Structural basis for the role of serine-rich repeat proteins from Lactobacillus reuteri in gut microbe-host interactions.

Lactobacillus reuteri, a Gram-positive bacterial species inhabiting the gastrointestinal tract of vertebrates, displays remarkable host adaptation. Previous mutational analyses of rodent strain L. reuteri 100-23C identified a gene encoding a predicted surface-exposed serine-rich repeat protein (SRRP100-23) that was vital for L. reuteri biofilm formation in mice. SRRPs have emerged as an important group of surface proteins on many pathogens, but no structural information is available in commensal bacteria. Here we report the 2.00-Å and 1.92-Å crystal structures of the binding regions (BRs) of SRRP100-23 and SRRP53608 from L. reuteri ATCC 53608, revealing a unique ß-solenoid fold in this important adhesin family. SRRP53608-BR bound to host epithelial cells and DNA at neutral pH and recognized polygalacturonic acid (PGA), rhamnogalacturonan I, or chondroitin sulfate A at acidic pH. Mutagenesis confirmed the role of the BR putative binding site in the interaction of SRRP53608-BR with PGA. Long molecular dynamics simulations showed that SRRP53608-BR undergoes a pH-dependent conformational change. Together, these findings provide mechanistic insights into the role of SRRPs in host-microbe interactions and open avenues of research into the use of biofilm-forming probiotics against clinically important pathogens.

Nanomechanics of Pectin-Linked ß-Lactoglobulin Nanofibril Bundles.

Nanofibrils of ß-lactoglobulin can be assembled into bundles by site-specific noncovalent cross-linking with high-methoxyl pectin (Hettiarachchi et al. Soft Matter 2016, 12, 756). Here we characterized the nanomechanical properties of bundles using atomic force microscopy and force spectroscopy. Bundles had Gaussian cross sections and a mean height of 17.4 ± 1.4 nm. Persistence lengths were calculated using image analysis with the mean-squared end-to-end model. The relationship between the persistence length and the thickness had exponents of 1.69-2.30, which is consistent with previous reports for other fibril types. In force spectroscopy experiments, the bundles stretched in a qualitatively different manner to fibrils, and some of the force curves were consistent with peeling fibrils away from bundles. The flexibility of pectin-linked nanofibril bundles is likely to be tunable by modulating the stiffness and length of fibrils and the ratio of pectin to fibrils, giving rise to a wide range of structures and functionalities.

A novel mycovirus from Aspergillus fumigatus contains four unique dsRNAs as its genome and is infectious as dsRNA.

We report the discovery and characterization of a double-stranded RNA (dsRNA) mycovirus isolated from the human pathogenic fungus Aspergillus fumigatus, Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1), which reveals several unique features not found previously in positive-strand RNA viruses, including the fact that it represents the first dsRNA (to our knowledge) that is not only infectious as a purified entity but also as a naked dsRNA. The AfuTmV-1 genome consists of four capped dsRNAs, the largest of which encodes an RNA-dependent RNA polymerase (RdRP) containing a unique GDNQ motif normally characteristic of negative-strand RNA viruses. The third largest dsRNA encodes an S-adenosyl methionine-dependent methyltransferase capping enzyme and the smallest dsRNA a P-A-S-rich protein that apparently coats but does not encapsidate the viral genome as visualized by atomic force microscopy. A combination of a capping enzyme with a picorna-like RdRP in the AfuTmV-1 genome is a striking case of chimerism and the first example (to our knowledge) of such a phenomenon. AfuTmV-1 appears to be intermediate between dsRNA and positive-strand ssRNA viruses, as well as between encapsidated and capsidless RNA viruses.

Getting the feel of food structure with atomic force microscopy.

This article describes the progress in the development of the atomic force microscope as an imaging tool and a force transducer, with particular reference to applications in food science. Use as an imaging tool has matured and emphasis is placed on the novel insights gained from the use of the technique to study food macromolecules and food colloids, and the subsequent applications of this new knowledge in food science. Use as a force transducer is still emerging and greater emphasis is given on the methodology and analysis. Where available, applications of force measurements between molecules or between larger colloidal particles are discussed, where they have led to new insights or solved problems related to food science. The future prospects of the technique in imaging or through force measurements are discussed.

