scholarly journals Crystalline S-Layer Protein Monolayers Induce Water Turbulences on the Nanometer Scale

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1147
Author(s):  
Rupert Tscheliessnig ◽  
Andreas Breitwieser ◽  
Uwe B. Sleytr ◽  
Dietmar Pum
Keyword(s):  
Cell Surface ◽  
Molecular Sieves ◽  
Cell Envelope ◽  
Functional Model ◽  
Ion Traps ◽  
Coarse Grained ◽  
Flow Profile ◽  
Natural Habitats ◽  
Bacterial Surface ◽  
Wide Range

Bacterial surface layers (S-layers) have been observed as the outermost cell envelope component in a wide range of bacteria and most archaea. They are one of the most common prokaryotic cell surface structures and cover the cells completely. It is assumed that S-layers provide selection advantages to prokaryotic cells in their natural habitats since they act as protective envelopes, as structures involved in cell adhesion and surface recognition, as molecular or ion traps, and as molecular sieves in the ultrafiltration range. In order to contribute to the question of the function of S-layers for the cell, we merged high-resolution cryo-EM and small-angle X-ray scattering datasets to build a coarse-grained functional model of the S-layer protein SbpA from Lysinibacillus sphaericus ATCC 4525. We applied the Navier–Stokes and the Poisson equations for a 2D section through the pore region in the self-assembled SbpA lattice. We calculated the flow field of water, the vorticity, the electrostatic potential, and the electric field of the coarse-grained model. From calculated local changes in the flow profile, evidence is provided that both the characteristic rigidity of the S-layer and the charge distribution determine its rheological properties. The strength of turbulence and pressure near the S-layer surface in the range of 10 to 50 nm thus support our hypothesis that the S-layer, due to its highly ordered repetitive crystalline structure, not only increases the exchange rate of metabolites but is also responsible for the remarkable antifouling properties of the cell surface. In this context, studies on the structure, assembly and function of S-layer proteins are promising for various applications in nanobiotechnology, biomimetics, biomedicine, and molecular nanotechnology.

scholarly journals Assembly and mechanisms of bacterial type IV secretion machines

2012 ◽  
Vol 367 (1592) ◽  
pp. 1073-1087 ◽  
Author(s):  
Ellen L. Zechner ◽  
Silvia Lang ◽  
Joel F. Schildbach
Keyword(s):  
Cell Surface ◽  
Cell Envelope ◽  
Recipient Cell ◽  
Antibiotic Resistance Genes ◽  
Effector Proteins ◽  
Type Iv Secretion ◽  
Host Cells ◽  
Type Iv ◽  
Wide Range ◽  
Cell Envelopes

Type IV secretion occurs across a wide range of prokaryotic cell envelopes: Gram-negative, Gram-positive, cell wall-less bacteria and some archaea. This diversity is reflected in the heterogeneity of components that constitute the secretion machines. Macromolecules are secreted in an ATP-dependent process using an envelope-spanning multi-protein channel. Similar to the type III systems, this apparatus extends beyond the cell surface as a pilus structure important for direct contact and penetration of the recipient cell surface. Type IV systems are remarkably versatile in that they mobilize a broad range of substrates, including single proteins, protein complexes, DNA and nucleoprotein complexes, across the cell envelope. These machines have broad clinical significance not only for delivering bacterial toxins or effector proteins directly into targeted host cells, but also for direct involvement in phenomena such as biofilm formation and the rapid horizontal spread of antibiotic resistance genes among the microbial community.

scholarly journals Discovery of Fibrillar Adhesins across Bacterial Species

2020 ◽  
Author(s):  
Vivian Monzon ◽  
Aleix Lafita ◽  
Alex Bateman
Keyword(s):  
Cell Surface ◽  
Bacterial Species ◽  
Domain Architecture ◽  
Surface Proteins ◽  
Host Cells ◽  
Bacterial Surface ◽  
Bacterial Phyla ◽  
C Terminus ◽  
Wide Range ◽  
Bacterial Proteomes

