame, 2016). A key protein in nucleoid organization of Gram-negative bacteria is the Histone-like Nucleoid Structuring protein (H-NS). Genome-wide binding studies have revealed that H-NS binds along the genome in long patches (Grainger et al., 2006; Kahramanoglou et al., 2011; Lucchini et al., 2006; Navarre, 2006; Oshima et al., 2006), which have been proposed to mediate the formation of genomic loops (Noom et al., 2007; van der Valk et al., 2014). H-NS is also an important regulator of global gene expression, implied in mediating global transcriptional responses to environmental stimuli (osmolarity, pH, temperature) (Atlung and Ingmer, 1997), and operating as xenogeneic silencer, silencing horizontally integrated DNA (Navarre et al., 2006). A large fraction of Escherichia coli and Salmonella genes (5–10%) is thus regulated (usually repressed) by the action of H-NS. H-NS operation is modulated by environmental stimuli and through interplay with other proteins (Atlung and Ingmer, 1997; Stoebel et al., 2008). In solution, the H-NS protein exists as a dimer, which oligomerizes at high concentrations (Ceschini et al., 2000; Spurio et al., 1997). H-NS consists of three structural domains: a C-terminal domain responsible for DNA binding (Shindo et al., 1995), a N-terminal dimerization domain (Bloch et al., 2003; Cerdan et al., 2003; Esposito et al., 2002; Ueguchi et al., 1996) and a central dimer-dimer interaction domain responsible for multimer formation (Arold et al., 2010; Leonard et al., 2009). These two interaction domains are connected by a long α-helix (Arold et al., 2010) (helix α3). H-NS exhibits two seemingly distinct DNA-binding modes: DNA bridging (Dame et al., 2006; Dame et al., 2000; Dame et al., 2001; Dame et al., 2002; Schneider et al., 2001), the condensation of DNA by intra- and inter- molecular DNA binding by H-NS and DNA stiffening, the rigidification of DNA through the formation of a H-NS-DNA filament (Amit et al., 2003; Dame and Wuite, 2003; Liu et al., 2010). These modes have been attributed to the basic functional H-NS unit (a dimer) binding to DNA either in cis or in trans (Wiggins et al., 2009; Joyeux and Vreede, 2013). H-NS paralogues StpA, Sfh, Hfp, and truncated derivatives such as H-NST, have been proposed to modulate H-NS function by forming heteromers with H-NS (Baños et al., 2008; Deighan et al., 2003; Müller et al., 2010; Williams et al., 1996; Williamson and Free, 2005), with DNA-binding properties different from homomeric H-NS. Members of the Hha/YmoA family of proteins are H-NS co-regulators with limited sequence homology to H-NS (Madrid et al., 2007). At many targets along the genome, H-NS and Hha co-localize. Localization of Hha at these sites is strictly H-NS dependent, whereas the genome-wide binding pattern of H-NS is only mildly affected by Hha (Ueda et al., 2013).

Although evidence has been put forward that the concentration of divalent ions determines the binding mode of H-NS (Liu et al., 2010), a mechanistic explanation is lacking. Moreover, the possible effect of co-regulators of H-NS, such as Hha, on these binding modes has remained unexplored. To obtain a better understanding of the molecular basis underlying the H-NS binding modes, it is crucial to determine the effects of ion valence and concentration, as well as the presence of helper proteins on both the stiffening and the bridging mode. Here, we investigate DNA stiffening on short DNA tethers using Tethered Particle Motion (TPM). As intramolecular DNA bridging does not occur on short DNA tethers, DNA stiffening can be uncoupled from DNA bridging. In addition, to accurately determine intermolecular DNA-bridging efficiencies in solution, we developed a sensitive quantitative bulk assay. Using these two assays, we unravel the assembly pathway of bridged DNA-H-NS-DNA complexes and the roles of mono- and divalent ions, helper proteins Hha and YdgT, and truncated H-NS derivatives. Finally, Molecular Dynamics (MD) simulations reveal that ions and interacting proteins directly alter H-NS structure from a ‘closed’ bridging incapable to an ‘open’ bridging capable conformation, thus providing a molecular understanding of the modulation of H-NS function.

Results

The role of Mg2+and H-NS multimerization in DNA bridging and DNA stiffening

In order to dissect the role of divalent ions in the formation of bridged and stiffened complexes, we applied a novel, sensitive, and quantitative DNA-bridging assay and carried out TPM experiments (providing a quantitative and selective readout of DNA stiffening). The DNA-bridging assay relies on immobilization of bait DNA on magnetic microparticles and the capture and detection of 32P labeled prey DNA if DNA-DNA bridge formation occurs (see Figure 1—figure supplement 4b for a schematic depiction of the assay). 80% of initial prey DNA is recovered at high H-NS concentrations (see Figure 1a). In the absence of either the H-NS protein or bait DNA, no prey DNA is recovered under our experimental conditions. Next, we used this assay to quantify the DNA-bridging efficiency of H-NS as a function of the amount of Mg2+ ions (see Figure 1b), reproducing the qualitative results of Liu et al. (2010) and providing independent confirmation of the previously observed effects. The concentration range from 0 to 10 mM Mg2+ is considered to be physiologically relevant (Hurwitz and Rosano, 1967). Importantly, the transition from no bridging to complete bridging is abrupt between 4–6 mM Mg2+, indicating that changes in Mg2+ concentration might drive a binary switch.

Figure 1 with 5 supplements see all
Modulation of H-NS function by ionic conditions.

(a) DNA-bridging efficiency as a function of H-NS concentration in the presence of 10 mM MgCl2. (b) DNA-bridging efficiency as a function of MgCl2 concentration. (c) DNA-bridging efficiency as a function of the KCl concentration. (d) Root Mean Square displacement (RMS) as a function of H-NS concentration, in the presence and absence of 10 mM MgCl2 (N > 70, per data point). (e) RMS of DNA as a function of H-NSY61DM64D in the presence and absence of MgCl2 (N > 70, for each point). (f) Extension of DNA as a function of the KCl concentration (N > 70, for each point). Error bars indicate standard deviation. Dashed lines are to guide the eye.

https://doi.org/10.7554/eLife.27369.003

Earlier studies have shown that H-NS binding along a single DNA molecule results in DNA stiffening (Amit et al., 2003; Liu et al., 2010). However, due to the co-occurrence of DNA bridging, previous studies were incapable of measuring DNA stiffening in the presence of Mg2+. Here, we used TPM to investigate DNA stiffening as a function of Mg2+ concentration. In TPM, the Root Mean Square displacement (RMS) of bead movement is a direct reflection of tether stiffness and length (Figure 1—figure supplement 4a). DNA-binding proteins can affect both, but previous studies have shown that the DNA contour length is not affected by binding of H-NS (Dame et al., 2006; Dame et al., 2001). Thus, an increase in stiffness due to H-NS binding translates into a higher RMS value of a DNA tether (Figure 1d). Here, we measured the effects of H-NS on DNA stiffness in the absence and presence of 10 mM Mg2+ and confirmed that H-NS stiffens DNA (Amit et al., 2003; Liu et al., 2010); importantly, our experiments reveal that Mg2+ does not affect the stiffness of the fully formed H-NS-DNA complexes at saturation, as in both conditions the RMS is the same (Figure 1d). Analysis of the binding characteristics using the McGhee-von Hippel equation revealed that the association constant of H-NS is somewhat reduced in the presence of Mg2+, while cooperativity increases under these conditions (Figure 3—figure supplement 1a,d). The reduction in DNA-binding affinity of H-NS may be attributed to shielding of the negatively charged phosphate backbone by Mg2+.

The cooperative binding of H-NS and DNA stiffening observed by TPM suggest that H-NS multimerizes along DNA, likely via the recently defined dimer-dimer interaction domain (Arold et al., 2010). Multimerization along DNA has been previously suggested (Esposito et al., 2002; Williams et al., 1996) but has never been conclusively demonstrated. To test this hypothesis, we generated a mutant, H-NSY61DM64D, predicted to have disrupted dimer-dimer interaction based on the H-NS1-83 crystal structure (Arold et al., 2010). Size exclusion chromatography showed that this H-NS mutant indeed exists solely as a dimer in solution independent of protein concentration (Figure 1—figure supplement 1b), whereas wild-type H-NS forms large multimeric structures (Figure 1—figure supplements 1a and Arold et al., 2010; Leonard et al., 2009). The multimerization behavior of both proteins was unaffected by the presence of Mg2+. Electrophoretic Mobility Shift Assay confirmed that the DNA binding of the H-NS mutant is intact (Figure 1—figure supplement 2). TPM experiments reveal that H-NSY61DM64D binding does not lead to the formation of stiff H-NS-DNA filaments (Figure 1e). The RMS is reduced compared to that of bare DNA, indicating not only that dimer-dimer interactions are disrupted, but also that individual H-NS dimers mildly distort DNA. DNA-bridging experiments reveal that H-NSY61DM64D is also incapable of forming DNA-H-NS-DNA complexes (Figure 1—figure supplement 3). This indicates that individual H-NSY61DM64D dimers do not form stable bridges and that dimer-mediated bridging, involving H-NS-dimer binding cooperativity due to high local DNA concentration adjacent to existing bridges (Dame et al., 2006; Dame et al., 2000), is insufficient to explain the formation of bridged DNA-H-NS-DNA complexes. The nature of the effect of Mg2+ on DNA-bridging efficiency is not understood. An increase in affinity would be expected if Mg2+ would only facilitate interactions between the DNA phosphate backbone and negatively charged residues on H-NS, but this is not observed (Figure 3—figure supplement 1). As Mg2+ does not affect the multimeric state of H-NS in solution (Figure 1—figure supplement 1), a model involving an effect on H-NS multimerization can be excluded. A structural effect of Mg2+ on individual units within H-NS filaments could explain the observed effects of Mg2+ on the bridging efficiency of H-NS.