Use of Atomic Force Microscopy to Study the Multi-Modular Interaction of Bacterial Adhesins to Mucins.

The mucus layer covering the gastrointestinal (GI) epithelium is critical in selecting and maintaining homeostatic interactions with our gut bacteria. However, the molecular details of these interactions are not well understood. Here, we provide mechanistic insights into the adhesion properties of the canonical mucus-binding protein (MUB), a large multi-repeat cell-surface adhesin found in Lactobacillus inhabiting the GI tract. We used atomic force microscopy to unravel the mechanism driving MUB-mediated adhesion to mucins. Using single-molecule force spectroscopy we showed that MUB displayed remarkable adhesive properties favouring a nanospring-like adhesion model between MUB and mucin mediated by unfolding of the multiple repeats constituting the adhesin. We obtained direct evidence for MUB self-interaction; MUB-MUB followed a similar binding pattern, confirming that MUB modular structure mediated such mechanism. This was in marked contrast with the mucin adhesion behaviour presented by Galectin-3 (Gal-3), a mammalian lectin characterised by a single carbohydrate binding domain (CRD). The binding mechanisms reported here perfectly match the particular structural organization of MUB, which maximizes interactions with the mucin glycan receptors through its long and linear multi-repeat structure, potentiating the retention of bacteria within the outer mucus layer.

Structure and biosynthesis of two exopolysaccharides produced by Lactobacillus johnsonii FI9785.

Exopolysaccharides were isolated and purified from Lactobacillus johnsonii FI9785, which has previously been shown to act as a competitive exclusion agent to control Clostridium perfringens in poultry. Structural analysis by NMR spectroscopy revealed that L. johnsonii FI9785 can produce two types of exopolysaccharide: EPS-1 is a branched dextran with the unusual feature that every backbone residue is substituted with a 2-linked glucose unit, and EPS-2 was shown to have a repeating unit with the following structure: -6)-α-Glcp-(1-3)-ß-Glcp-(1-5)-ß-Galf-(1-6)-α-Glcp-(1-4)-ß-Galp-(1-4)-ß-Glcp-(1-. Sites on both polysaccharides were partially occupied by substituent groups: 1-phosphoglycerol and O-acetyl groups in EPS-1 and a single O-acetyl group in EPS-2. Analysis of a deletion mutant (ΔepsE) lacking the putative priming glycosyltransferase gene located within a predicted eps gene cluster revealed that the mutant could produce EPS-1 but not EPS-2, indicating that epsE is essential for the biosynthesis of EPS-2. Atomic force microscopy confirmed the localization of galactose residues on the exterior of wild type cells and their absence in the ΔepsE mutant. EPS2 was found to adopt a random coil structural conformation. Deletion of the entire 14-kb eps cluster resulted in an acapsular mutant phenotype that was not able to produce either EPS-2 or EPS-1. Alterations in the cell surface properties of the EPS-specific mutants were demonstrated by differences in binding of an anti-wild type L. johnsonii antibody. These findings provide insights into the biosynthesis and structures of novel exopolysaccharides produced by L. johnsonii FI9785, which are likely to play an important role in biofilm formation, protection against harsh environment of the gut, and colonization of the host.

Structural basis for adaptation of lactobacilli to gastrointestinal mucus.

The mucus layer covering the gastrointestinal (GI) epithelium is critical in selecting and maintaining homeostatic interactions with our gut bacteria. However, the underpinning mechanisms of these interactions are not understood. Here, we provide structural and functional insights into the canonical mucus-binding protein (MUB), a multi-repeat cell-surface adhesin found in Lactobacillus inhabitants of the GI tract. X-ray crystallography together with small-angle X-ray scattering demonstrated a 'beads on a string' arrangement of repeats, generating 174 nm long protein fibrils, as shown by atomic force microscopy. Each repeat consists of tandemly arranged Ig- and mucin-binding protein (MucBP) modules. The binding of full-length MUB was confined to mucus via multiple interactions involving terminal sialylated mucin glycans. While individual MUB domains showed structural similarity to fimbrial proteins from Gram-positive pathogens, the particular organization of MUB provides a structural explanation for the mechanisms in which lactobacilli have adapted to their host niche by maximizing interactions with the mucus receptors, potentiating the retention of bacteria within the mucus layer. Together, this study reveals functional and structural features which may affect tropism of microbes across mucus and along the GI tract, providing unique insights into the mechanisms adopted by commensals and probiotics to adapt to the mucosal environment.

