Selected publications

Azulay DN, Ghrayeb M, Ktorza IBS, Nir I, Nasser R, Harel YS, Chai L. Colloidal-like aggregation of a functional amyloid protein. Physical Chemistry Chemical Physics [Internet]. 2020;22 :23286-23294. Publisher's VersionAbstract

Functional amyloid proteins are self-secreted by microbial cells that aggregate into extracellular networks and provide microbial colonies with mechanical stability and resistance to antibiotic treatment. In order to understand the formation mechanism of functional amyloid networks, their aggregation has been studied in vitro under different physical conditions, such as temperature, salt concentration, and pH. Typical aggregates' morphologies include fibers or plaques, the latter resembling amyloid aggregates in neurodegenerated brains. Here, we studied the pH-reduction-induced aggregation of TasA, an extracellular functional amyloid appearing as fibers in biofilms of the soil bacterium, Bacillus subtilis. We used turbidity and zeta potential measurements, electron microscopy, atomic force microscopy, and static light scattering measurements, to characterize the aggregates of TasA and to compare them with colloidal aggregates. We further studied the aggregation of TasA in the presence of negatively charged nanoparticles and showed that nanoparticles co-aggregated with TasA, and that the co-aggregation was hindered sterically. Based on these studies, we concluded that, similarly to colloidal aggregation, TasA aggregation occurs due to surface potential modulations and that the aggregation is followed by a rearrangement process. Shedding light on the aggregation mechanism of TasA, our results can be used for the design of TasA aggregation inhibitors and promoters.

Nir I, Lybman A, Hayet S, Azulay DN, Ghrayeb M, Liddaweih S, Chai L. Bacillus subtilis biofilms characterized as hydrogels. Insights on water uptake and water binding in biofilms. Soft Matter [Internet]. 2020. Publisher's VersionAbstract

Biofilms are aggregates of cells that form on surfaces or at the air-water interface. Cells in a biofilm are encased in a self-secreted extracellular matrix (ECM) that provides them with mechanical stability and protects them from antibiotic treatment. From a soft matter perspective, biofilms are regarded as colloidal hydrogels, with the cells playing the role of colloids and the ECM compared with a cross-linked hydrogel. Here, we examined whole biofilms of the soil bacterium Bacillus subtilis utilizing methods that are commonly used to characterize hydrogels in order to evaluate the uptake of water and the water properties in the biofilms. Specifically, we studied wild-type as well ECM mutants, lacking the protein TasA and the exopolysaccharide (EPS). We characterized the morphology and mesh size of biofilms using electron microscopy, studied the state of water in the biofilms using differential scanning calorimetry, and finally, we tested the biofilms' swelling properties. Our study revealed that Bacillus subtilis biofilms resemble cross-linked hydrogels is their morphology and swelling properties. Strikingly, we discovered that all the water in biofilms was bound water and there was no free water in the biofilms. Water binding was mostly related with the presence of solutes and much less so with the major ECM components, the protein TasA and the polysaccharide EPS. This study sheds light on water uptake and water binding in biofilms and it is therefore important for the understanding of solute transport and enzymatic function inside biofilms.

Lester-Zer N, Ghrayeb M, Chai L. Nanomechanical properties of steric zipper globular structures. Proceedings of the National Academy of Sciences of the United States of America [Internet]. 2019. Publisher's VersionAbstract

The term amyloid defines a group of proteins that aggregate into plaques or fibers. Amyloid fibers gained their fame mostly due to their relation with neurodegenerative diseases in humans. However, secreted by lower organisms, such as bacteria and fungi, amyloid fibers play a functional role: for example, when they serve as cement in the extracellular matrix of biofilms. Originating either in humans or in microorganisms, the sequence of amyloid proteins is decorated with hexapeptides with high propensity to form fibers, known as steric zippers. We have found that steric zippers form globular structures on route to making fibers and exhibit a characteristic force–distance (F-D) fingerprint when pulled with an atomic force microscope (AFM) tip. Particularly, the F-D pulling curves showed force plateau steps, suggesting that the globular structures were composed of chains that were unwound like a yarn ball. Force plateau analysis showed that the F-D characteristic parameters were sequence sensitive, representing differences in the packing of the hexapeptides within the globules. These unprecedented findings show that steric zippers exhibit a characteristic nanomechanical signature in solution in addition to previously observed characteristic crystallographic structure. Getting to the fundamental interactions that govern the unzipping of full-length amyloid fibers may initiate the development of antiamyloid methods that target the physical in addition to the structural properties of steric zippers.