Mg2+alters H-NS structure

To investigate the role of Mg2+ on individual H-NS dimers we carried out MD simulations of an H-NS dimer in both the absence and presence of Mg2+, using our previously established model of a full-length H-NS dimer (van der Valk et al., 2014). Visual inspection of the H-NS dimer simulations at 50 mM KCl reveals that H-NS changes from an ‘open’ extended conformation into more compact ‘closed’ shapes (see Figure 2a for snapshots from these simulations, Figure 2—figure supplement 1 for examples of the ‘closed’ conformation, or Figure 2—video 1 for a movie of one such simulation). The three domains in H-NS interact, and these inter-domain interactions are facilitated by partial unfolding and buckling of the long central α helix (helix α3) connecting the dimerization and dimer-dimer interaction domains. The average distance between the donor and acceptor of all helical hydrogen bonds (O-H distance) in helix α3 indicates that the buckle forms in region Glu42-Ala49 (Figure 2b). By analyzing the O-H distance between residues Ser45 and Ala49 in time, key residues at the site of buckle formation (see Figure 2—figure supplement 3), we found that buckles can be reversible and irreversible, within the simulation time scale of 50 ns. Reversible buckles, caused by thermal fluctuations, typically last a few nanoseconds and occur several times during a single simulation run (see green line in Figure 2—figure supplement 3 for an example). Irreversible buckles, stabilized by inter-domain interactions, do not return to a helical conformation during our simulations (see red line in Figure 2—figure supplement 3 for an example). To characterize the interactions that occur during the simulations, we generated contact maps that show the probability of finding interactions between residues, with a contact defined as the minimum distance between two residues being 0.6 nm or less, see Materials and methods for details of this analysis (Figure 2—figure supplement 2a). These maps reveal that the DNA-binding domain interacts with other parts of the protein complex. In absence of Mg2+, the DNA-binding domain interacts with the dimerization domain, rendering the DNA-binding QGR motif (residues 112–114) (Gordon et al., 2011) of one DNA-binding domain inaccessible (see the snapshots in Figure 2a). Although the simulations were performed in absence of DNA, these observations suggest that DNA bridging is not possible in such a conformation, as the H-NS dimer can bind DNA only through its remaining/second DNA-binding domain. In this ‘closed’ conformation, interactions occur between the IRT residues at position 10–12 and the AMDEQGK residues at position 122–128. These interactions are hydrophilic in nature, supplemented by a salt bridge between R11 and D124 or E125. In the presence of Mg2+ interactions between the DNA-binding domain and the dimerization domain no longer occur (see the snapshots in Figure 2a or the movie in Figure 2—video 2), The absence of such interactions is further illustrated by the contact map in Figure 2—figure supplement 2b and in higher detail in Figure 2—figure supplement 5. The likelihood of finding Mg2+ interacting with (i.e. being within 0.6 nm of) H-NS residues, indicated by PMg2+, revealed that Mg2+ has a preference for glutamate residues in region 22–35 (Figure 2c, Figure 2—figure supplement 8), where the ions shield this region from interacting with the DNA-binding domains. The Mg2+ ions transiently interact with the glutamate residues, with residence times in the order of a few ns (as seen in Figure 2—video 2). Furthermore, Mg2+ ions interact with region 98–105 (sequence DENGE), right next to the DNA-binding QGR motif (Figure 2c). The presence of Mg2+ stabilizes the ‘open’ conformation of H-NS, ensuring that DNA bridging can occur. Furthermore, we noted that Mg2+ is also located close to the buckle and may directly stabilize helix α3 through interactions with Glu42, Glu43, Glu44, and Ser45 (Figure 2—figure supplement 7), resulting in an ‘open’, bridging capable, H-NS conformation (see Figure 2—videos 1 and 2). These data suggest that Mg2+ modulates H-NS by shielding interactions between the DNA-binding domain and dimerization domain, and by influencing the conformation of helix α3. Based on these observations, we designed an H-NS mutant predicted to bridge DNA independent of Mg2+. We therefore generated a mutant in which several of the amino acids involved in buckle formation (E43,E44,S45) were substituted with alanines. In our DNA-bridging assay, H-NSE43A,E44A,S45A retains its ability to bridge DNA, but indeed achieves high DNA recovery (±50%) in the absence of Mg2+ (Figure 2—figure supplement 9a). Low concentrations of Mg2+ are sufficient to reach saturated DNA bridging (up to 80% DNA recovery) (Figure 2—figure supplement 9a). This observation independently confirms our model that the stretch of glutamates at the buckle is responsible for Mg2+ sensing and Mg2+-dependent bridging by H-NS. Additionally, we note that the DNA-binding affinity of H-NE43A,E44A,S45A is not significantly altered and that its DNA binding cooperativity is similar to that of wildtype H-NS in the absence of Mg2+ (Figure 2—figure supplement 9b, Figure 3—figure supplement 1d). Yet, in the presence of Mg2+, wild-type H-NS exhibits a far more cooperative DNA binding (Figure 3—figure supplement 1d). This suggests that the transition between the ‘open’ and ‘closed’ conformation of H-NS promotes lateral filament formation by H-NS.

Figure 2 with 11 supplements see all
Conformation of the H-NS dimer as a function of osmolarity.

(a) Snapshots depicting representative conformations of H-NS in the simulations with 50 mM KCl (top) and 10 mM MgCl2 +50 mM KCl (bottom) (For the full movies depicting these effects see Figure 2—videos 1 and 2, for other examples of the ‘closed’ conformations of H-NS see Figure 2—figure supplement 1). The buckle region is highlighted in red and the domains are colored blue, green and brown for the dimerization domain, the dimer-dimer interface and the DNA-binding domain, respectively. The conserved motif involved in DNA binding is highlighted as ball-stick models. Mg2+ ions are shown as dark gray orbs. The protein is shown in ribbon representation with a transparent surface. The atomic radii in the protein were set to 3 A to smooth the surface. (b) Location of buckle in helix α3. The average distance dO-N between donor and acceptor in the helical hydrogen bond in helix α3 is plotted as a function of the residue index of the acceptor. The dashed black line in the graphs indicates the distance threshold for forming a hydrogen bond. Time traces of these distances are given in Figure 2—figure supplement 3. (c) Location of Mg2+ on H-NS. The probability of finding Mg2+ ions within 0.6 nm of an H-NS residue, PMg2+, is plotted as function of the residue index for the three systems containing Mg2+.

https://doi.org/10.7554/eLife.27369.009

Modulation of DNA bridging by osmotic factors

Although it has long been known that the expression of some H-NS controlled genes (such as the proU operon) is modulated by the osmolarity of the medium (Cairney et al., 1985), the underlying mechanism remains undetermined. Previous studies have revealed that the H-NS DNA stiffening mode is mildly sensitive to the KCl concentration (Amit et al., 2003; Liu et al., 2010). Using TPM, we were able to confirm these observations. The reduction in DNA stiffening is gradual (Dame and Wuite, 2003) and modest (Figure 1f). It is thus questionable whether the multimerization of H-NS along DNA alone is sufficient to explain its role in repression of transcription (and modulation thereof). Could the modulation of gene repression be due to ionic effects on DNA-bridging efficiency? Using our DNA-bridging assay, we observed complete abolishment of H-NS DNA bridging by KCl at concentrations exceeding 120 mM (Figure 1c), a binary response, similar to what we observed for the Mg2+ titration. This in vitro observation mirrors the in vivo response of the ProU operon, at which KCl concentrations exceeding 100 mM are required to alleviate H-NS-mediated repression (Cairney et al., 1985). Control experiments using K-glutamate (Figure 1—figure supplement 5) confirm that K+, and not the counter-ion, is responsible for the observed effects, even though the counter ion may affect the DNA-binding affinity of the protein (Figure 1—figure supplements 5c and Leirmo et al., 1987) This strong and abrupt effect on DNA bridging, while leaving DNA stiffening essentially unaffected, might indicate that H-NS reverts to the ‘closed’ conformation by the addition of K+. To investigate this effect at a structural level we performed MD simulations at high KCl concentrations. The presence of 130 mM KCl alters interactions between the various domains in H-NS (see contact maps in Figure 2—figure supplement 2c and d). In addition to interactions between the DNA-binding domain and the dimerization domain, the two DNA-binding domains in the dimer interact with each other. Moreover, the DNA-binding domains interact with helix α3. In particular regions 98–105 (KYSYVDENGE) and 123–129 (EQGKS) are involved in these interactions. The average distance between the donors and acceptors in the hydrogen bonds within helix α3 (Figure 2b) indicates that that buckles in helix α3 also occur at a high KCl concentration, at the same location as determined by low-salt conditions. These observations indicate that the ‘closed’ state can have multiple forms (see Figure 2—figure supplement 1 for snapshots), but that all these conformations block the DNA-binding motif QGR from interacting with DNA. The presence of Mg2+ does not significantly alter the occurrence of buckles (Figure 2b). Instead, Mg2+ is capable of deterring interactions between the DNA-binding domain and the dimerization domain by shielding residues in the dimerization domain involved in these interactions (Figure 2c, Figure 2—figure supplement 8). However, the probability of interactions occurring between the DNA-binding domain and other parts of the protein is reduced significantly in the presence of Mg2+ (Figure 2—figure supplement 2 and Figure 2—figure supplement 5). High K+ concentrations therefore inhibit H-NS bridging by promoting the ‘closed’ conformation of H-NS even in the presence of Mg2+ and elucidates the modulatory and regulatory effects of KCl and osmolarity.

Modulation of DNA bridging and DNA stiffening by truncated H-NS variants

In addition to environmental factors such as osmolarity, H-NS activity is affected by interactions with other proteins in vivo. Members of the Hha/YmoA protein family, such as Hha and YdgT, are known to cooperate with H-NS in repression of genes (Baños et al., 2008), while other proteins such as H-NST are capable of inhibiting H-NS function (Liu et al., 2010), likely by hampering H-NS multimerization. To systematically investigate the latter mechanism, we designed and synthesized truncated H-NS derivatives, targeting the H-NS dimerization domain (H-NS1-58) or dimer-dimer interaction domain (H-NS56-83). Interfering with H-NS dimerization, through the addition of H-NS1-58 in DNA-bridging experiments, we observed a reduction in DNA recovery from 75% to 20% at ratios higher than 1: 3 H-NS1-58/ H-NS (Figure 3a). Similarly, targeting the dimer-dimer interaction domain (through H-NS56-82) resulted in complete abolishment of DNA bridging (Figure 3a). Next, we investigated the effects of H-NS derivatives on H-NS DNA stiffening using TPM. Only at very high H-NS derivative concentrations (30-fold excess) reduction of DNA stiffening was observed (Figure 3b). These experiments reveal that both H-NS dimerization and dimer-dimer interactions can be effectively targeted for inhibition of H-NS activity and that the respective domains are crucial to the formation of bridged filaments. This suggests that natural H-NS inhibitors such as H-NST operate by disrupting DNA bridging and provides clues for rational design of artificial peptide inhibitors of H-NS.

Figure 3 with 2 supplements see all
Modulation of H-NS function by protein cofactors.

(a) DNA bridging efficiency as a function of inhibiting peptides targeting either the dimerization domain (H-NS1-58) and multimerization domain (H-NS56-82). (b) Root Mean Square displacement (RMS) as a function of inhibiting peptides targeting either the dimerization (H-NS1-58) and multimerization (H-NS56-82) (N > 70, for each point). (c) DNA bridging efficiency as a function of Mg2+ concentration in the presence and absence of 4 µM Hha or 2 µM YdgT. (d) RMS of DNA in the presence of H-NS, H-NS-Hha, and H-NS-YdgT. Dashed lines are to guide the eye (N > 60, for each point).

https://doi.org/10.7554/eLife.27369.021

Modulation of H-NS by Hha and YdgT

Gene regulation by H-NS often occurs in conjunction with other proteins; these co-regulators are known to interact with H-NS at specific loci along the genome. Two such proteins, Hha, and YdgT, are members of the Hha/YmoA (Madrid et al., 2007) family of proteins. In order to understand the modulation of H-NS function by these proteins we investigated their influence on the H-NS DNA binding modes. We observed that Hha, when added at equimolar concentrations, enhances DNA bridging by H-NS at low Mg2+ concentrations (Figure 3c). A similar enhancement of H-NS-mediated DNA bridging was observed with the Hha paralogue, YdgT. While Hha and YdgT promote DNA bridging to a similar extent, YdgT promotes DNA bridging at significantly lower concentrations, likely due to a higher affinity for H-NS. At higher concentrations of YdgT the effect on H-NS-mediated bridging closely resembles the bridging profile obtained for H-NSE43A,E44A,S45A (Figure 3—figure supplement 2). To determine whether enhanced DNA bridging is due to structural changes in H-NS-DNA filaments, we investigated the effects of Hha and YdgT on DNA stiffening (Figure 3d). TPM experiments show a mild increase in H-NS mediated DNA stiffening in the presence of Hha. We observe a negative offset in RMS in the presence of YdgT, indicating a more compact conformation. Specifically, this is evident in TPM experiments containing H-NS, YdgT, and Mg2+, where in the presence of Mg2+ and YdgT, H-NS causes ‘DNA collapse’ in TPM (data not shown), similar to earlier observations for H-NS in the presence of Mg2+ without (Liu et al., 2010; Wang et al., 2014) or with Hha added (Wang et al., 2014). This ‘DNA collapse’ is attributed to H-NS-mediated DNA bridge formation. One possible explanation for the effects of Hha and YdgT, is that they effectively increase the DNA-binding affinity of H-NS (Ali et al., 2013). To investigate whether Hha affects H-NS conformation, we performed MD simulations, incorporating structural information from the recently resolved H-NS1-43-Hha co-crystal structure (Ali et al., 2013). Our MD simulations reveal that Hha does not prevent buckles in helix α3 (see Figure 2b). Instead Hha alters the interactions between the dimerization domain and the DNA-binding domain (Figure 2—figure supplement 2) by blocking access to parts of dimerization domain. This hypothesis is further supported by interactions between Hha and other parts of H-NS, including the DNA-binding domain and helix α3 (Figure 2—figure supplement 6). In the presence of Mg2+ and Hha, the contacts between the DNA-binding domain and dimerization domain are reduced even further. This shows that Hha modulates H-NS function by stabilizing the ‘open’ -bridging capable- conformation of H-NS.