Trehalose-containing hydrocolloid edible films prepared in the presence of transglutaminase.

In this article, edible hydrocolloid films were prepared by using Citrus pectins and the protein phaseolin in the presence of microbial transglutaminase, an enzyme able to catalyze isopeptide bonds between endo-protein-reactive glutamine and lysine residues. For the first time, trehalose, a nonreducing homodisaccharide into which two glucose units are linked together by a α-1,1-glycosidic linkage, was used as a component of hydrocolloid films constituted of both proteins and carbohydrates. Our data have demonstrated that these films act as very effective barriers to gases, especially to CO2 . They also present a high antioxidant capability as measured by the 2,2-diphenyl-1-picrylhydrazyl scavenging assay. In addition, the films were characterized using Atomic Force Microscopy, a powerful tool used to evaluate film surface topography and roughness. The results of our experiments clearly indicate that the trehalose-containing films prepared both in the presence and absence of transglutaminase are composed of nanoparticles with a smooth surface, having similar roughness values (Rα). In conclusion, according to barrier and antioxidant properties and to their structure, it is possible to consider the trehalose-containing films as innovative bioplastics potentially able to protect different kinds of foods.

Mining the "glycocode"--exploring the spatial distribution of glycans in gastrointestinal mucin using force spectroscopy.

Mucins are the main components of the gastrointestinal mucus layer. Mucin glycosylation is critical to most intermolecular and intercellular interactions. However, due to the highly complex and heterogeneous mucin glycan structures, the encoded biological information remains largely encrypted. Here we have developed a methodology based on force spectroscopy to identify biologically accessible glycoepitopes in purified porcine gastric mucin (pPGM) and purified porcine jejunal mucin (pPJM). The binding specificity of lectins Ricinus communis agglutinin I (RCA), peanut (Arachis hypogaea) agglutinin (PNA), Maackia amurensis lectin II (MALII), and Ulex europaeus agglutinin I (UEA) was utilized in force spectroscopy measurements to quantify the affinity and spatial distribution of their cognate sugars at the molecular scale. Binding energy of 4, 1.6, and 26 aJ was determined on pPGM for RCA, PNA, and UEA. Binding was abolished by competition with free ligands, demonstrating the validity of the affinity data. The distributions of the nearest binding site separations estimated the number of binding sites in a 200-nm mucin segment to be 4 for RCA, PNA, and UEA, and 1.8 for MALII. Binding site separations were affected by partial defucosylation of pPGM. Furthermore, we showed that this new approach can resolve differences between gastric and jejunum mucins.

The adsorption-desorption behaviour and structure function relationships of bile salts.

The digestion of dietary components in the human gastrointestinal (GI) tract is a complex, dynamic, inherently heterogeneous process. A key aspect of the digestion of lipid in the GI tract is the combined action of bile salts, lipase and colipase in hydrolysing and solubilising dispersed lipid. The bile salts are a mixture of steroid acid conjugates with surfactant properties. In order to examine whether the different bile salts have different interfacial properties their dynamic interfacial behaviour was characterised. Differences in the adsorption behaviour to solid hydrophobic surfaces of bile salt species were studied using dual polarisation interferometry and atomic force microscopy (AFM) under physiological conditions. Specifically, the cholates adsorbed more slowly and a significant proportion were irreversibly adsorbed following buffer rinsing; whereas the deoxycholates and chenodeoxycholates adsorbed more rapidly and desorbed to a greater extent following buffer rinsing. The conjugating groups (taurine, glycine) did not influence the behaviour. AFM showed that the interfacial structures that remained following buffer rinsing were also different between these two groups. In addition, the adsorption-desorption behaviour affected the adsorption of colipase to a solid surface. This supports the idea that cooperative adsorption occurs between certain bile salts and colipase to facilitate the adsorption and activity of pancreatic lipase in order to restore lipolytic activity in the presence of bile salts. This study provides insights into how differences in bile salt structure could affect lipase activity and solubilisation of lipolysis products and other lipid-soluble bioactive molecules.

