Macromolecular interactions of the bacterial division FtsZ protein: from quantitative biochemistry and crowding to reconstructing minimal divisomes in the test tube

Depletion-Induced Self-Assembly of Colloidal Particles on a Solid Substrate

We investigate the depletion contributions to the self-assembly of microcolloids on solid substrates. The assembly is driven by the exclusion of nanoparticles and nonadsorbing polymers from the depletion zone between the microcolloids in the liquid and the underlying substrate. The model system consists of 1 μm polystyrene particles that we deposit on a flat glass slab in an electrolyte solution. Using polystyrene nanoparticles and poly(acrylic acid) polymers as depleting agents, we demonstrate in our experiments that nanoparticle concentrations of 0.5% (w/v) support well-ordered packing of microcolloids on glass, while the presence of polymers leads to irregular aggregate deposition structures. A mixture of nanoparticles and polymers enhances the formation of colloidal aggregate and particulate surface coverage compared to using the polymers alone as a depletion agent. Moreover, tuning the polymer ionization state from pH 4 to 9 modifies the polymer conformational state and radius of gyration, which in turn alters the microcolloid deposition from compact multilayers to flocculated structures. Our study provides entropic strategies for manipulating particulate assembly on substrates from dispersed to continuous coatings.

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.

Benzodioxane-benzamides as promising inhibitors of Escherichia coli FtsZ

The conserved process of cell division in bacteria has been a long-standing target for antimicrobials, although there are few examples of potent broad-spectrum compounds that inhibit this process. Most currently available compounds acting on division are directed towards the FtsZ protein, a self-assembling GTPase that is a central element of the division machinery in most bacteria. Benzodioxane-benzamides are promising candidates, but poorly explored in Gram-negatives. We have tested a number of these compounds on E. coli FtsZ and found that many of them significantly stabilized the polymers against disassembly and reduced the GTPase activity. Reconstitution in crowded cell-like conditions showed that FtsZ bundles were also susceptible to these compounds, including some compounds that were inactive on protofilaments in dilute conditions. They efficiently killed E. coli cells defective in the AcrAB efflux pump. The activity of the compounds on cell growth and division generally showed a good correlation with their effect in vitro, and our experiments are consistent with FtsZ being the target in vivo. Our results uncover the detrimental effects of benzodioxane-benzamides on permeable E. coli cells via its central division protein, implying that lead compounds may be found within this class for the development of antibiotics against Gram-negative bacteria.

Simplified Equilibrium Model for Exploring the Combined Influences of Concentration, Aggregate Shape, Excluded Volume, and Surface Adsorption upon Aggregation Propensity and Distribution of Globular Macromolecules

A mesoscopic model for the equilibrium self-association of a globular macromolecule that may form oligomers of various shapes and unlimited sizes is presented. Allowance is made within this model for the effects of variation in the free energy of subunit contact within an oligomer of specified size and different shapes, the free energy of adsorption of an oligomer of specified size and shape to a planar surface, and the free energy of nonspecific excluded volume interaction between an oligomer of specified size and shape and an inert species occupying a specified fraction of total volume. The model is analytically soluble and permits rapid calculation and analysis of the effects of variation in each of the three free energy parameters upon the concentration dependence of the weight-average stoichiometry of the oligomer, the fraction of total macromolecule that is adsorbed, and the fraction of differently shaped oligomers that are adsorbed and in free solution.

Biophysical Reviews' "Meet the Editors Series"-a profile of Germán Rivas

German Rivas is an executive editor of the IUPAB Biophysical Reviews journal based in Spain. As the head of the Department of Structural and Chemical Biology at the Center for Biological Research (CIB) Margarita Salas (one of the largest research institutes devoted to life sciences of the Spanish National Research Council (CSIC)), he leads a research program aimed at understanding the structure function relationship of large macromolecular complexes (involved in bacterial cell division) when placed in physiologically complex and "crowded" media toward their reconstitution from the bottom up in cell-like compartments. In this "Meet the Editors'" piece, he briefly describes his research interests and history.

In vitro assembly, positioning and contraction of a division ring in minimal cells

Constructing a minimal machinery for autonomous self-division of synthetic cells is a major goal of bottom-up synthetic biology. One paradigm has been the E. coli divisome, with the MinCDE protein system guiding assembly and positioning of a presumably contractile ring based on FtsZ and its membrane adaptor FtsA. Here, we demonstrate the full in vitro reconstitution of this machinery consisting of five proteins within lipid vesicles, allowing to observe the following sequence of events in real time: 1) Assembly of an isotropic filamentous FtsZ network, 2) its condensation into a ring-like structure, along with pole-to-pole mode selection of Min oscillations resulting in equatorial positioning, and 3) onset of ring constriction, deforming the vesicles from spherical shape. Besides demonstrating these essential features, we highlight the importance of decisive experimental factors, such as macromolecular crowding. Our results provide an exceptional showcase of the emergence of cell division in a minimal system, and may represent a step towards developing a synthetic cell.