Discussion

It has been known for many years that H-NS binding induces gene silencing. H-NS activity in vivo is modulated by physico-chemical factors (osmolarity, pH, temperature) and interaction partners. These findings support the hypothesis that H-NS plays a role in environmental adaptation. However, mechanistically it is unclear how functional modulation of H-NS by such factors is achieved. Based on our findings, we conclude that H-NS is incapable of bridging or stiffening DNA as dimers. H-NS dimers bind DNA in cis (Dame et al., 2006; Dame et al., 2000) and associate side-by-side along DNA, likely via the recently identified dimer-dimer interaction domain (Arold et al., 2010), resulting in DNA stiffening. This process is cooperative as H-NS dimers interact with neighbors, as well as with DNA. Our studies reveal that H-NS-DNA filaments are structurally very similar, independent of the presence of Mg2+ (Figure 1d). But functionally, these H-NS-DNA filaments are distinct. H-NS can be ‘activated’ by Mg2+, which promotes a conformational change, rendering both DNA-binding domains of H-NS dimers accessible for DNA bridging. In our model, the assembly of bridged complexes proceeds in distinct steps: (1) nucleation (Lang et al., 2007) (binding of an H-NS dimer at a high affinity site), (2) lateral filament growth by H-NS dimer-dimer interactions (leading to DNA stiffening) and (3) bridging of the assembled filament to bare DNA provided in trans (Figure 4). Each step can potentially be modulated by osmolarity and protein interaction partners. Here, we show that these factors most effectively target DNA bridging.

Model of H-NS complex assembly.

(a) H-NS nucleates at preferred DNA sequences in the genome. (b) H-NS laterally multimerizes laterally along the DNA in the ‘closed’ conformation. (c) In the presence of Mg2+ or other H-NS modulators such as Hha, H-NS switches to the ‘open’, bridging capable conformation. (d) H-NS forms DNA bridges in trans. The red asterisk indicates the buckle location. Mg2+ ions are shown as green orbs.

https://doi.org/10.7554/eLife.27369.024

What are the implications of our observations? Our observations add to the large body of evidence showing that regulation of transcription via H-NS is complex, and that it does not proceed via a single, simple, well-defined mechanism. The most straightforward form of repression by H-NS is via occlusion of RNA polymerase from the promoter (Lim et al., 2012; Prosseda et al., 2004; Göransson et al., 1990). Whether this mechanism of repression involves lateral filament formation or bridging is unclear. It is expected that both types of complexes assembled at a promoter site can in principle occlude RNA polymerase. A second mechanism of repression is to trap RNA polymerase at the promoter, preventing promoter escape (Schröder and Wagner, 2000; Shin et al., 2005). RNA polymerase trapping likely involves DNA bridging of promoter upstream and downstream elements (Dame et al., 2002; Shin et al., 2005). A third mechanism of repression by H-NS is to interfere with RNA polymerase progression during active transcription by intragenic binding (Dole et al., 2004). In this model, both modes could interfere with transcription. However, it was suggested recently that only bridged filaments are capable of interfering with transcription (Kotlajich et al., 2015), with lateral filaments likely being disassembled as RNA polymerase encounters them. Generally, the type of complex formed by H-NS is expected to depend on the type and number of ions, combined with local DNA conformation (dependent on DNA sequence or DNA topology), and the presence of modulating proteins. The interplay between these factors will determine the strength of the complex, and degree of repression. Thus, different H-NS repressed genes are expected to be subject to different types of modulation, providing a key to a coordinated response in gene expression to altered conditions and selectivity for the interplay with specific co-regulators at specific target regions.

Materials and methods

Construction of expression vectors

H-NS expression vector

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The vector pRD18 for expression of H-NS was constructed by inserting the PCR amplified hns gene into the pET3His overexpression vector using NdeI and XhoI restriction sites. Using the XhoI restriction site, the encoded protein does not contain a C-terminal His-tag.

H-NSY61DM64D expression vector

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The vector pRD69 for expression of H-NSY61DM64D was constructed by inserting a PCR fragment containing the hns gene mutated to encode aspartic acid instead of tyrosine/methionine at position 61 and 64 into pET3His using NdeI and XhoI restriction sites.

Hha expression vector

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The vector pRD38 for expression of N-terminally His tagged Hha was constructed by inserting a PCR fragment containing the hha gene into pET3His using XhoI and BamHI restriction sites.

YdgT expression vector

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The vector pRD39 for expression of N-terminally His tagged YdgT was constructed by inserting a PCR fragment containing the ydgT gene into pET3His using XhoI and BamHI restriction sites.

Protein overproduction and purification

H-NS/H-NSY61DM64D/H-NSE43A,E44A,S45A. BL21 (DE3) (RRID: WB-STRAIN: HT115(DE3)) Δhns::kan/frt pLysE (NT201, our lab) cells transformed with plasmids expressing H-NS/H-NS mutants were grown to an OD600 of 0.4, and induced for 2 hr using IPTG (500 μM). For the H-NE43A,E44A,S45A protein, the cells were co-transformed with pRD252, coding for LacI to help suppress leaky expression of H-NE43A,E44A,S45A. The cells were pelleted and lysed by sonication in 100 mM NH4Cl, 20 mM Tris pH 7.2, 10% glycerol, 8 mM β-mercaptoethanol, 3 mM benzamidine). The soluble fraction was loaded onto a P11 column and eluted using a 100 mM-1 M NH4Cl gradient, the protein eluted at 280 mM NH4Cl. The peak fractions were dialysed to buffer B (identical to buffer A, but containing 130 mM NaCl instead of NH4Cl) by overnight dialysis. The dialysate was loaded onto a heparin column (GE Healthcare) and eluted using a 130 mM-1 M NaCl gradient, the protein eluted at 350 mM NaCl. The pooled peak fractions were dialysed to buffer B and concentrated using a 1 ml Resource-Q column (GE Healthcare). The purity of the protein was verified on an SDS-PAGE gel. The protein concentration was determined using a Bicinchoninic Acid assay (Pierce BCA protein assay kit, Thermo Scientific).

H-NS1-58

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BL21 (DE3) (RRID: WB-STRAIN: HT115(DE3)) Δhns::kan/frt pLysE (NT210, our lab) cells transformed with plasmids expressing H-NS/H-NS mutants were grown to an OD600 of 0.4, and induced for 2 hr using IPTG (500 μM). The cells were pelleted and lysed by sonication in 100 mM NaCl, 20 mM Tris pH 7.2, 10% glycerol, 8 mM β-mercaptoethanol, 3 mM benzamidine). The soluble fraction was heated to 65°C for 10 min and then spun down at 10.000 RPM for 10 min. The supernatant was collected and a 1:1 ratio saturated ammonium sulfate (50 mM Tris pH 7.2, 4M ammonium sulfate) was gradually added to the cooled sample. The sample was spun down at 8.000 RPM for 15 min and a 1:1 ratio of 5 mM Tris pH 7.2, 15% glycerol was added to the supernatant. To remove further impurities, the sample was run through a 1 ml hydrophobic interaction column and 1 ml Blue-agarose column (the protein should not bind to either of these column) before finally binding the protein to 1 ml Resource-Q column (GE Healthcare). The protein was eluted with a 25 mM −1M gradient of NaCl, the protein eluted at roughly 380 mM NaCl. The purity of the protein was verified on an SDS-PAGE gel. The protein concentration was determined using a Bicinchoninic Acid assay (Pierce BCA protein assay kit, Thermo Scientific).

Hha/YdgT

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BL21 (DE3) (RRID: WB-STRAIN: HT115(DE3)) Δhns::frt, hha::kan, pLysE (our lab) cells transformed with plasmids pRD38/pRD39 expressing hha/ydgT were grown at 37°C to an OD600 of 0.4, and induced for two hours using IPTG (500 μM). The cells were pelleted and lysed in 20 mM HEPES pH 7.9, 1 M KCl, 10% glycerol, 8 mM β-mercaptoethanol. The soluble fraction was loaded onto a Ni-column. The column was first washed with buffer D (20 mM HEPES pH 7.9, 0.5 M KCl, 10% glycerol, 8 mM β-mercaptoethanol). The protein was then eluted using a 0 mM-0.5 M Imidazole gradient, the protein eluted at 300 mM Imidazole. The peak fractions were dialysed to buffer E (identical to buffer D, but containing 100 mM KCl) by overnight dialysis. The sample was then loaded onto pre-equilibrated SP Hi-Trap-column and Ni-column connected in series. After loading the samples on the column, the SP Hi-Trap -column was disconnected and the protein was eluted from the Ni-column using a 0–0.5 M imidazole gradient. The purity of the protein was verified on an SDS-PAGE gel. The protein concentration was determined using a Bicinchoninic Acid assay.

Peptide production and purification

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A truncated form of H-NS (H-NS56-82) was synthesized by way of automated solid phase synthesis using standard protocols via Fmoc-strategy. Purification was performed by RP-HPLC with a Gemini 5µ C18 reversed phase column. Identity of the peptides was determined via MALDI-MS. The purity was determined by means of analytical RP-HPLC. The peptide was freeze dried and dissolved in 20 mM Tris pH 7.2, 300 mM KCl, 10% glycerol, 8 mM β-mercaptoethanol. The peptide concentration was determined using a Bicinchoninic Acid assay (Pierce BCA protein assay kit, Thermo Scientific).

Size exclusion chromatography

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Size exclusion chromatography was done using a Superose-12 column with a flow of 0.3 ml/min, pre-equilibrated with 10 mM Tris-HCl, 50 mM KCl, 5% glycerol containing or lacking 10 mM MgCl2. The absorbance of the eluting fractions was measured at 215 nm. These experiments were performed in triplicate.