Controlled release of protein from viable Lactococcus lactis cells.

Overexpression of the lactococcal CsiA protein affects the cell wall integrity of growing cells and leads to leakage of intracellular material. This property was optimized and exploited for the targeted release of biologically active compounds into the extracellular environment, thereby providing a new delivery system for bacterial proteins and peptides. The effects of different levels of CsiA expression on the leakage of endogenous lactate dehydrogenase and nucleic acids were measured and related to the impact of CsiA expression on Lactococcus lactis cell viability and growth. A leakage phenotype was obtained from cells expressing both recombinant and nonrecombinant forms of CsiA. As proof of principle, we demonstrated that CsiA promotes the efficient release of the heterologous Listeria bacteriophage endolysin LM4 in its active form. Under optimized conditions, native and heterologous active-molecule release is possible without affecting cell viability. The ability of CsiA to release intracellular material by controlled lysis without the requirement for an external lytic agent provides a technology for the control of both the extent of lysis and its timing. Taken together, these results demonstrate the potential of this novel approach for applications including product recovery in industrial fermentations, food processing, and medical therapy.

Recognition of galactan components of pectin by galectin-3.

It has been reported that modified forms of pectin possess anticancer activity. To account for this bioactivity, it has been proposed that fragments of pectin molecules can act by binding to and inhibiting the various roles of the mammalian protein galectin 3 (Gal3) in cancer progression and metastasis. Despite this clear molecular hypothesis and evidence for the bioactivity of modified pectin, the structural origins of the "bioactive fragments" of pectin molecules are currently ill defined. By using a combination of fluorescence microscopy, flow cytometry, and force spectroscopy, it has been possible to demonstrate, for the first time, specific binding of a pectin galactan to the recombinant form of human Gal3. Present studies suggest that bioactivity resides in the neutral sugar side chains of pectin polysaccharides and that these components could be isolated and modified to optimize bioactivity.

Probing the in situ competitive displacement of protein by nonionic surfactant using atomic force microscopy.

Force-distance data obtained from an atomic force microscope have been used to follow the in situ displacement of beta-lactoglobulin from tetradecane droplets by Tween 20 (polyoxyethylenesorbitan monolaurate). Interpretation of the force-distance curves has shown that the slope of the region, traditionally termed the constant compliance region, is a useful indicator of droplet deformation within a given experiment. The magnitude of this slope can be used to monitor how the deformability of the droplet changes upon addition of surfactant. It has been found that, immediately after initial addition of surfactant, there is an increase in magnitude of this slope, indicating a stiffening of the droplet, attributed to a stiffening of the protein network formed at the surface of the droplet. Subsequent additions of Tween 20 reduce the magnitude of the slope until an equilibrium value is reached, where the interface becomes surfactant-dominated. These observations suggest that it is possible to monitor in situ the displacement of protein from individual oil droplets. The data have been interpreted in terms of the "orogenic" model of displacement, which is based on studies made on model interfaces. These data have been compared to those obtained using the more traditional techniques of dilatational rheology, surface loading, and surface potential measurements for analogous beta-lactoglobulin-stabilized droplets or emulsions.

Adsorption of bile salts and pancreatic colipase and lipase onto digalactosyldiacylglycerol and dipalmitoylphosphatidylcholine monolayers.

