Atomic Force Microscopy Imaging of DNA under Macromolecular Crowding Conditions

Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo

The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.

Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles

Cell-free protein synthesis is an important tool for studying gene expression and harnessing it for applications. In cells, gene expression is regulated in part by the spatial organization of transcription and translation. Unfortunately, current cell-free approaches are unable to control the organization of molecular components needed for gene expression, which limits the ability to probe and utilize its effects. Here, we show, using complementary computational and experimental approaches, that macromolecular crowding can be used to control the spatial organization and translational efficiency of gene expression in cell-sized vesicles. Computer simulations and imaging experiments reveal that, as crowding is increased, DNA plasmids become localized at the inner surface of vesicles. Ribosomes, in contrast, remain uniformly distributed, demonstrating that crowding can be used to differentially organize components of gene expression. We further carried out cell-free protein synthesis reactions in cell-sized vesicles and quantified mRNA and protein abundance. At sufficiently high levels of crowding, we observed localization of mRNA near vesicle surfaces, a decrease in translational efficiency and protein abundance, and anomalous scaling of protein abundance as a function of vesicle size. These results are consistent with high levels of crowding causing altered spatial organization and slower diffusion. Our work demonstrates a straightforward way to control the organization of gene expression in cell-sized vesicles and provides insight into the spatial regulation of gene expression in cells.

Crowding-induced polymer trapping in a channel

In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effective polymer-corner attraction due to the depletion effect. This phenomenon is referred to as polymer trapping. The occurrence of polymer trapping requires a minimum volume fraction of crowders, ϕ^{*}, which scales as ϕ^{*}∼(a_{c}/L_{p})^{1/3} for a_{c}≫a_{m} and ϕ^{*}∼(a_{c}/L_{p})^{1/3}(a_{c}/a_{m})^{1/2} for a_{c}≪a_{m}, where a_{c} is the crowder diameter, a_{m} is the monomer diameter, and L_{p} is the polymer persistence length. For DNA, ϕ^{*} is estimated to be around 0.25 for crowders with a_{c}=2nm. We find that ϕ^{*} also strongly depends on the shape of the channel cross section, and ϕ^{*} is much smaller for a triangle channel than a square channel. The polymer trapping leads to a nearly fully stretched polymer conformation along a channel corner, which may have practical applications, such as full stretching of DNA for the nanochannel-based genome mapping technology.

Crowding-induced interactions of ring polymers

Macromolecular crowding and the presence of surfaces can significantly impact the spatial organization of biopolymers. While the importance of crowding-induced depletion interactions in biology has been recognized, much remains to be understood about the effect of crowding on biopolymers such as DNA plasmids. A fundamental problem highlighted by recent experiments is to characterize the impact of crowding on polymer-polymer and polymer-surface interactions. Motivated by the need for quantitative insight, we studied flexible ring polymers in crowded environments using Langevin dynamics simulations. The simulations demonstrated that crowding can lead to compaction of isolated ring polymers and enhanced interactions between two otherwise repulsive polymers. Using umbrella sampling, we determined the potential of mean force (PMF) between two ring polymers as a function of their separation distance at different volume fractions of crowding particles, φ. An effective attraction emerged at φ≈ 0.4, which is similar to the degree of crowding in cells. Analogous simulations showed that crowding can lead to strong adsorption of a ring polymer to a wall, with an effective attraction to the wall emerging at a smaller volume fraction of crowders (φ≈ 0.2). Our results reveal the magnitude of depletion interactions in a biologically-inspired model and highlight how crowding can be used to tune interactions in both cellular and cell-free systems.

Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers

BACKGROUND

DNA bridging promoted by the H-NS protein, combined with the compaction induced by cellular crowding, plays a major role in the structuring of the E. coli genome. However, only few studies consider the effects of the physical interplay of these two factors in a controlled environment.

METHODS

We apply a single molecule technique (Magnetic Tweezers) to study the nanomechanics of compaction and folding kinetics of a 6 kb DNA fragment, induced by H-NS bridging and/or PEG crowding.

RESULTS

In the presence of H-NS alone, the DNA shows a step-wise collapse driven by the formation of multiple bridges, and little variations in the H-NS concentration-dependent unfolding force. Conversely, the DNA collapse force observed with PEG was highly dependent on the volume fraction of the crowding agent. The two limit cases were interpreted considering the models of loop formation in a pulled chain and pulling of an equilibrium globule respectively.

CONCLUSIONS

We observed an evident cooperative effect between H-NS activity and the depletion of forces induced by PEG.

GENERAL SIGNIFICANCE

Our data suggest a double role for H-NS in enhancing compaction while forming specific loops, which could be crucial in vivo for defining specific mesoscale domains in chromosomal regions in response to environmental changes.

Solid-Liquid Interface Structure of Muscovite Mica in SrCl2 and BaCl2 Solutions

The structure of the solid-liquid interface formed by muscovite mica in contact with two divalent ionic solutions (SrCl₂ and BaCl₂) is determined using in situ surface X-ray diffraction using both specular and non-specular crystal truncation rods. The 0.5 monolayer of monovalent potassium present at the surface after cleavage is replaced by approximately 0.25 monolayer of divalent ions, closely corresponding to ideal charge compensation within the Stern layer in both cases. The adsorption site of the divalent ions is determined to be in the surface ditrigonal cavities with minor out-of-plane relaxations that are consistent with their ionic radii. The divalent ions are adsorbed in a partly hydrated state (partial solvation sphere). The liquid ordering induced by the presence of the highly ordered crystalline mica is limited to the first 8-10 Å from the topmost crystalline surface layer. These results partly agree with previous studies in terms of interface composition, but there are significant differences regarding the structural details of these interfaces.