DNA substrates

DNA preparation

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All experiments were performed using a random, AT-rich, 685 bp (32% GC) DNA substrate (Laurens et al., 2012). The DNA substrate was generated by PCR, and the PCR products were purified using a GenElute PCR Clean-up kit (Sigma-Aldrich). If required, DNA was 32P-labeled as described previously (Wagner et al., 2011).

DNA-bridging assay

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Streptavidin-coated paramagnetic Dynabeads M280 (Invitrogen) were washed once with 100 μL of 1xPBS and twice with Coupling Buffer (CB: 20 mM Tris-HCl pH 8.0, 2 mM EDTA, 2 M NaCl, 2 mg/mL BSA(ac), 0.04% Tween20) according to manufacturer instructions. After washing, the beads were resuspended in 200 µL CB containing 100 nM biotinylated DNA. Next, the bead suspensions were incubated for 30 min on a rotary shaker (1000 rpm) at 25°C. After incubation, the beads were washed twice with Incubation buffer (IB: 10 mM Tris-HCl pH 8.0, 50 mM KCl, 10* mM MgCl2, 5% v/v Glycerol, 1 mM DTT and 1 mM Spermidine) before resuspension in IB and addition of ±8000 cpm of radioactively labeled 32P 685 bp DNA. Radioactive DNA was supplemented with unlabeled 685 bp DNA to maintain a constant (20 nM) DNA concentration. The DNA-bridging protein H-NS (concentrations indicated in the text), and if applicable Hha or YdgT were added and the mixture was incubated for 30 min on a shaker (1000 rpm) at 25°C. To remove unbridged prey DNA, the beads were washed with IB, before resuspension in 12 μL stop buffer (10 mM Tris pH 8.0, 1 mM EDTA, 200 mM NaCl, 0.2% SDS). All samples were quantified through liquid scintillation counting over 10 min. All values recovered from the DNA-bridging assay were corrected for background signal (using a sample lacking H-NS), and normalized to a reference sample containing the amount of labeled 32P 685 bp DNA used in the assay. The samples were then run on a 5% 0.5x TBE gel to ensure DNA integrity. DNA bridging was calculated based on a reference sample containing 2 µL of prey DNA. All DNA-bridging experiments were performed in triplicate. Unless indicated otherwise all DNA-bridging experiments were performed in the presence of 10 mM of MgCl2 and 3,3 µM of H-NS (10% more H-NS than is required for saturation - see Figure 1A). Each experiment contains 50 mM KCl, to which additional KCl or K-glutamate are added depending on the experimental condition tested.

Tethered particle motion experiments

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Tethered particle motion experiments were performed as reported previously (Driessen et al., 2014; van der Valk et al., 2017). Flow cells were prepared as described with minor modifications (Driessen et al., 2014; van der Valk et al., 2017). Here, before flowing in protein diluted in the experimental buffer (10 mM Tris-HCl pH 8.0, 50 mM KCl, 10 mM MgCl2/EDTA, 5% v/v Glycerol, 1 mM DTT) the flow cell was washed using 4 flow cell volumes with the experimental buffer. Next, the flow cell was incubated for 10 min with protein solution before sealing the flow cell. The flow cell was maintained at a constant temperature of 25°C. Measurements were started 10 min after the introduction of protein solution. TPM experiments were done at least in duplicate. The data were analyzed as previously described (Driessen et al., 2014; van der Valk et al., 2017). The RMS was first converted to persistence length(Lp) using Equation 1 (Göransson et al., 1990):

(1) RMS=233- 156(1+0.08Lp)0.45

Lp values were then used to calculate the fractional coverage (Equation 2) (Göransson et al., 1990):

(2) nϑ=1Lp, measured-1Lp, naked1Lp, saturated-1Lp, naked

The fractional coverage (d) was fit using the McGhee-von Hippel model for cooperative lattice binding (Equation 3-5) (McGhee and von Hippel, 1974):

(3) ϑc=K1-d2ω+11-d+ϑ-R2ω-11-dn-11-n+1ϑ+R2(1-d)2

where

(4) R=(1-n+1ϑ)2+4ωϑ(1-d)

and

d=nϑ

Here, the association constant(K) is described as a function of the protein concentration (c) and a cooperativity parameter (ω).

To this end, weighted orthogonal distance regression (ODR) was performed to estimate the parameters of the nonlinear implicit equation describing the cooperative ligand binding. The binding site size (n) of H-NS was fixed to a value of 30 bp during regression, which corresponds to values determined previously (Dame et al., 2006; Amit et al., 2003). The association constant (K) and the cooperativity parameter (ω) were assumed to be positive real numbers. A custom fitting routine was implemented in Fortran and makes use of the ODRPACK library (Boggs et al., 1992).

Molecular dynamics simulations

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The starting conformation of the full-length H-NS dimer was constructed as described previously (van der Valk et al., 2014). The system was placed in a periodic dodecahedron box with a distance of at least 0.8 nm between the box edge and the most extended atom of the protein dimer, followed by the addition of water and ions. With this system we performed Molecular Dynamics (MD) simulations of full length H-NS at different concentrations of KCl, and MgCl2 and with the addition of Hha, summing up to a total of six different systems. Hha was added by aligning the crystal structure containing the H-NS – Hha complex (PDB code 4ICG [Ali et al., 2013]) with the full-length structural model and copying the Hha molecules. System size ranged from 513457 atoms for the Hha systems to around 1,135,000 atoms for the other four systems.

Interactions between atoms were described by the AMBER99-SB-ILDN force field (Lindorff-Larsen et al., 2010), in combination with the TIP3P water model (Jorgensen et al., 1983). Long-range electrostatic interactions were treated via the Particle Mesh Ewald method (Darden et al., 1993; Essmann et al., 1995) with a short-range electrostatic cutoff distance at 1.1 nm. Van der Waals interactions were cut off at 1.1 nm. Preparation of the systems consisted of energy minimization equilibration of the solvent. Energy minimization was performed by the conjugate gradient method. After energy minimization, the positions of water molecules and ions were equilibrated by a 1 ns molecular dynamics run at a temperature of 298 K and a pressure of 1 bar in which the heavy atoms in the protein were position-restrained with a force constant in each direction of 1000 kJ/mol nm. After preparation, we performed 16 50 ns runs for each system, varying initial conditions by assigning new random starting velocities drawn from the Maxwell-Boltzmann distribution at 298 K. All simulations were performed with GROMACS v.4.6.3 (Pronk et al., 2013) at the Dutch National Supercomputer with the leap-frog integration scheme and a time step of 2 fs, using LINCS (Hess et al., 1997) to constrain all bonds. All simulations were performed in the isothermal-isobaric ensemble at a pressure of 1 bar, using the v-rescale thermostat (Bussi et al., 2007) and the Parrinello-Rahman barostat (Parrinello and Rahman, 1981).

Frames were stored every 10 ps. The first 10 ns of each simulation are excluded from analysis, unless stated otherwise. Analysis focused on determining contacts between domains, between H-NS and Hha, between H-NS and ions, and helical hydrogen bonds. Contact maps of interactions between residues in the H-NS dimer system were obtained by first calculating the minimum distance between each residue pair in the system. A residue pair is counted to be in contact if they are at a minimum distance of 0.6 nm or less. The probability of a contact is then calculated as the average over all 16 simulations (excluding the first 10 ns) and displayed as a contact probability matrix. We used a modified version of the g_mdmat tool in GROMACS (Pronk et al., 2013) in combination with Perl scripts to generate contact maps. To determine the location of ions with respect to the H-NS system, we calculated the minimum distance between each residue in the H-NS dimer and the ions and counted a contact if the distance between an H-NS residue and an ion is 0.6 nm or less. These contact probabilities (PMg2+, PK+ and PCl-) are averaged over all 16 simulations and the two monomers. A similar procedure was performed to determine the probability of contacts between H-NS and Hha, PHha, and between H-NS domains, with P1-40 indicating the probability of finding the DNA-binding domain (residues 96–137) close to the dimerization domain (residues 1–40). P96-137 indicates the probability of finding the dimerization domain close to the DNA-binding domain.

To determine the location of the buckle in helix α3, we calculated the helical hydrogen bond distances dO-N for residues 22–67 in each monomer between the backbone carbonyl oxygen O of residue i and the backbone amide nitrogen N of residue i + 4. A hydrogen bond is counted to be in contact if they are at a minimum distance of 0.35 nm or less. These probabilities are averaged over all 16 simulations (excluding the first 10 ns) and the two monomers. Snapshots and movies were generated with PyMOL.

References

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Decision letter

  1. Gisela Storz
    Reviewing Editor; National Institute of Child Health and Human Development, United States

In the interests of transparency, eLife includes the editorial decision letter and accompanying author responses. A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included.

[Editors’ note: a previous version of this study was rejected after peer review, but the authors submitted for reconsideration. The first decision letter after peer review is shown below.]

Thank you for submitting your work entitled "Environment driven conformational changes modulate the function of H-NS" for consideration by eLife. Your article has been favorably evaluated by Kevin Struhl (Senior Editor) and three reviewers, one of whom is a member of our Board of Reviewing Editors. The reviewers have opted to remain anonymous.

Our decision has been reached after consultation between the reviewers. Based on these discussions and the individual reviews below, we regret to inform you that your work will not be considered for publication in eLife.

All three of the reviewers found the proposed model for the switch in H-NS binding modes to be interesting and important. However, they also thought that either a true functional (in vivo) experiment or a definitive test of the DNA-binding domain sequestration model would be required for publication in eLife. The reviewers hope their comments, particularly the very detailed and thoughtful comments of reviewer 3, will help you to improve the manuscript.

Reviewer #1:

The question of how the nucleoid protein H-NS is modulated by a range of different environmental signals has long been unanswered. In this study, van der Valk et al. developed and carried out novel methodologies to assay the impact of H-NS on DNA bridging and DNA stiffening at different concentrations of Mg2+ and K+ and in the presence of the H-NS co-regulators Hha and YdgT. The authors also examined the consequences of truncating H-NS and carried out molecular dynamic simulations of the effects of these conditions on the H-NS dimer. The results of these assays and modeling, led the authors to conclude that "H-NS switches between a "closed" and an "open", bridging-competent conformation driven by environmental cues and interaction partners. This model is extremely attractive, however in my opinion the authors have not tested their interesting ideas in sufficient depth. The study would be a more substantial contribution with additional experiments and discussion to address the following:

1) Many of the conclusions are based on molecular dynamic simulations. The authors should carry out independent experiments such as fluorescence quenching, to test the predictions of these simulations.

2) The authors examined the "modulation of DNA bridging by osmotic factors", but infer that the model is relevant to a range of environmental signals. This should be tested. As a minor point the authors should comment on how the concentrations of Mg2+ and K+ tested in vitro compare to the concentrations found to modulate H-NS activity in the cell.

3) The authors observe disparate effects of Hha and YdgT with respect to DNA stiffening. How do these differences relate to effects of Hha and YdgT in vivo? Can Hha really be a proxy for YdgT in the molecular simulations?

4) The authors make very general statements about the implications of their observations? Ideally, the contributions of filament formation versus bridging to the regulation of specific promoters should be examined.