It is increasingly recognized that changes in the composition of the oil-water interface can markedly affect pancreatic lipase adsorption and function. To understand interfacial mechanisms determining lipase activity, we investigated the adsorption behavior of bile salts and pancreatic colipase and lipase onto digalactosyldiacylglycerol (DGDG) and dipalmitoylphosphatidylcholine (DPPC) monolayers at the air-water interface. The results from Langmuir trough and pendant drop experiments showed that a DGDG interface was more resistant to the adsorption of bile salts, colipase, and lipase compared to that of DPPC. Atomic force microscopy (AFM) images showed that the adsorption of bile salts into a DPPC monolayer decreased the size of the liquid condensed (LC) domains while there was no visible topographical change for DGDG systems. The results also showed that colipase and lipase adsorbed exclusively onto the mixed DPPC-bile salt regions and not the DPPC condensed phase. When the colipase and lipase were in excess, they fully covered the mixed DPPC-bile salt regions. However, the colipase and lipase coverage on the mixed DGDG-bile salt monolayer was incomplete and discontinuous. It was postulated that bile salts adsorbed into the DPPC monolayers filling the gaps between the lipid headgroups and spacing out the lipid molecules, making the lipid hydrocarbon tails more exposed to the surface. This created hydrophobic patches suitable for the binding of colipase and lipase. In contrast, bile salts adsorbed less easily into the DGDG monolayer because DGDG has a larger headgroup, which has strong intermolecular interactions and the ability to adopt different orientations at the interface. Thus, there are fewer hydrophobic patches that are of sufficient size to accommodate the colipase on the mixed DGDG-bile salt monolayer compared to the mixed DPPC-bile salt regions. The results from this work have reinforced the hypothesis that the interfacial molecular packing of lipids at the oil-water interface influences the adsorption of bile salts, colipase, and lipase, which in turn impacts the rate of lipolysis.

Mapping specific adhesive interactions on living human intestinal epithelial cells with atomic force microscopy.

Specific molecular-receptor interactions with gut epithelium cells are important in understanding bioactivity of food components and drugs, binding of commensal microflora, attachment and initiation of defense mechanisms against pathogenic bacteria and for development of targeted delivery systems to the gut. However, methods for probing such interactions are lacking. Methodology has been developed and validated to measure specific molecular-receptor interactions on living human colorectal cancer cells as in vitro models for the gut epithelium. Atomic force microscopy (AFM) was used to measure ligand-receptor interactions and to map receptor locations on cell surfaces. Measurements were made using silica beads attached to the AFM tip-cantilever assembly, which were functionalized by coupling of ligands to the bead surface. Wheat germ agglutinin (WGA) binds to the glycosylated extracellular domain III of the epidermal growth factor receptor. Methodology was tested by measuring binding of WGA to the surface of confluent monolayers of living Caco-2 human intestinal epithelial cells. The measured modal detachment force of 125 pN is typical of values expected for single molecule interactions. Adhesive events were used to map the location of binding sites on the cell surface revealing heterogeneity in their distribution within and between cells within the monolayer.

Isolation and characterization of a theta-type cryptic plasmid from Bifidobacterium longum FI10564.

A number of bifidobacterial species of human origin were screened for the presence of cryptic plasmids. One strain, Bifidobacterium longum FI10564, harbored plasmids of approximately 2.2 kb, 3.6 kb, and 4.9 kb in size. The smallest plasmid, pFI2576 (2,197 bp), was studied in detail and its complete nucleotide sequence was determined. Computer-assisted analysis of this novel plasmid (G+C content 62%) identified 9 putative open reading frames (orfs), 3 of which were shown to be probable genes. These putative genes are arranged in an operon-like structure, in which the overlapping orfs 1 and 2 encode putative Rep proteins and are highly homologous to the rep genes of the B. longum plasmid pMB1 (1,847 bp). The mechanism of replication of pFI2576 was investigated using Southern blot analysis of whole cell lysates, with and without S1 nuclease treatment, and atomic force microscopy (AFM). The results indicate that pFI2576 is likely to use the theta mode of replication.

Detection of transglucosidase-catalyzed polysaccharide synthesis on a surface in real time using surface plasmon resonance spectroscopy.