An enhancer sequence in the intrinsically disordered region of FtsZ promotes polymer‐guided substrate processing by ClpXP protease

The essential bacterial division protein in Escherichia coli, FtsZ, assembles into the FtsZ-ring at midcell and recruits other proteins to the division site to promote septation. A region of the FtsZ amino acid sequence that links the conserved polymerization domain to a C-terminal protein interaction site was predicted to be intrinsically disordered and has been implicated in modulating spacing and architectural arrangements of FtsZ filaments. While the majority of cell division proteins that directly bind to FtsZ engage either the polymerization domain or the C-terminal interaction site, ClpX, the recognition and unfolding component of the bacterial ClpXP proteasome, has a secondary interaction with the predicted intrinsically disordered region (IDR) of FtsZ when FtsZ is polymerized. Here, we use NMR spectroscopy and reconstituted degradation reactions in vitro to demonstrate that this linker region is indeed disordered in solution and, further, that amino acids in the IDR of FtsZ enhance the degradation in polymer-guided interactions.

Liposomes encapsulating artificial cytosol as drug delivery system

The fabrication of cell models containing artificial cytosol is challenging. Herein we constructed an artificial cytosol contained cell model by electroformation method. Agarose was selected as the main component of the artificial cytosol, and sucrose was added into the agarose to regulate the sol viscosity and the phase transition temperature. The viscosity of the sol with the mass ratio (agarose-sucrose) 1:9 was closest to the natural cytosol. DSPC/20 mol% cholesterol was used to form large unilamellar vesicles (LUVs) as cell model compartment. The rhodamine release experiment confirmed that the unique release profile of agarose-sucrose@LUVs is suitable as a drug carrier. Doxorubicin is loaded in the agarose-sucrose@LUVs, and their half maximum inhibition concentration on HeLa cells is 0.016 μmol L^-1, which means 28.7 times increase in inhibition efficiency over free doxorubicin.

Cell-free biogenesis of bacterial division proto-rings that can constrict liposomes

A major challenge towards the realization of an autonomous synthetic cell resides in the encoding of a division machinery in a genetic programme. In the bacterial cell cycle, the assembly of cytoskeletal proteins into a ring defines the division site. At the onset of the formation of the Escherichia coli divisome, a proto-ring consisting of FtsZ and its membrane-recruiting proteins takes place. Here, we show that FtsA-FtsZ ring-like structures driven by cell-free gene expression can be reconstituted on planar membranes and inside liposome compartments. Such cytoskeletal structures are found to constrict the liposome, generating elongated membrane necks and budding vesicles. Additional expression of the FtsZ cross-linker protein ZapA yields more rigid FtsZ bundles that attach to the membrane but fail to produce budding spots or necks in liposomes. These results demonstrate that gene-directed protein synthesis and assembly of membrane-constricting FtsZ-rings can be combined in a liposome-based artificial cell.

Godino et al. show that FtsA-FtsZ ring-like structures driven by cell-free gene expression can be reconstituted on planar membranes and inside liposome compartments. These cytoskeletal structures constrict the liposome, generating elongated membrane necks and budding vesicles. This study represents a step forward to realizing genetic programming of synthetic cell division.

Reconstituting bacterial cell division assemblies in crowded, phase-separated media

Here we have summarized several strategies to reconstruct complexes containing the FtsZ protein, a central element of the cell division machinery in most bacteria, and to test their functional organization in minimal membrane systems and cell-like containers, as vesicles and droplets produced by microfluidics. These synthetic systems have been devised to mimic elements of the intracellular complexity, as excluded volume effects due to natural crowding, and macromolecular condensation resulting from biologically regulated liquid-liquid phase separation, in media of known and controllable composition. This integrative approach has allowed to demonstrate that macromolecular phase separation and crowding may also help to dynamically organize FtsZ in the intracellular space thus modulating its functional reactivity in cell division.