AbstractBackgroundFibrillar adhesins are long multidomain proteins attached at the cell surface and composed of at least one adhesive domain and multiple tandemly repeated domains, which build an elongated stalk that projects the adhesive domain beyond the bacterial cell surface. They are an important yet understudied class of proteins that mediate interactions of bacteria with their environment. This study aims to characterize fibrillar adhesins in a wide range of bacterial phyla and to identify new fibrillar adhesin-like proteins to improve our understanding of host-bacteria interactions.ResultsBy careful search for fibrillar adhesins in the literature and by computational analysis we identified 75 stalk domains and 24 adhesive domains. Based on the presence of these domains in the UniProt Reference Proteomes database, we identified and analysed 3,388 fibrillar adhesin-like proteins across species of the most common bacterial phyla. We found that the bacterial proteomes with the highest fraction of fibrillar adhesins include several known pathogens. We further enumerate the adhesive and stalk domain combinations found in nature and demonstrate that fibrillar adhesins have complex and variable domain architectures, which differ across species. By analysing the domain architecture of fibrillar adhesins we show that in Gram positive bacteria adhesive domains are mostly positioned at the N-terminus of the protein with the cell surface anchor at the C-terminus, while their positions are more variable in Gram negative bacteria. We provide an open repository of fibrillar adhesin-like proteins and domains to facilitate downstream studies of this class of bacterial surface proteins.ConclusionThis study provides a domain-based characterization of fibrillar adhesins and demonstrates that they are widely found across the main bacterial phyla. We have discovered numerous novel fibrillar adhesins and improved the understanding of how pathogens might adhere to and subsequently invade into host cells.

scholarly journals Adsorption of Components of the Plasma Kinin-Forming System on the Surface ofPorphyromonas gingivalisInvolves Gingipains as the Major Docking Platforms

2010 ◽  
Vol 79 (2) ◽  
pp. 797-805 ◽  
Author(s):  
Maria Rapala-Kozik ◽  
Grazyna Bras ◽  
Barbara Chruscicka ◽  
Justyna Karkowska-Kuleta ◽  
Aneta Sroka ◽  
...  
Keyword(s):  
Cell Surface ◽  
Cell Envelope ◽  
Periodontal Pathogen ◽  
Kinin System ◽  
Relative Significance ◽  
Proteolytic Activation ◽  
Bacterial Surface ◽  
Enhanced Production ◽  
Direct Binding ◽  
Kallikrein Kinin System

ABSTRACTEnhanced production of proinflammatory bradykinin-related peptides, the kinins, has been suggested to contribute to the pathogenesis of periodontitis, a common inflammatory disease of human gingival tissues. In this report, we describe a plausible mechanism of activation of the kinin-generating system, also known as the contact system or kininogen-kallikrein-kinin system, by the adsorption of its plasma-derived components such as high-molecular-mass kininogen (HK), prekallikrein (PK), and Hageman factor (FXII) to the cell surface of periodontal pathogenPorphyromonas gingivalis. The adsorption characteristics of mutant strains deficient in selected proteins of the cell envelope suggested that the surface-associated cysteine proteinases, gingipains, bearing hemagglutinin/adhesin domains (RgpA and Kgp) serve as the major platforms for HK and FXII adhesion. These interactions were confirmed by direct binding tests using microplate-immobilized gingipains and biotinylated contact factors. Other bacterial cell surface components such as fimbriae and lipopolysaccharide were also found to contribute to the binding of contact factors, particularly PK. Analysis of kinin release in plasma upon contact withP. gingivalisshowed that the bacterial surface-dependent mechanism is complementary to the previously described kinin generation system dependent on HK and PK proteolytic activation by the gingipains. We also found that severalP. gingivalisclinical isolates differed in the relative significance of these two mechanisms of kinin production. Taken together, these data show the importance of this specific type of bacterial surface-host homeostatic system interaction in periodontal infections.

scholarly journals Discovery of fibrillar adhesins across bacterial species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Vivian Monzon ◽  
Aleix Lafita ◽  
Alex Bateman
Keyword(s):  
Cell Surface ◽  
Bacterial Species ◽  
Domain Architecture ◽  
Surface Proteins ◽  
Bacterial Surface ◽  
Bacterial Phyla ◽  
Gram Positive Bacteria ◽  
Invasion Mechanisms ◽  
C Terminus ◽  
Wide Range

Abstract Background Fibrillar adhesins are long multidomain proteins that form filamentous structures at the cell surface of bacteria. They are an important yet understudied class of proteins composed of adhesive and stalk domains that mediate interactions of bacteria with their environment. This study aims to characterize fibrillar adhesins in a wide range of bacterial phyla and to identify new fibrillar adhesin-like proteins to improve our understanding of host-bacteria interactions. Results Through careful literature and computational searches, we identified 82 stalk and 27 adhesive domain families in fibrillar adhesins. Based on the presence of these domains in the UniProt Reference Proteomes database, we identified and analysed 3,542 fibrillar adhesin-like proteins across species of the most common bacterial phyla. We further enumerate the adhesive and stalk domain combinations found in nature and demonstrate that fibrillar adhesins have complex and variable domain architectures, which differ across species. By analysing the domain architecture of fibrillar adhesins, we show that in Gram positive bacteria, adhesive domains are mostly positioned at the N-terminus and cell surface anchors at the C-terminus of the protein, while their positions are more variable in Gram negative bacteria. We provide an open repository of fibrillar adhesin-like proteins and domains to enable further studies of this class of bacterial surface proteins. Conclusion This study provides a domain-based characterization of fibrillar adhesins and demonstrates that they are widely found in species across the main bacterial phyla. We have discovered numerous novel fibrillar adhesins and improved our understanding of pathogenic adhesion and invasion mechanisms.