Reviewer #2:

In this manuscript van der Valk and colleagues present evidence that certain ions and important regulatory factors from E. coli promote the ability of H-NS to bridge DNA molecules. The new in vitro DNA bridging assay they develop is elegant and is used to show that Mg and KCl above a certain concentration can promote DNA bridging by H-NS. The findings with Mg are consistent with the original findings from the Kenney and Yan labs. The authors go on to use the same in vitro assay to show that KCl and regulatory proteins that promote the activities of H-NS, including Hha and YdgT, also promote DNA bridging by H-NS. These findings are new. Finally, based on molecular dynamics simulations the authors suggest that Mg, K, and Hha influence bridging through a common mechanism. This proposed mechanism involves interacting directly with H-NS and blocking an otherwise inhibitory interaction between an oligomerization determinant and a DNA-binding determinant of the protein. The work is interesting but falls somewhat short. Additional biophysical experiments would be needed to strengthen the case that certain ions and proteins promote bridging by altering the distance between specific regions of H-NS. Furthermore, there are no in vivo or in vitro tests of the physiological relevance of Hha or YdgT's ability to promote bridging by H-NS.

1) For the H-NS (Y61D; M64D) double mutant that is predicted to be defective for dimer-dimer interactions, it would be important to show the EMSA analysis of its ability to bind DNA (currently mentioned as data not shown, subsection “The role of Mg2+ and H-NS multimerization in DNA bridging and DNA stiffening”, last paragraph). Ideally, the authors should also test whether this particular mutant is defective in vivo.

2) The modulation of DNA bridging and stiffening by truncated H-NS variants is interesting (subsection “Modulation of DNA bridging and DNA stiffening by truncated H-NS variants”). However, the authors should be careful about extrapolating the findings with these fragments of H-NS to other proteins such as H-NST. I think if the authors want to make strong claims about H-NST, then it would be better to directly test whether or not H-NST influences bridging (perhaps with the one from EPEC as it appears to have the most potent activity).

Reviewer #3:

Van der Valk et al. report new insights into the mechanism and regulation of DNA bridging by the bacterial transcriptional regulator H-NS. Specifically, the authors determined how magnesium, osmolarity, and Hha/YdgT modulate a switch between bridged H-NS filaments (H-NS filaments binding two distinct DNA segments) and stiffened H-NS filaments (N-HS binding to a single DNA segment). These two different modes of H-NS binding affect gene expression differently, and understanding both the physical basis for the switch and how it is regulated are crucial questions in the field of bacterial gene regulation. Van der Valk et al. propose and provide support for a novel hypothesis that the switch in binding modes involves sequestration or release of one of the two DNA-binding domains in an H-NS dimer by the N-terminal dimerization domain. Using a new, quantitative bridging assay, the authors report that magnesium and the H-NS modulators Hha/YdgT favor the bridging conformation whereas KCl and truncated H-NS derivatives that mimic other H-NS modulators decrease bridging at high concentrations. In contrast, stiffened filaments were only disrupted by interactions in the dimer-dimer interaction domain. Using molecular dynamics simulations to observe H-NS conformational changes with or without these factors, the authors found that a bulge in the central H-NS α-helix could facilitate interactions between the DNA-binding domain and the dimerization domain, resulting in a closed conformation that disfavors bridging. Factors that favor bridging appear to disfavor interactions between the DNA binding domain and dimerization domain, and results in a more open conformation. These results suggest a mechanism by which factors that influence H-NS filament conformations act by altering the sequestration of the DNA-binding domain.

The authors' findings significantly advance understanding of H-NS filament formation and its regulation, but their presentation in the submitted manuscript will be largely inaccessible to a general audience without revisions to the text and figures. Additionally, one relatively straightforward experiment would greatly increase the relevance of the findings to in vivo regulation. All these changes are achievable within a reasonable time and would make the manuscript suitable for high-profile publication.

1) Both the TPM and bridging assays need to be better explained in the text and figures. For starters, the ability of readers to understand each assay would be immensely aided by simply graphics that illustrate the assay and what is being measured. For the TPM assay, what is the physical difference in bead behavior between 0% and 100% coverage? This could be illustrated. For the bridging assay, what is the difference between no bridging and complete bridging? Is it just one H-NS dimer bridge between the two DNAs – or more than one bridge? This could be illustrated. For example, an earlier paper from this group provided an excellent illustration of the assay used (Figure 1 of Dame et al. 2006. Nature. 444:387). For both assays, what is the source of the DNA used (why was it chosen and where it is from)? Is the DNA from a gene naturally regulated by H-NS? These DNAs should be described, and perhaps shown as sequence in a supplemental figure, rather than referring readers to another paper.

The first paragraph of the subsection “The role of Mg2+ and H-NS multimerization in DNA bridging and DNA stiffening” should be rewritten to better explain the goals and set-up of the two assays, and the logic for why the experiments were carried out as described so that readers diverse backgrounds can follow the description.

2) One main conclusion is that Mg2+ ions interact with residues 22-35 of H-NS based on molecular dynamics. Do the authors believe this is principally an ionic interaction or some type of coordination of Mg2+ by these residues? Could this interaction be abolished by a mutation in H-NS? It would enhance the paper to discuss the properties of this interaction, but more experiments are not necessary. Is there precedence in the literature for Mg2+ interacting with proteins in a similar manner? If so, examples would be useful to cite and discuss.

a) The authors should also stipulate explicitly that the simulations were performed in the absence of DNA, and discuss whether the conclusions derived from simulations in the absence of DNA can be used to infer the behavior of H-NS in the presence of DNA. The current simulation provides evidence that the conformation of an H-NS dimer is dynamic in solution, but would this effect be different when H-NS is bound to DNA? A discussion of this question would make the results more complete.

b) Additionally, it is unclear why the authors' results in Figure 1 lead them to test the Mg2+ binding to H-NS. Did they favor this model because the high [Mg2+] does not inhibit DNA binding (subsection “The role of Mg2+ and H-NS multimerization in DNA bridging and DNA stiffening”, last paragraph)?

3) The authors propose that high K+ can disrupt the bridging of H-NS, which they relate to changes in the cell during osmotic stress. Although this observation is interesting, the authors should rule out the possibility that the high [Cl-] could destabilize H-NS DNA interaction rather than high [K+] destabilizing the bridging interaction, since it is known that Cl- can destabilize protein-DNA interactions (Leirmo S, et al. 1987. Biochemistry 26:2095.). The authors should repeat the experiment in Figure 1C and F with potassium glutamate to test ionic conditions that actually correspond to the in vivo osmotic stress response. If K+ is responsible for the changes in bridging, then the potassium glutamate result will show a similar decrease in bridging as KCl.

4) The discussion on the Hha/YdgT effect on H-NS binding affinity is unclear because the experiment is not described well. The results are also confusing in that Hha and YdgT both increase bridging, but only Hha enhances binding affinity (by their assay). This result does not support the hypothesis put forth in the subsection “Modulation of H-NS by Hha and YdgT”, that both Hha and YdgT increase the binding affinity of H-NS. A clearer description of the results is needed to communicate the differences and similarities between the Hha and YdgT effects accurately. Additionally, a diagram illustrating how Hha and YdgT are proposed to affect filaments and a representation of this experiment also might improve the accessibility of the results. For Figure 3—figure supplement 1, including a graphical representation of coverage would immensely help in understanding the results.

a) It is surprising that Hha and H-NS together do not show cooperative DNA binding. The authors should discuss how these new results can be reconciled with previous publications showing that Hha (along with H-NS) is necessary for silencing of genes (e.g., Ali, S. S., et al. 2013. JBC. 288: 13356; Banos, R. C., et al. 2009. PLoS Genetics. 5:e1000513.) The results presented in those papers suggest that cooperative binding is necessary for forming a filament that can silence genes (a bridged filament), which would also suggest that filaments containing Hha and H-NS should cooperatively form a bridged filament. The result that Hha disrupts cooperative binding is inconsistent with that hypothesis, so the authors should discuss alternative mechanisms to explain how Hha and H-NS together silence genes.

[Editors’ note: what now follows is the decision letter after the authors submitted for further consideration.]

Thank you for resubmitting your work entitled "Environment driven conformational changes modulate H-NS DNA bridging activity" for further consideration at eLife. Your revised article has been evaluated by Kevin Struhl as the Senior Editor and Gisela Storz as the Reviewing Editor, and three reviewers.

There continues to be enthusiasm for your study, but after discussion, the reviewers feel the following additional revisions are critical for the study to live up to its potential as a significant advance.

1) Experimental tests of the predictions of the molecular dynamics simulations need to be carried out. This should involve mutating the residues (i.e. glutamates to serines) expected to interact with ions like Mg2+ and mutating residue R11 expected to destabilise the closed H-NS conformation. Assaying the effects of such mutations, using the experimental tools applied in Figure 1, should reveal differences in magnesium modulation of HNS binding as predicted by the simulations.

2) Downplay the hha/ydgT experiments, as they are not yet fully developed, and focus the paper on Mg2+ induced changes.

Each of the reviewers’ comments is also included below.

Reviewer #1:

In this revised manuscript van der Valk and colleagues present evidence that certain ions and important regulatory factors from E. coli promote the ability of H-NS to bridge DNA molecules. Key components of the manuscript include use of an elegant biochemical assay to demonstrate that Mg, as well as the regulatory factors Hha and YdgT promote DNA-bridging by H-NS. They also show that K inhibits DNA-bridging by H-NS, and that truncated derivatives of H-NS can modulate the ability of H-NS to bridge the DNA--findings that have implications for naturally occurring inhibitors of H-NS, such as H-NST. Based on molecular dynamics simulations the authors suggest that Mg and Hha promote bridging through a common mechanism. This proposed mechanism involves interacting directly with H-NS and blocking an otherwise inhibitory interaction between an oligomerization determinant and a DNA-binding determinant of the protein. In my earlier review I had indicated that additional biophysical experiments would be needed to strengthen the case that certain ions and proteins influence bridging by altering the distance between specific regions of H-NS. The authors didn't comment on this concern but indicate in their response to reviewer 1 that Alexa555 labelling of H-NS is problematic. Thus, a limitation of both the original and the current study is that there are no independent experimental tests of the predictions from the molecular dynamics simulations used to develop the highly interesting model the authors propose.

In my earlier review I had also indicated there are no in vivo or in vitro tests of the physiological relevance of Hha or YdgT's ability to promote bridging by H-NS. The authors didn't comment on my concern but indicate in response to reviewer 1 that they are conducting a separate single-molecule study to test the effects of different bridging efficiencies on RNA polymerase progression.

The authors adequately addressed my specific comments. In particular, they now provide in vitro analysis of the ability of HNS (Y61D;M64D) to bind DNA by EMSA. They also attempted to test the effects of H-NST (from EPEC) on bridging by H-NS in vitro, but ran into problems with H-NST solubility.

Additional independent experiments would strengthen the case that certain ions and proteins influence bridging by altering the distance between specific regions of H-NS.

Reviewer #2:

The paper by van der Valk, et al., systematically explores the effects of ions and accessory proteins on the multimerization and binding mode of H-NS on DNA. To do this they use a combination of a novel "bridging assay" (a pulldown of radioactive bait), molecular dynamics simulations, and TPM (tethered particle motion) assays.

Novel findings include that H-NS contains a "hinge" that allows it to go from an open to a closed conformation. In the closed conformation one of the DNA binding domains is proposed to be inaccessible because it interacts with the N-terminal "head" domain of the H-NS dimer. The primary determinants of whether the molecule is in an open or closed conformation are ions like K+ and Mg2+ as well as accessory molecules like Hha. This paper attempts to unify findings from many other previous publications into a single model.