Treadmilling analysis reveals new insights into dynamic FtsZ ring architecture

FtsZ, the primary protein of the bacterial Z ring guiding cell division, has been recently shown to engage in intriguing treadmilling dynamics along the circumference of the division plane. When coreconstituted in vitro with FtsA, one of its natural membrane anchors, on flat supported membranes, these proteins assemble into dynamic chiral vortices compatible with treadmilling of curved polar filaments. Replacing FtsA by a membrane-targeting sequence (mts) to FtsZ, we have discovered conditions for the formation of dynamic rings, showing that the phenomenon is intrinsic to FtsZ. Ring formation is only observed for a narrow range of protein concentrations at the bilayer, which is highly modulated by free Mg²⁺ and depends upon guanosine triphosphate (GTP) hydrolysis. Interestingly, the direction of rotation can be reversed by switching the mts from the C-terminus to the N-terminus of the protein, implying that the filament attachment must have a perpendicular component to both curvature and polarity. Remarkably, this chirality switch concurs with previously shown inward or outward membrane deformations by the respective FtsZ mutants. Our results lead us to suggest an intrinsic helicity of FtsZ filaments with more than one direction of curvature, supporting earlier hypotheses and experimental evidence.

FtsZ is a tubulin homologue and the primary protein of the bacterial Z ring that guides cell division. In vivo, but also in reconstituted systems, FtsZ shows an intriguing treadmilling dynamic along circular tracks of approximately 1 micrometer in diameter. In cells, this treadmilling along the circumference of the division site is suggested to dynamically guide peptidoglycan—and thus new cell wall—synthesis. In vitro, when reconstituted along with its membrane adaptor FtsA on flat supported membranes, FtsZ self-organizes into similarly treadmilling vortices as observed in vivo but with a clear chirality. With the aim of thoroughly investigating these dynamics, revealing the origin of chirality, and potentially relating it to a membrane-transforming ability of FtsZ, we reconstituted different membrane-targeted mutants of FtsZ on flat membranes. In this minimized system, we found that dynamic ring formation is an intrinsic feature of FtsZ without the need of any other protein. However, self-organization into dynamic treadmilling only occurs within a specific protein, cation, and guanosine triphosphate (GTP) concentration range. Our work led us to propose that the observed chirality of FtsZ treadmilling may be explained by an inherent helical character of the filaments with more than one direction of curvature.

Microenvironments created by liquid-liquid phase transition control the dynamic distribution of bacterial division FtsZ protein

The influence of membrane-free microcompartments resulting from crowding-induced liquid/liquid phase separation (LLPS) on the dynamic spatial organization of FtsZ, the main component of the bacterial division machinery, has been studied using several LLPS systems. The GTP-dependent assembly cycle of FtsZ is thought to be crucial for the formation of the septal ring, which is highly regulated in time and space. We found that FtsZ accumulates in one of the phases and/or at the interface, depending on the system composition and on the oligomerization state of the protein. These results were observed both in bulk LLPS and in lipid-stabilized, phase-separated aqueous microdroplets. The visualization of the droplets revealed that both the location and structural arrangement of FtsZ filaments is determined by the nature of the LLPS. Relocation upon depolymerization of the dynamic filaments suggests the protein may shift among microenvironments in response to changes in its association state. The existence of these dynamic compartments driven by phase transitions can alter the local composition and reactivity of FtsZ during its life cycle acting as a nonspecific modulating factor of cell function.

FtsZ Polymers Tethered to the Membrane by ZipA Are Susceptible to Spatial Regulation by Min Waves

Bacterial cell division is driven by an FtsZ ring in which the FtsZ protein localizes at mid-cell and recruits other proteins, forming a divisome. In Escherichia coli, the first molecular assembly of the divisome, the proto-ring, is formed by the association of FtsZ polymers to the cytoplasmic membrane through the membrane-tethering FtsA and ZipA proteins. The MinCDE system plays a major role in the site selection of the division ring because these proteins oscillate from pole to pole in such a way that the concentration of the FtsZ-ring inhibitor, MinC, is minimal at the cell center, thus favoring FtsZ assembly in this region. We show that MinCDE drives the formation of waves of FtsZ polymers associated to bilayers by ZipA, which propagate as antiphase patterns with respect to those of Min as revealed by confocal fluorescence microscopy. The emergence of these FtsZ waves results from the displacement of FtsZ polymers from the vicinity of the membrane by MinCD, which efficiently competes with ZipA for the C-terminal region of FtsZ, a central hub for multiple interactions that are essential for division. The coupling between FtsZ polymers and Min is enhanced at higher surface densities of ZipA or in the presence of crowding agents that favor the accumulation of FtsZ polymers near the membrane. The association of FtsZ polymers to the membrane modifies the response of FtsZ to Min, and comigrating Min-FtsZ waves are observed when FtsZ is free in solution and not attached to the membrane by ZipA. Taken together, our findings show that the dynamic Min patterns modulate the spatial distribution of FtsZ polymers in controlled minimal membranes. We propose that ZipA plays an important role in mid-cell recruitment of FtsZ orchestrated by MinCDE.