Solid-Liquid Interface Structure of Muscovite Mica in CsCl and RbBr Solutions

The solid-liquid interface formed by single terminated muscovite mica in contact with two different ionic solutions is analyzed using surface X-ray diffraction. Specular and nonspecular crystal truncation rods of freshly cleaved mica immersed in CsCl or RbBr aqueous solution were measured. The half monolayer of the surface potassium ions present after the cleavage is completely replaced by the positive ions (Cs⁺ or Rb⁺) from the solution. These ions are located in the ditrigonal surface cavities with small outward relaxations with respect to the bulk potassium position. We find evidence for the presence of a partly ordered hydration shell around the surface Cs⁺ or Rb⁺ ions and partly ordered negative ions in the solution. The lateral liquid ordering induced by the crystalline surface vanishes at distances larger than 5 Å from the surface.

Do RNA viruses require genome cyclisation for replication?

Complementary sequences at the 5' and 3' ends of the dengue virus RNA genome are essential for viral replication, and are believed to cyclise the genome through long-range base pairing in cis. Although consistent with evidence in the literature, this view neglects possible biologically active multimeric forms that are equally consistent with the data. Here, we propose alternative multimeric structures, and suggest that multigenome noncovalent concatemers are more likely to exist under cellular conditions than single cyclised monomers. Concatemers provide a plausible mechanism for the dengue virus to overcome the single-stranded (+)-sense RNA virus dilemma, and can potentially assist genome transport from the virus-induced vesicles into the cytosol.

Structure of metaphase chromosomes: a role for effects of macromolecular crowding

In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

Macromolecular crowding regulates assembly of mRNA stress granules after osmotic stress: new role for compatible osmolytes

The massive uptake of compatible osmolytes such as betaine, taurine, and myo-inositol is a protective response shared by all eukaryotes exposed to hypertonic stress. Their accumulation results mostly from the expression of specific transporters triggered by the transcriptional factor NFAT5/TonEBP. This allows the recovery of the cell volume without increasing intracellular ionic strength. In this study we consider the assembly and dissociation of mRNA stress granules (SGs) in hypertonic-stressed cells and the role of compatible osmolytes. In agreement with in vitro results obtained on isolated mRNAs, both macromolecular crowding and a high ionic strength favor the assembly of SGs in normal rat kidney epithelial cells. However, after hours of constant hypertonicity, the slow accumulation in the cytoplasm of compatible osmolytes via specific transporters both reduces macromolecular crowding and ionic strength, thus leading to the progressive dissociation of SGs. In line with this, when cells are exposed to hypertonicity to accumulate a large amount of compatible osmolytes, the formation of SGs is severely impaired, and cells increase their chances of survival to another hypertonic episode. Altogether, these results indicate that the impact of compatible osmolytes on the mRNA-associated machineries and especially that associated with SGs may play an important role in cell resistance and adaption to hyperosmolarity in many tissues like kidney and liver.

Kinetic study on the reentrant condensation of oligonucleotide in trivalent salt solution

The reentrant condensation of 21-bp oligonucleotide in the presence of spermidine was investigated by laser light scattering and capillary electrophoresis. 21-bp oligonucleotide showed a bimodal distribution in 1 × TE buffer, with the slow mode being the characteristic diffusion of polyelectrolyte in solution without enough salt. At the fixed spermidine concentration, the reentry of oligonucleotide underwent aggregation, phase separation, and disassociation in sequence with time, and the kinetics was extremely slow. For example, it took more than 1200 h (50 days) for the reentry to complete at 21 mM spermidine. Higher spermidine concentration led to faster kinetics. After reentry, the slow mode disappeared, and the charges of oligonucleotide were at least partially neutralized. No prominent charge inversion was observed. The kinetics of oligonucleotide reentry in the presence of spermidine gained insight in the interactions of polyelectrolyte in aqueous solution.

Macromolecular crowding can account for RNase-sensitive constraint of bacterial nucleoid structure

The shape and compaction of the bacterial nucleoid may affect the accessibility of genetic material to the transcriptional machinery in natural and synthetic systems. To investigate this phenomenon, the nature and contribution of RNA and protein to the compaction of nucleoids that had been gently released from Escherichia coli cells were investigated using fluorescent and transmission electron microscopy. We propose that the removal of RNA from the bacterial nucleoid affects nucleoid compaction by altering the branching density and molecular weight of the nucleoid. We show that a common detergent in nucleoid preparations, Brij 58, plays a previously unrecognized role as a macromolecular crowding agent. RNA-free nucleoids adopt a compact structure similar in size to exponential-phase nucleoids when the concentration of Brij 58 is increased, consistent with our hypothesis. We present evidence that control and protein-free nucleoids behave similarly in solutions containing a macromolecular crowding agent. These results show that the contribution to DNA compaction by nucleoid-associated proteins is small when compared to macromolecular crowding effects.

Specific DNA-protein interactions on mica investigated by atomic force microscopy

DNA processing by site-specific proteins on surface remains a challenging issue for nanobioscience applications and, in particular, for high-resolution imaging by atomic force microscopy (AFM). To obtain high-resolution conditions, mica, an atomically flat and negatively charged surface, is generally used. However, even though many specific DNA/protein interactions have already been observed by AFM, little is known about DNA accessibility to specific enzymes on mica. Here we measured the accessibility of adsorbed DNA to restriction endonucleases (EcoRI and EcoRV) using AFM. By increasing the concentration of divalent or multivalent salts, DNA adsorption on mica switches from weak to strong binding. Interestingly, while the accessibility of strongly bound DNA was inhibited, loosely adsorbed DNA was efficiently cleaved on mica. This result opens new perspective to study DNA/protein interaction by AFM or to modify specifically DNA on surface.