I see the paper has been through at least one round of review already. I think it's in pretty good shape.

I'm not entirely convinced their models are correct regarding Hha vs. YdgT (see Figure 3). It makes little sense that by having less affinity for H-NS, that Hha in some way disrupts multimerization while YdgT (which has more affinity) promotes more multimerization, but of the closed H-NS conformer. They may be over-interpreting and making a model from limited data without thinking of alternatives. Furthermore, if Hha disrupts cooperativity, would not the HNS multimerization domain mutant (Y61DM64D) act the same as H-NS plus Hha? How does the mutant abolish bridging while Hha promotes it?

Another issue I have is that in their proposed "closed" conformation I see no way the central dimerization domain would be available for making an H-NS oligomer. The central dimerization domain would also be made inaccessible to binding a new dimer of H-NS. Perhaps they could explain it better?

I think the molecular dynamics simulations are interesting and they propose that certain residues in the protein interact with ions like Mg2+ to modulate the conformation of the molecule. It would be nice to see more simulations with "mutant" H-NS or even experimental data where the glutamates in question were changed to serine. I don't believe, however, those experiments are critical for publication.

Reviewer #3:

This is an interesting paper that adds important mechanistic detail to the known changes in H-NS:DNA complexes induced by a change in the availability of Mg2+, other divalent cations, and H-NS-like proteins.

Overall, this paper represents an important contribution to the field and I am supportive of publication. However, I think that the paper suffers in two ways and attempts could be made to resolve these issues.

First, the reliance on molecular dynamics is a potential weakness in my opinion. To me, this seems like an excellent way to generate a hypothesis that can be tested experimentally (see subsection “Mg2+ alters H-NS structure”) but this has not been done yet. Second, the paper attempts to deal with two issues; the role of cations and the role of interaction partners. As a result, I feel that the paper falls just short of "nailing" either story. In some ways, the Discussion reflects this and mostly ignores the interaction partners.

For me, it would be great to see a paper focused on cation interactions bolstered by a couple of simple experiments testing the predictions of the molecular dynamics. I appreciate that the paper has already been through one round of revision and so this idea may not be greeted enthusiastically by the authors or journal. With this in mind, it may be possible for the authors to rewrite the subsection “Modulation of DNA bridging and DNA stiffening by truncated H-NS variants” so that it is presented as a test of the molecular dynamics predictions. E.g. would some of these truncated H-NS proteins block some of the intramolecular interactions predicted by the dynamics?

https://doi.org/10.7554/eLife.27369.026

Author response

[Editors’ note: the author responses to the first round of peer review follow.]

All three of the reviewers found the proposed model for the switch in H-NS binding modes to be interesting and important. However, they also thought that either a true functional (in vivo) experiment or a definitive test of the DNA-binding domain sequestration model would be required for publication in eLife. The reviewers hope their comments, particularly the very detailed and thoughtful comments of reviewer 3, will help you to improve the manuscript.

Reviewer #1:

The question of how the nucleoid protein H-NS is modulated by a range of different environmental signals has long been unanswered. In this study, van der Valk et al. developed and carried out novel methodologies to assay the impact of H-NS on DNA bridging and DNA stiffening at different concentrations of Mg2+ and K+ and in the presence of the H-NS co-regulators Hha and YdgT. The authors also examined the consequences of truncating H-NS and carried out molecular dynamic simulations of the effects of these conditions on the H-NS dimer. The results of these assays and modeling, led the authors to conclude that "H-NS switches between a "closed" and an "open", bridging-competent conformation driven by environmental cues and interaction partners. This model is extremely attractive, however in my opinion the authors have not tested their interesting ideas in sufficient depth. The study would be a more substantial contribution with additional experiments and discussion to address the following:

1) Many of the conclusions are based on molecular dynamic simulations. The authors should carry out independent experiments such as fluorescence quenching, to test the predictions of these simulations.

Because of the delicate balance between the open and closed conformation of H-NS and the small size of the protein, it is not feasible to investigate this system using fluorescent tags, as these are far too invasive. Indeed, it has been reported earlier that fluorescently labeling H-NS with N-(1-pyrenyl)maleimide dramatically affects its functionality (Schroder et al., Biochem Biophys Res Comm 282, 2001). We have independently confirmed these findings and found that Alexa555 labeling of H-NS at C21 abrogates the DNA bridging capacity of H-NS, while it does not hamper DNA binding (confirmed by EMSA; see Author response image 1 – panel A) or DNA stiffening (confirmed by TPM; see Author response image 1 –panel B)).

Author response image 1
DNA binding and activity of H-NS and H-NSC21Alexa555.

(A) Electrophoretic mobility shift assay using a 32P labeled (AT-rich) curved DNA substrate as described in Dame et al., Bioch., 2001. (B) The root mean squared (RMS) displacement of a DNA tether bound by H-NS and H-NSC21Alexa555 as measured by TPM.

2) The authors examined the "modulation of DNA bridging by osmotic factors", but infer that the model is relevant to a range of environmental signals. This should be tested. As a minor point the authors should comment on how the concentrations of Mg2+ and K+ tested in vitro compare to the concentrations found to modulate H-NS activity in the cell.

Indeed we believe that the model is of generic value and could also explain the effect of other modulatory factors. It would be interesting to test additional factors, but we feel that this goes beyond the scope of the current studies, in which we aim to establish a framework using a series of well-defined and ‘simple’ modulatory factors. It is helpful to give the reader an impression of the concentrations of Mg2+ and K+ relevant to the cell. Whereas information on the effects of K+ in relation to the well-characterized osmoresponsive proU operon is known, little is currently known of the in vivoeffects of Mg2+ on H-NS functionality, beyond the observation that the Mg2+ stimulon (Minagawa et al., J. Bact, 2003) and some of the genes targeted by H-NS overlap. In order to describe the range of ion concentrations relevant in vivo, we have now included the following sentences in the Results section:

“The concentration range from 0 – 10 mM Mg2+ is considered to be physiologically relevant.”

And,

“This in vitroobservation mirrors the in vivoresponse of the ProU operon, at which KCl concentrations exceeding 100 mM are required to alleviate H-NS-mediated repression.”

3) The authors observe disparate effects of Hha and YdgT with respect to DNA stiffening. How do these differences relate to effects of Hha and YdgT in vivo? Can Hha really be a proxy for YdgT in the molecular simulations?

We agree that, given the high sequence identity and homology, the differences between Hha and YdgT in their ability to modulate H-NS function are striking. At this point it is not possible to correlate the distinct effects to in vivodata since data addressing the effects of Hha or YdgT alone on H-NS are unavailable. In the field, Hha and YdgT are considered interchangeable and their functions overlapping, but our data, for the first time, show that these small differences in sequence have substantial effects on how H-NS function is modulated. This observation may have important implications as it suggests that Hha- and YdgT-H-NS heteromers may have distinct target specificity.

4) The authors make very general statements about the implications of their observations? Ideally, the contributions of filament formation versus bridging to the regulation of specific promoters should be examined.

This issue has been addressed in the recent article by Kotlajich, M. V. et al., eLife, 2015. In their studies it was discovered that bridged complexes – and not filaments – reduce transcription by interfering with RNA polymerase progression. In our study we have shown that bridging efficiency – and not filament formation – is modulated by various regulatory factors. Thus our studies provide a rationale for the conditional impact of H-NS on transcription observed in Kotlajich et al. Currently, we are setting up single-molecule transcription experiments in which we can study the effect of different bridging efficiencies – obtained under different experimental conditions – RNA polymerase progression. The extent of these studies goes beyond the scope of the current work.

Reviewer #2:

In this manuscript van der Valk and colleagues present evidence that certain ions and important regulatory factors from E. coli promote the ability of H-NS to bridge DNA molecules. The new in vitro DNA bridging assay they develop is elegant and is used to show that Mg and KCl above a certain concentration can promote DNA bridging by H-NS. The findings with Mg are consistent with the original findings from the Kenney and Yan labs. The authors go on to use the same in vitro assay to show that KCl and regulatory proteins that promote the activities of H-NS, including Hha and YdgT, also promote DNA bridging by H-NS. These findings are new. Finally, based on molecular dynamics simulations the authors suggest that Mg, K, and Hha influence bridging through a common mechanism. This proposed mechanism involves interacting directly with H-NS and blocking an otherwise inhibitory interaction between an oligomerization determinant and a DNA-binding determinant of the protein. The work is interesting but falls somewhat short. Additional biophysical experiments would be needed to strengthen the case that certain ions and proteins promote bridging by altering the distance between specific regions of H-NS. Furthermore, there are no in vivo or in vitro tests of the physiological relevance of Hha or YdgT's ability to promote bridging by H-NS.

1) For the H-NS (Y61D; M64D) double mutant that is predicted to be defective for dimer-dimer interactions, it would be important to show the EMSA analysis of its ability to bind DNA (currently mentioned as data not shown, subsection “The role of Mg2+ and H-NS multimerization in DNA bridging and DNA stiffening”, last paragraph). Ideally, the authors should also test whether this particular mutant is defective in vivo.

We have included as supplementary information the results of an EMSA, which show that indeed the DNA binding capacity of the H-NS mutant is not severely affected (whereas binding is no longer cooperative). We have also attempted to introduce these two mutations in the endogenous hns gene with little success; during the λ red recombination procedure at the marker selection stage, the mutated gene repeatedly reverted to the wild type sequence. This suggests that the H-NS double mutant is not only defective in DNA compaction and organization, but perturbs cellular function in such a way that it severely decreases cell viability. This hypothesis is supported by random mutagenesis studies (Ueguchi, C. et al., J. Mol Biol, 1997), in which no mutations were found in the H-NS dimer-dimer interaction domain (a.a. residues 56-83), even though mutations were obtained throughout all other domains of H-NS.

2) The modulation of DNA bridging and stiffening by truncated H-NS variants is interesting (subsection “Modulation of DNA bridging and DNA stiffening by truncated H-NS variants”). However, the authors should be careful about extrapolating the findings with these fragments of H-NS to other proteins such as H-NST. I think if the authors want to make strong claims about H-NST, then it would be better to directly test whether or not H-NST influences bridging (perhaps with the one from EPEC as it appears to have the most potent activity).

We invested a large amount of time into cloning and purifying the natural truncated H-NS variant and H-NS modulator, H-NST (the EPEC variant), and tested this protein in our assays.

We initially focused on obtaining an untagged variant of this protein. As described earlier by Williamson and Free (MolMic, 2005), we were unable to obtain this protein in soluble form, despite our use of different types of mild detergents to enhance solubility. We therefore resorted to purifying and testing the soluble, tagged variant described by Williamson and Free, which in their hands somewhat reduced binding of H-NS to DNA in vitro. This tagged protein in our hands still suffers from solubility issues and were therefore only able to obtain it at low concentration.