Biological systems that involve enzyme catalysis at surfaces, particularly strategically important ones that involve insoluble substrates/products such as the cell wall and the starch granule, require analyses beyond classical solution state enzymology. Using a model system, we have demonstrated the real-time measurement of transglucosidase activity on a surface using surface plasmon resonance (SPR) spectroscopy. We monitored the extension of a (partially carboxymethylated) dextran surface with alternansucrase and sucrose as a glycosyl donor. Conditions were used where surface polymer synthesis rates were a function of enzyme concentration and proportional to the extent of enzyme binding to the surface. A method to determine the turnover number of the enzyme on the surface was also developed. The presence of a new amorphous polysaccharide was observed optically, detected by lectin binding and imaged by atomic force microscopy. This surface method will have utility in a wide range of carbohydrate enzyme systems including screens.

Unravelling the nanostructure of strawberry fruit pectins by endo-polygalacturonase digestion and atomic force microscopy.

Pectins analysed by AFM are visualized as individual chains, branched or unbranched, and aggregates. To investigate the nature of these structures, sodium carbonate soluble pectins from strawberry fruits were digested with endo-polygalacturonase M2 from Aspergillus aculeatus and visualized by AFM. A gradual decrease in the length of chains was observed as result of the treatment, reaching a minimum LN value of 22nm. The branches were not visible after 2h of enzymatic incubation. The size of complexes also diminished significantly with the enzymatic digestion. A treatment to hydrolyse rhamnogalacturonan II borate diester bonds neither affected chains length or branching nor complex size but reduced the density of aggregates. These results suggest that chains are formed by a mixture of homogalacturonan and more complex molecules composed by a homogalacturonan unit linked to an endo-PG resistant unit. Homogalacturonan is a structural component of the complexes and rhamnogalacturonan II could be involved in their formation.

Structural changes in cell wall pectins during strawberry fruit development.

Strawberry (Fragaria × anannasa Duch.) is one of the most important soft fruit. Rapid loss of firmness occurs during the ripening process, resulting in a short shelf life and high economic losses. To get insight into the role of pectin matrix in the softening process, cell walls from strawberry fruit at two developmental stages, unripe-green and ripe-red, were extracted and sequentially fractionated with different solvents to obtain fractions enriched in a specific component. The yield of cell wall material as well as the per fresh weight contents of the different fractions decreased in ripe fruit. The largest reduction was observed in the pectic fractions extracted with a chelating agent (trans-1,2- diaminocyclohexane-N,N,N'N'-tetraacetic acid, CDTA fraction) and those covalently bound to the wall (extracted with Na2CO3). Uronic acid content of these two fractions also decreased significantly during ripening, but the amount of soluble pectins extracted with phenol:acetic acid:water (PAW) and water increased in ripe fruit. Fourier transform infrared spectroscopy of the different fractions showed that the degree of esterification decreased in CDTA pectins but increased in soluble fractions at ripen stage. The chromatographic analysis of pectin fractions by gel filtration revealed that CDTA, water and, mainly PAW polyuronides were depolymerised in ripe fruit. By contrast, the size of Na2CO3 pectins was not modified. The nanostructural characteristics of CDTA and Na2CO3 pectins were analysed by atomic force microscopy (AFM). Isolated pectic chains present in the CDTA fractions were significantly longer and more branched in samples from green fruit than those from red fruit. No differences in contour length were observed in Na2CO3 strands between samples of both stages. However, the percentage of branched chains decreased from 19.7% in unripe samples to 3.4% in ripe fruit. The number of pectin aggregates was higher in green fruit samples of both fractions. These results show that the nanostructural complexity of pectins present in CDTA and Na2CO3 fractions diminishes during fruit development, and this correlates with the solubilisation of pectins and the softening of the fruit.

Visualisation of xanthan conformation by atomic force microscopy.

Direct visual evidence obtained by atomic force microscopy demonstrates that when xanthan is adsorbed from aqueous solution onto the heterogeneously charged substrate mica, its helical conformation is distorted. Following adsorption it requires annealing for several hours to restore its ordered helical state. Once the helix state reforms, the AFM images obtained showed clear resolution of the periodicity with a value of 4.7nm consistent with the previously predicted models. In addition, the images also reveal evidence that the helix is formed by a double strand, a clarification of an ambiguity of the xanthan ultrastructure that has been outstanding for many years.