Azulay DN, Chai L. Calcium Carbonate Formation in the Presence of Biopolymeric Additives. Journal of Visualized Experiments [Internet]. 2019;(147). Publisher's VersionAbstract

Biomineralization is the formation of minerals in the presence of organic molecules, often related with functional and/or structural roles in living organisms. It is a complex process and therefore a simple, in vitro, system is required to understand the effect of isolated molecules on the biomineralization process. In many cases, biomineralization is directed by biopolymers in the extracellular matrix. In order to evaluate the effect of isolated biopolymers on the morphology and structure of calcite in vitro, we have used the vapor diffusion method for the precipitation of calcium carbonate, scanning electron microscopy and micro Raman for the characterization, and ultraviolet-visible (UV/Vis) absorbance for measuring the quantity of a biopolymer in the crystals. In this method, we expose the isolated biopolymers, dissolved in a calcium chloride solution, to gaseous ammonia and carbon dioxide that originate from the decomposition of solid ammonium carbonate. Under the conditions where the solubility product of calcium carbonate is reached, calcium carbonate precipitates and crystals are formed. Calcium carbonate has different polymorphs that differ in their thermodynamic stability: amorphous calcium carbonate, vaterite, aragonite, and calcite. In the absence of biopolymers, under clean conditions, calcium carbonate is mostly present in the calcite form, which is the most thermodynamically stable polymorph of calcium carbonate. This method examines the effect of the biopolymeric additives on the morphology and structure of calcium carbonate crystals. Here, we demonstrate the protocol through the study of an extracellular bacterial protein, TapA, on the formation of calcium carbonate crystals. Specifically, we focus on the experimental set up, and characterization methods, such as optical and electron microscopy as well as Raman spectroscopy.

Abbasi R, Mousa R, Dekel N, Amartely H, Danieli T, Lebendiker M, Levi-Kalisman Y, Shalev DE, Metanis N, Chai L. The bacterial extracellular matrix protein TapA is a two‐domain partially disordered protein. CHEMBIOCHEM [Internet]. 2018. Publisher's VersionAbstract

Biofilms are aggregates of microbial cells that form on surfaces and at interfaces and are encased in an extracellular matrix. In biofilms made by the soil bacterium Bacillus subtilis, the protein TapA mediates the assembly of the functional amyloid protein TasA into extracellular fibers and it also anchors these fibers to the cell surface. Here we used circular dichroism and NMR to show that, unlike the structured TasA, TapA is disordered. In addition, TapA is composed of two weakly interacting domains, a disordered C‐terminal domain and a more structured N‐terminal domain. These two domains also exhibited different structural changes in response to changes in external conditions, such as increased temperatures and the presence of lipid vesicles. While the two TapA domains weakly interacted in solution, their cooperative interaction with lipid vesicles prevented the vesicles' disruption, that was otherwise observed in the presence of the C‐terminal domain alone. Our findings therefore suggest that the two‐domain composition of TapA is important for its interaction with a single or with multiple partners in the extracellular matrix in biofilms.

Azulay DN, Abbasi R, Ktorza IBS, Remennik S, M AR, Chai L. Biopolymers from a Bacterial Extracellular Matrix Affect the Morphology and Structure of Calcium Carbonate Crystals. Crystal Growth and Design [Internet]. 2018;18 (9) :5582–5591. Publisher's VersionAbstract

Biomineralization is a mineral precipitation process occurring in the presence of organic molecules and used by various organisms to serve a structural and/or a functional role. Many biomineralization processes occur in the presence of extracellular matrices that are composed of proteins and polysaccharides. Recently, there is growing evidence that bacterial biofilms induce CaCO3 mineralization and that this process may be related with their extracellular matrix (ECM). In this study we explore, in vitro, the effect of two bacterial ECM proteins, TasA and TapA, and an exopolysaccharide, EPS, on calcium carbonate crystallization. We have found that all the three biopolymers induce the formation of complex CaCO3 structures. The crystals formed in the presence of the EPS are very diverse in morphology and they are either calcite or vaterite in structure. However, more uniformly sized calcite crystals are formed in the presence of the proteins; these crystals are composed of single crystalline domains that assemble together into spherulites (in the presence of TapA) or dumbbell-like shapes (in the presence of TasA). Our results suggest the EPS affects the nucleation of calcium carbonate when it induces the formation of vaterite crystals and that unlike EPS, the proteins stabilize preformed calcite nuclei and induce their aggregation into complex calcite structures. Biomineralization processes induced by bacterial ECM macromolecules make biofilms more robust and difficult to remove when they form, for example, on pipes and filters in water desalination systems or on ship hulls. Understanding the formation conditions and mechanism of formation of calcium carbonate in the presence of bacterial biopolymers may lead to the design of suitable mineralization inhibitors.