Nevertheless, we tested the effect of adding this protein in the H-NS-DNA stiffening assay up to 8 µM tagged H-NST. In this range we observed no clear effect on DNA stiffness. Note that also with the H-NS1-58 peptide (which most resembles H-NST) the effect on DNA stiffness was mild, but significant in the range between 5-10 µM. Next, we investigated the effect of tagged H-NST on the H-NS-DNA bridging efficiency. In the bridging assay concentrations of up to 3 µM tagged H-NST can be achieved, while maintaining an identical buffer composition throughout the titration range. No significant reduction in bridging efficiency could be observed for tagged H-NST, whereas H-NS1-58 maximally perturbs H-NS mediated bridging at a concentration of 1 µM. The low perturbation efficiency of tagged H-NST in our assays mirrors the smaller effect of tagged H-NST compared to wtH-NST on H-NS mediated repression, observed in vivo by Williamson and Free.

The limited solubility of H-NST underscores the importance of using mimics with high solubility, such as the natural H-NS truncated derivatives used in our studies, to be able to investigate fundamental mechanistic aspects of H-NS activity crucial to its functional modulation.

We have softened the statement referred to by this reviewer by deleting the word ‘strongly’.

Reviewer #3:

[…] The authors' findings significantly advance understanding of H-NS filament formation and its regulation, but their presentation in the submitted manuscript will be largely inaccessible to a general audience without revisions to the text and figures. Additionally, one relatively straightforward experiment would greatly increase the relevance of the findings to in vivo regulation. All these changes are achievable within a reasonable time and would make the manuscript suitable for high-profile publication.

1) Both the TPM and bridging assays need to be better explained in the text and figures. For starters, the ability of readers to understand each assay would be immensely aided by simply graphics that illustrate the assay and what is being measured. For the TPM assay, what is the physical difference in bead behavior between 0% and 100% coverage? This could be illustrated. For the bridging assay, what is the difference between no bridging and complete bridging? Is it just one H-NS dimer bridge between the two DNAs – or more than one bridge? This could be illustrated. For example, an earlier paper from this group provided an excellent illustration of the assay used (Figure 1 of Dame et al. 2006. Nature. 444:387). For both assays, what is the source of the DNA used (why was it chosen and where it is from)? Is the DNA from a gene naturally regulated by H-NS? These DNAs should be described, and perhaps shown as sequence in a supplemental figure, rather than referring readers to another paper.

The first paragraph of the subsection “The role of Mg2+ and H-NS multimerization in DNA bridging and DNA stiffening” should be rewritten to better explain the goals and set-up of the two assays, and the logic for why the experiments were carried out as described so that readers diverse backgrounds can follow the description.

We have added a figure to better illustrate how the assays used work (Figure 1—figure supplement 4). We have also modified the Materials and methods to include the following to further elucidate the minutia of the experiment: “and normalized to a reference sample containing the amount of labeled 32P 685 bp DNA used in the assay.” The DNA substrate is now referred to as “a random, AT rich, 685 bp (32% GC) DNA substrate” in the subsection “DNA preparation”.

2) One main conclusion is that Mg2+ ions interact with residues 22-35 of H-NS based on molecular dynamics. Do the authors believe this is principally an ionic interaction or some type of coordination of Mg2+ by these residues? Could this interaction be abolished by a mutation in H-NS? It would enhance the paper to discuss the properties of this interaction, but more experiments are not necessary.

The simulations suggest that the interaction between Mg2+ and the glutamate residues in region 22-35 is mainly ionic, as the residence time of Mg2+ ions at those residues is relatively short, in the order of a few ns.

We altered the main text to include this information (lines 191 – 198):

“The likelihood of finding Mg2+ interacting with (i.e. being within 0.6 nm of) H-NS residues, indicated by PMg2+, revealed that Mg2+ has a preference for glutamate residues in region 22-35 (Figure 2C), where the ions shield this region from interacting with the DNA binding domains. The magnesium ions transiently interact with the glutamate residues, with residence times in the order of a few ns (as illustrated in Figure 2—figure supplement 5).”

Is there precedence in the literature for Mg2+ interacting with proteins in a similar manner? If so, examples would be useful to cite and discuss.

We were unable to find any cases where Mg2+ interacts with proteins in a similar manner. However, we do suspect that similar interactions occur on other proteins, potentially modulating also their function.

a) The authors should also stipulate explicitly that the simulations were performed in the absence of DNA, and discuss whether the conclusions derived from simulations in the absence of DNA can be used to infer the behavior of H-NS in the presence of DNA. The current simulation provides evidence that the conformation of an H-NS dimer is dynamic in solution, but would this effect be different when H-NS is bound to DNA? A discussion of this question would make the results more complete.

This has now been addressed in the Results section where we have added:

“Even though the simulations were performed in absence of DNA, these observations indicate that DNA bridging is no longer possible in such a conformation, as the H-NS dimer can bind DNA only through its remaining/second DNA binding domain.”

b) Additionally, it is unclear why the authors' results in Figure 1 lead them to test the Mg2+ binding to H-NS. Did they favor this model because the high [Mg2+] does not inhibit DNA binding (subsection “The role of Mg2+ and H-NS multimerization in DNA bridging and DNA stiffening”, last paragraph)?

A motivation of testing the direct effect of Mg2+ on H-NS dimer structure has now been included:

“As Mg2+ does not affect the multimeric state of H-NS in solution (Figure 1—figure supplement 1), a model involving an effect on H-NS multimerization can be excluded. A structural effect of Mg2+ on individual units within H-NS filaments could explain the observed effects of Mg2+ on the bridging efficiency of H-NS.”

3) The authors propose that high K+ can disrupt the bridging of H-NS, which they relate to changes in the cell during osmotic stress. Although this observation is interesting, the authors should rule out the possibility that the high [Cl-] could destabilize H-NS DNA interaction rather than high [K+] destabilizing the bridging interaction, since it is known that Cl- can destabilize protein-DNA interactions (Leirmo S, et al. 1987. Biochemistry 26:2095.). The authors should repeat the experiment in Figure 1C and F with potassium glutamate to test ionic conditions that actually correspond to the in vivo osmotic stress response. If K+ is responsible for the changes in bridging, then the potassium glutamate result will show a similar decrease in bridging as KCl.

This is an important point. We have carried out additional experiments to determine the effects of potassium-glutamate on DNA bridging and DNA stiffening by H-NS. The experiments reveal that potassium glutamate, similar to our findings with potassium chloride, reduces the DNA bridging efficiency, yet that higher concentrations of this salt are needed to achieve the same effects (see Figure 1—figure supplement 5A and B). Throughout this concentration range DNA stiffening is only mildly affected (as seen with KCl), indicating that the intrinsic binding of H-NS to DNA is minimally affected by altered potassium glutamate concentrations. We have also investigated the effects of potassium-glutamate on the DNA binding affinity of H-NS. Here we found that, unlike our expectations based on literature (Leirmo et al., Biochemistry, 1987), potassium-glutamate reduces the DNA binding affinity of H-NS as seen in the figure below in panels C and D. The observation that despite a low DNA binding affinity DNA bridging is enhanced, supports our findings that the observed effects of ions on DNA bridging is direct, and mediated by a structural change in the protein. These findings further strengthen our conclusions that it is indeed DNA bridging and not DNA stiffening that is sensitive to environmental stimuli.

4) The discussion on the Hha/YdgT effect on H-NS binding affinity is unclear because the experiment is not described well. The results are also confusing in that Hha and YdgT both increase bridging, but only Hha enhances binding affinity (by their assay). This result does not support the hypothesis put forth in the subsection “Modulation of H-NS by Hha and YdgT”, that both Hha and YdgT increase the binding affinity of H-NS. A clearer description of the results is needed to communicate the differences and similarities between the Hha and YdgT effects accurately. Additionally, a diagram illustrating how Hha and YdgT are proposed to affect filaments and a representation of this experiment also might improve the accessibility of the results.

We have altered this part of the text to correct for this inadvertent omission. It now reads as follows:

“One possible explanation for the effects of Hha and YdgT, is that they effectively increase the DNA binding affinity of H-NS47. We find that the affinity of H-NS is significantly enhanced by Hha, but it is not significantly altered by YdgT (Figure 3—figure supplement 1D).”

We have also added “Figure 3—figure supplement 2: Schematic depiction of the effects of Hha and YdgT.” To more clearly explain our findings with Hha and YdgT.

For Figure 3—figure supplement 1, including a graphical representation of coverage would immensely help in understanding the results.

a) It is surprising that Hha and H-NS together do not show cooperative DNA binding. The authors should discuss how these new results can be reconciled with previous publications showing that Hha (along with H-NS) is necessary for silencing of genes (e.g., Ali, S. S., et al. 2013. JBC. 288: 13356; Banos, R. C., et al. 2009. PLoS Genetics. 5:e1000513.) The results presented in those papers suggest that cooperative binding is necessary for forming a filament that can silence genes (a bridged filament), which would also suggest that filaments containing Hha and H-NS should cooperatively form a bridged filament. The result that Hha disrupts cooperative binding is inconsistent with that hypothesis, so the authors should discuss alternative mechanisms to explain how Hha and H-NS together silence genes.

Indeed, earlier studies of H-NS and Hha clearly demonstrate functional interactions between Hha and H-NS required for gene silencing. However, these studies provide direct information only on the effect of Hha on the affinity of H-NS, and not on cooperativity of H-NS binding arising from the interaction with Hha. Altered cooperativity, i.e. an altered propensity to form protein-DNA filaments, is reported for the first time in our work as we are capable of accurately quantifying this aspect of H- NS binding. This was not possible with the methods employed by previous studies (such as those employed by Ali, S. S., et al. 2013. JBC. 288: 13356). We have updated the text and added an illustrative figure to explain how Hha lowers the cooperativity of H-NS DNA binding (Figure 3—figure supplement 2):

“The absence of cooperativity observed in the presence of Hha, indicates that Hha (unlike YdgT) interferes with filament formation. A higher effective affinity of H-NS- Hha to DNA compared to DNA bound H-NS-Hha may favor nucleation over filament formation (Figure 3—figure supplement 2B).”

It is also important to note that there exists no discrepancy between our findings concerning the cooperativity of DNA binding and DNA bridging as these two occur at significantly different H-NS concentrations (150 nM H-NS for DNA binding, whereas bridging only begins at roughly 3 μM H-NS).

[Editors' note: the author responses to the re-review follow.]

There continues to be enthusiasm for your study, but after discussion, the reviewers feel the following additional revisions are critical for the study to live up to its potential as a significant advance.

1) Experimental tests of the predictions of the molecular dynamics simulations need to be carried out. This should involve mutating the residues (i.e. glutamates to serines) expected to interact with ions like Mg2+ and mutating residue R11 expected to destabilise the closed H-NS conformation. Assaying the effects of such mutations, using the experimental tools applied in Figure 1, should reveal differences in magnesium modulation of HNS binding as predicted by the simulations.

In light of this suggestion we have cloned and purified several H-NS derivatives to test the occurrence of predicted structural changes in response to altered physico-chemical conditions:

a) H-NSE42S, E43S, E44S (a mutant with α helix 3 predicted to be stable)

b) H-NSE43A, E44A, S45A (another mutant with α helix 3 predicted to be stable)

c) H-NSR11E (a mutation that should prevent the closed conformation by removing an important salt bridge)

We investigated these H-NS derivatives in both our DNA bridging and Tethered Particle Motion assays. These experiments yielded the following results:

a) H-NSE42S, E43S, E44S: No DNA binding is observed for this H-NS derivative, likely due to misfolding of the protein.

b) H-NSE43A, E44A, S45A: This H-NS derivative is capable of bridging DNA in the absence of Mg2+ (as seen in Figure 2—figure supplement 9A), confirming both our MD simulations and our model

c) H-NSR11E:The intrinsic DNA binding affinity of this mutant is drastically reduced to such an extent that in the presence of Mg2+ no binding to DNA is observed (as seen in Author response image 2). This finding corroborates the findings of previous studies in vivo by Ueguchi et al.(Journal of Molecular Biology 1996) and in vitro by Bloch et al. (Nature Structural Biology 2003), in which it was shown that altering R11 perturbs H-NS function, likely by hampering its DNA binding activity.