Charged Molecules Modulate the Volume Exclusion Effects Exerted by Crowders on FtsZ Polymerization

We have studied the influence of protein crowders, either combined or individually, on the GTP-induced FtsZ cooperative assembly, crucial for the formation of the dynamic septal ring and, hence, for bacterial division. It was earlier demonstrated that high concentrations of inert polymers like Ficoll 70, used to mimic the crowded cellular interior, favor the assembly of FtsZ into bundles with slow depolymerization. We have found, by fluorescence anisotropy together with light scattering measurements, that the presence of protein crowders increases the tendency of FtsZ to polymerize at micromolar magnesium concentration, being the effect larger with ovomucoid, a negatively charged protein. Neutral polymers and a positively charged protein also diminished the critical concentration of assembly, the extent of the effect being compatible with that expected according to pure volume exclusion models. FtsZ polymerization was also observed to be strongly promoted by a negatively charged polymer, DNA, and by some unrelated polymers like PEGs at concentrations below the crowding regime. The influence of mixed crowders mimicking the heterogeneity of the intracellular environment on the tendency of FtsZ to assemble was also studied and nonadditive effects were found to prevail. Far from exactly reproducing the bacterial cytoplasm environment, this approach serves as a simplified model illustrating how its intrinsically crowded and heterogeneous nature may modulate FtsZ assembly into a functional Z-ring.

Evidence That Bacteriophage λ Kil Peptide Inhibits Bacterial Cell Division by Disrupting FtsZ Protofilaments and Sequestering Protein Subunits

The effects of Kil peptide from bacteriophage λ on the assembly of Escherichia coli FtsZ into one subunit thick protofilaments were studied using combined biophysical and biochemical methods. Kil peptide has recently been identified as the factor from bacteriophage λ responsible for the inhibition of bacterial cell division during lytic cycle, targeting FtsZ polymerization. Here, we show that this antagonist blocks FtsZ assembly into GTP-dependent protofilaments, producing a wide distribution of smaller oligomers compared with the average size of the intact protofilaments. The shortening of FtsZ protofilaments by Kil is detectable at concentrations of the peptide in the low micromolar range, the mid-point of the inhibition being close to its apparent affinity for GDP-bound FtsZ. This antagonist not only interferes with FtsZ assembly but also reverses the polymerization reaction. The negative regulation by Kil significantly reduces the GTPase activity of FtsZ protofilaments, and FtsZ polymers assembled in guanosine-5'-[(α,β)-methyleno]triphosphate are considerably less sensitive to Kil. Our results suggest that, at high concentrations, Kil may use an inhibition mechanism involving the sequestration of FtsZ subunits, similar to that described for other inhibitors like the SOS response protein SulA or the moonlighting enzyme OpgH. This mechanism is different from those employed by the division site selection antagonists MinC and SlmA. This work provides new insight into the inhibition of FtsZ assembly by phages, considered potential tools against bacterial infection.

MinC protein shortens FtsZ protofilaments by preferentially interacting with GDP-bound subunits

The interaction of MinC with FtsZ and its effects on FtsZ polymerization were studied under close to physiological conditions by a combination of biophysical methods. The Min system is a widely conserved mechanism in bacteria that ensures the correct placement of the division machinery at midcell. MinC is the component of this system that effectively interacts with FtsZ and inhibits the formation of the Z-ring. Here we report that MinC produces a concentration-dependent reduction in the size of GTP-induced FtsZ protofilaments (FtsZ-GTP) as demonstrated by analytical ultracentrifugation, dynamic light scattering, fluorescence correlation spectroscopy, and electron microscopy. Our experiments show that, despite being shorter, FtsZ protofilaments maintain their narrow distribution in size in the presence of MinC. The protein had the same effect regardless of its addition prior to or after FtsZ polymerization. Fluorescence anisotropy measurements indicated that MinC bound to FtsZ-GDP with a moderate affinity (apparent KD ∼10 μM at 100 mm KCl and pH 7.5) very close to the MinC concentration corresponding to the midpoint of the inhibition of FtsZ assembly. Only marginal binding of MinC to FtsZ-GTP protofilaments was observed by analytical ultracentrifugation and fluorescence correlation spectroscopy. Remarkably, MinC effects on FtsZ-GTP protofilaments and binding affinity to FtsZ-GDP were strongly dependent on ionic strength, being severely reduced at 500 mM KCl compared with 100 mM KCl. Our results support a mechanism in which MinC interacts with FtsZ-GDP, resulting in smaller protofilaments of defined size and having the same effect on both preassembled and growing FtsZ protofilaments.