Malishev R, Abassi R, Jelinek R, Chai L. Bacterial model membranes reshape fibrillation of a functional amyloid protein. Biochemistry [Internet]. 2018;57 (35) :5230–5238. Publisher's VersionAbstract

Biofilms are aggregates of cells that form surface-associated communities. The cells in biofilms are interconnected with an extracellular matrix, a network that is made mostly of polysaccharides, proteins, and sometimes nucleic acids. Some extracellular matrix proteins form fibers, termed functional amyloid or amyloid-like, to differentiate their constructive function from disease-related amyloid fibers. Recent functional amyloid assembly studies have neglected their interaction with membranes, despite their native formation in a cellular environment. Here, we use TasA, a major matrix protein in biofilms of the soil bacterium Bacillus subtilis, as a model functional amyloid protein and ask whether the bacterial functional amyloid interacts with membranes. Using biochemical, spectroscopic, and microscopic tools, we show that TasA interacts distinctively with bacterial model membranes and that this interaction mutually influences the morphology and structure of the protein and the membranes. At the protein level, fibers of similar structure and morphology are formed in the absence of membranes and in the presence of eukaryotic model membranes. However, in the presence of bacterial model membranes, TasA forms disordered aggregates with a different β sheet signature. At the membrane level, fluorescence microscopy and anisotropy measurements indicate that bacterial membranes deform more considerably than eukaryotic membranes upon interaction with TasA. Our findings suggest that TasA penetrates bacterial more than eukaryotic model membranes and that this leads to membrane disruption and to reshaping the TasA fiber formation pathway. Considering the important role of TasA in providing integrity to biofilms, our study may direct the design of antibiofilm drugs to the protein–membrane interface.

TalStern, Kaner I, Zer NL, Shoval H, Dror D, Manevitch Z, Chai L, Brill-Karniely Y, Benny O. Rigidity of polymer micelles affects interactions with tumor cells. Journal of Controlled Release [Internet]. 2017;257 :40-50. Publisher's VersionAbstract

Controlling the interaction of drug delivery systems (DDS) with tissues is critical for the success of therapies. Specifically in cancer, due to the high density of the tumors, tissue penetration of DDS is critical and may be challenging. In previous work we have shown that Solidified Polymer Micelles (SPMs) rapidly internalize into cells and tissues. Using AFM analysis, in the present work we measured differences in rigidity of SPM compared with Wet Polymer Micelles (WPM). We further examined whether the semi-solid form of hydrated SPMs has an effect on the interaction with tumor cells both in mono-layer systems and in multi-layer clusters of cells as spheroids. For that we have performed detailed characterization of SPM compared to WPM, including examinations of particle size, stability, drug release kinetics and cell transcytosis, in melanoma A-375 cells. Cell uptake measurements were done using fluorescent signal analysis, FACS and microscopy imaging, showing enhanced abilities of SPMs to penetrate cells and tissues. A simple physical model is presented that well agrees with the experiments and provides insight about the role of particle rigidity in the engulfment mechanism. We conclude that particle rigidity enhances cellular uptake and tissue penetration and that SPMs have a promising potential as an effective and highly permeable DDS. Our findings can be important in future rational design of DDS for particle adjustment to specific tissues and pathologies.

Chai L, Romero D, Kayatekin C, Akabayov B, Vlamakis H, Losick R, Kolter R. Isolation, characterization, and aggregation of a structured bacterial matrix precursor. Journal of Biological Chemistry [Internet]. 2013;288 :17559-17568. Publisher's VersionAbstract

Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms.

Chai L, Vlamakis H, Kolter R. Extracellular signal regulation of cell differentiation in biofilms. MRS Bulletin [Internet]. 2011;36 (5) :374-379. Publisher's VersionAbstract

Bacteria often live in the form of surface-associated communities of cells termed biofilms. Within biofilms, there is a division of labor in which genetically identical cells differentiate to serve distinct functions. This cellular differentiation results from a response to extracellular signals that occur due to changes in the local environment of a cell or in response to signaling molecules that the cells themselves produce. In this review, we discuss differentiation in biofilms, focusing on the molecular mechanisms that regulate differentiation in the bacterium Bacillus subtilis. In this organism, there is a subpopulation of cells within a biofilm that produces a signal, while a different subpopulation of cells responds to it. Studying what signals cells use to communicate with each other within a biofilm will allow for better design of strategies to prevent and disrupt biofilms.