Author response image 2
DNA binding by the H-NS derivative H-NSR11E measured by the Root Mean Square displacement of DNA.

2) Downplay the hha/ydgT experiments, as they are not yet fully developed, and focus the paper on Mg2+ induced changes.

We have modified the text accordingly.

Each of the reviewers’ comments is also included below.

Reviewer #1:

In this revised manuscript van der Valk and colleagues present evidence that certain ions and important regulatory factors from E. coli promote the ability of H-NS to bridge DNA molecules. Key components of the manuscript include use of an elegant biochemical assay to demonstrate that Mg, as well as the regulatory factors Hha and YdgT promote DNA-bridging by H-NS. They also show that K inhibits DNA-bridging by H-NS, and that truncated derivatives of H-NS can modulate the ability of H-NS to bridge the DNA--findings that have implications for naturally occurring inhibitors of H-NS, such as H-NST. Based on molecular dynamics simulations the authors suggest that Mg and Hha promote bridging through a common mechanism. This proposed mechanism involves interacting directly with H-NS and blocking an otherwise inhibitory interaction between an oligomerization determinant and a DNA-binding determinant of the protein. In my earlier review I had indicated that additional biophysical experiments would be needed to strengthen the case that certain ions and proteins influence bridging by altering the distance between specific regions of H-NS. The authors didn't comment on this concern but indicate in their response to reviewer 1 that Alexa555 labelling of H-NS is problematic. Thus, a limitation of both the original and the current study is that there are no independent experimental tests of the predictions from the molecular dynamics simulations used to develop the highly interesting model the authors propose.

In my earlier review I had also indicated there are no in vivo or in vitro tests of the physiological relevance of Hha or YdgT's ability to promote bridging by H-NS. The authors didn't comment on my concern but indicate in response to reviewer 1 that they are conducting a separate single-molecule study to test the effects of different bridging efficiencies on RNA polymerase progression.

The authors adequately addressed my specific comments. In particular, they now provide in vitro analysis of the ability of HNS (Y61D;M64D) to bind DNA by EMSA. They also attempted to test the effects of H-NST (from EPEC) on bridging by H-NS in vitro, but ran into problems with H-NST solubility.

Additional independent experiments would strengthen the case that certain ions and proteins influence bridging by altering the distance between specific regions of H-NS.

In light of the reviewer’s suggestion we have designed an H-NS mutant that is predicted to directly affect the ability of H-NS to form the open and closed conformations.

In this mutant, we sought to abrogate the ability of H-NS to attain a closed conformation. In this light, we substituted the glutamic acids E43, E44, and serine S45 with Alanines to prevent the closed conformation. The DNA bridging assay (Figure 2—figure supplement 9) shows that this mutant indeed can bridge DNA in a Mg2+ independent manner. We note that there is a strong similarity in the Mg2+ dependence of the H-NSE43A,E44A,S45A protein and wildtype H-NS in the presence of 4 µM YdgT. This similarity further supports our idea that YdgT and Hha promote the open conformation of H-NS to enhance its bridging efficiency.

Reviewer #2:

[…] I'm not entirely convinced their models are correct regarding Hha vs. YdgT (see Figure 3). It makes little sense that by having less affinity for H-NS, that Hha in some way disrupts multimerization while YdgT (which has more affinity) promotes more multimerization, but of the closed H-NS conformer. They may be over-interpreting and making a model from limited data without thinking of alternatives. Furthermore, if Hha disrupts cooperativity, would not the HNS multimerization domain mutant (Y61DM64D) act the same as H-NS plus Hha? How does the mutant abolish bridging while Hha promotes it?

Indeed, as the reviewer summarizes, we find that Hha antagonizes the cooperativity inherent to H-NS DNA binding and multimerization. However, different from the results for the H-NS multimerization mutant (Y61DM64D), we find that H-NS + Hha is still capable of multimerization along the DNA (Figure 3). We agree with the referee that the disparate behaviour of the two related proteins, Hha and YdgT, is unexpected and hard to explain at a molecular mechanistic level based on the currently available information (unfortunately a H-NS-YdgT co-crystal structure is lacking). Therefore, we have significantly reduced the text in relation to our structural interpretation of these observations, and have removed the model in the accompanying figure.

Another issue I have is that in their proposed "closed" conformation I see no way the central dimerization domain would be available for making an H-NS oligomer. The central dimerization domain would also be made inaccessible to binding a new dimer of H-NS. Perhaps they could explain it better?

This is an astute question posed by the reviewer. We agree that the closed conformation in the shown simulation snapshots appears quite compact. It is important to realize that the structure is dynamic and that different physico-chemical conditions drive a bias within the population of proteins towards either open or closed conformation.

Interestingly, we found similar cooperativity in DNA binding by H-NS in the “open” conformation (H-NSE43A,E44A,S45A as seen in Figure 3—figure supplement 1D) and the “closed” conformation (wildtype H-NS in the absence of Mg2+ as seen in Figure 3—figure supplement 1D). Only in the presence of Mg2+ does H-NS show a very high level of cooperative DNA binding (Figure 3—figure supplement 1D). This indicates that cooperativity by H-NS is not promoted by either the “closed” or “open” conformations, but by the transition between the two states.

I think the molecular dynamics simulations are interesting and they propose that certain residues in the protein interact with ions like Mg2+ to modulate the conformation of the molecule. It would be nice to see more simulations with "mutant" H-NS or even experimental data where the glutamates in question were changed to serine. I don't believe, however, those experiments are critical for publication.

We agree with the reviewer that an experimental test of our structural model (and the specific residues of importance for the structural changes and Mg2+ sensing in the protein) significantly strengthens our observations. We have therefore designed and generated an H-NS derivative, in which the glutamic acids E43, E44, and S45 are substituted with Alanines. These mutations are predicted to prevent buckle formation and to result in a stable a-helix structure. This prevents the occurrence of the closed conformation, and is expected to result in a high efficiency of DNA bridging, which is not dependent on Mg2+. Our bridging assay (Figure 2—figure supplement 9) shows that this mutant indeed bridges DNA in a Mg2+ independent manner. See also our reply above.

Reviewer #3:

This is an interesting paper that adds important mechanistic detail to the known changes in H-NS:DNA complexes induced by a change in the availability of Mg2+, other divalent cations, and H-NS-like proteins.

Overall, this paper represents an important contribution to the field and I am supportive of publication. However, I think that the paper suffers in two ways and attempts could be made to resolve these issues.

First, the reliance on molecular dynamics is a potential weakness in my opinion. To me, this seems like an excellent way to generate a hypothesis that can be tested experimentally (see subsection “Mg2+ alters H-NS structure”) but this has not been done yet. Second, the paper attempts to deal with two issues; the role of cations and the role of interaction partners. As a result, I feel that the paper falls just short of "nailing" either story. In some ways, the Discussion reflects this and mostly ignores the interaction partners.

For me, it would be great to see a paper focused on cation interactions bolstered by a couple of simple experiments testing the predictions of the molecular dynamics. I appreciate that the paper has already been through one round of revision and so this idea may not be greeted enthusiastically by the authors or journal. With this in mind, it may be possible for the authors to rewrite the subsection “Modulation of DNA bridging and DNA stiffening by truncated H-NS variants” so that it is presented as a test of the molecular dynamics predictions. E.g. would some of these truncated H-NS proteins block some of the intramolecular interactions predicted by the dynamics?

We have taken the reviewers comment to heart, but we fear that this is a misrepresentation of our experiments with truncated H-NS proteins. Instead we chose to directly test the model described by the MD simulations by generating an H-NS mutant predicted to persist in the “open” conformation. In this light, we substituted the glutamic acids E43, E44, and S45 with Alanines to prevent the closed conformation. Our bridging assay (Figure 2—figure supplement 9) shows that this mutant indeed bridges DNA in a Mg2+ independent manner.

https://doi.org/10.7554/eLife.27369.027

Article and author information

Author details

  1. Ramon A van der Valk

    Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
    Contribution
    Conceptualization, Formal analysis, Supervision, Validation, Investigation, Visualization, Methodology, Writing—original draft, Writing—review and editing
    Competing interests
    No competing interests declared
  2. Jocelyne Vreede

    Computational Chemistry, Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, Netherlands
    Contribution
    Conceptualization, Resources, Data curation, Software, Formal analysis, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing—review and editing
    Competing interests
    No competing interests declared
  3. Liang Qin

    Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
    Contribution
    Formal analysis, Validation, Investigation, Visualization
    Competing interests
    No competing interests declared
  4. Geri F Moolenaar

    Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
    Contribution
    Conceptualization, Resources, Validation, Investigation, Methodology, Project administration
    Competing interests
    No competing interests declared
  5. Andreas Hofmann

    Institute for Theoretical Physics, University of Heidelberg, Heidelberg, Germany
    Contribution
    Software, Formal analysis, Investigation, Methodology
    Competing interests
    No competing interests declared
  6. Nora Goosen

    Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
    Contribution
    Conceptualization, Resources, Validation, Investigation, Methodology, Project administration
    Competing interests
    No competing interests declared
  7. Remus T Dame

    1. Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
    2. Centre for Microbial Cell Biology, Leiden University, Leiden, Netherlands
    Contribution
    Conceptualization, Data curation, Formal analysis, Supervision, Funding acquisition, Visualization, Methodology, Writing—original draft, Project administration, Writing—review and editing
    For correspondence
    rtdame@chem.leidenuniv.nl
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9863-1692

Funding

NanonextNL of the Government of the Netherland and 130 partners

  • Ramon A van der Valk
  • Geri F Moolenaar
  • Remus T Dame

Netherlands Organisation for Scientific Research (VIDI 864.08.001)

  • Ramon A van der Valk
  • Geri F Moolenaar
  • Nora Goosen
  • Remus T Dame

Netherlands Organisation for Scientific Research (Athena grant 700.58.802)

  • Jocelyne Vreede

Human Frontier Science Program (RGP0014/2014)

  • Andreas Hofmann
  • Remus T Dame

China Scholarship Council (No. 201506880001)

  • Liang Qin

Netherlands Organisation for Scientific Research (VICI 016.160.613)

  • Remus T Dame

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

We thank Bas de Mooij for his assistance in standardizing the bridging assay, Wim Jesse and Alexander Kros for synthesizing the H-NS56-83 peptide and their assistance during its purification. We also thank Rosalie Driessen for her assistance with data analysis and all group members for valued discussions. JV acknowledges the use of the Dutch National Supercomputer Cartesius for the MD simulations.

Reviewing Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Publication history

  1. Received: April 3, 2017
  2. Accepted: September 25, 2017
  3. Accepted Manuscript published: September 26, 2017 (version 1)
  4. Version of Record published: October 18, 2017 (version 2)

Copyright

© 2017, van der Valk et al.

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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