scholarly journals Continuous, Topologically Guided Protein Crystallization Controls Bacterial Surface Layer Self-Assembly

2019 ◽  
Author(s):  
Colin J. Comerci ◽  
Jonathan Herrmann ◽  
Joshua Yoon ◽  
Fatemeh Jabbarpour ◽  
Xiaofeng Zhou ◽  
...  
Keyword(s):  
Surface Layer ◽  
Cell Surface ◽  
Self Assembly ◽  
Cell Envelope ◽  
Protein Crystallization ◽  
Bacterial Surface ◽  
Cell Surface Structures ◽  
Complicated Topology ◽  
Layer Assembly

AbstractBacteria assemble the cell envelope using localized enzymes to account for growth and division of a topologically complicated surface1–3. However, a regulatory pathway has not been identified for assembly and maintenance of the surface layer (S-layer), a 2D crystalline protein coat surrounding the curved 3D surface of a variety of bacteria4,5. By specifically labeling, imaging, and tracking native and purified RsaA, the S-layer protein (SLP) fromC. crescentus, we show that protein self-assembly alone is sufficient to assemble and maintain the S-layerin vivo. By monitoring the location of newly produced S-layer on the surface of living bacteria, we find that S-layer assembly occurs independently of the site of RsaA secretion and that localized production of new cell wall surface area alone is insufficient to explain S-layer assembly patterns. When the cell surface is devoid of a pre-existing S-layer, the location of S-layer assembly depends on the nucleation characteristics of SLP crystals, which grow by capturing RsaA molecules freely diffusing on the outer bacterial surface. Based on these observations, we propose a model of S-layer assembly whereby RsaA monomers are secreted randomly and diffuse on the lipopolysaccharide (LPS) outer membrane until incorporated into growing 2D S-layer crystals. The complicated topology of the cell surface enables formation of defects, gaps, and grain boundaries within the S-layer lattice, thereby guiding the location of S-layer assembly without enzymatic assistance. This unsupervised mechanism poses unique challenges and advantages for designing treatments targeting cell surface structures or utilizing S-layers as self-assembling macromolecular nanomaterials. As an evolutionary driver, 2D protein self-assembly rationalizes the exceptional S-layer subunit sequence and species diversity6.

scholarly journals Patterns in Nature—S-Layer Lattices of Bacterial and Archaeal Cells

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 869
Author(s):  
Dietmar Pum ◽  
Andreas Breitwieser ◽  
Uwe B. Sleytr
Keyword(s):  
Cell Envelope ◽  
Hexagonal Lattice ◽  
Basic Research ◽  
Surface Layers ◽  
Uniform Size ◽  
Bacterial Surface ◽  
Wide Range ◽  
Cell Dimensions ◽  
Size And Morphology ◽  
Unit Cell Dimensions

Bacterial surface layers (S-layers) have been observed as the outermost cell envelope component in a wide range of bacteria and most archaea. S-layers are monomolecular lattices composed of a single protein or glycoprotein species and have either oblique, square or hexagonal lattice symmetry with unit cell dimensions ranging from 3 to 30 nm. They are generally 5 to 10 nm thick (up to 70 nm in archaea) and represent highly porous protein lattices (30–70% porosity) with pores of uniform size and morphology in the range of 2 to 8 nm. Since S-layers can be considered as one of the simplest protein lattices found in nature and the constituent units are probably the most abundantly expressed proteins on earth, it seems justified to briefly review the different S-layer lattice types, the need for lattice imperfections and the discussion of S-layers from the perspective of an isoporous protein network in the ultrafiltration region. Finally, basic research on S-layers laid the foundation for applications in biotechnology, synthetic biology, and biomimetics.

In vitro assembly of 2-D crystals from partially purified EA1 protein secreted by Bacillus anthracis strain Delta Sterne-1

1994 ◽  
Vol 52 ◽  
pp. 276-277
Author(s):  
Mary Beth Downs ◽  
Wilson Ribot ◽  
Joseph W. Farchaus
Keyword(s):  
Cell Wall ◽  
Molecular Sieves ◽  
Cell Envelope ◽  
Single Species ◽  
Supporting Cell ◽  
Surface Layers ◽  
Rabbit Igg ◽  
In Vitro Assembly ◽  
Covalently Linked

Many bacteria possess surface layers (S-layers) that consist of a two-dimensional protein lattice external to the cell envelope. These S-layer arrays are usually composed of a single species of protein or glycoprotein and are not covalently linked to the underlying cell wall. When removed from the cell, S-layer proteins often reassemble into a lattice identical to that found on the cell, even without supporting cell wall fragments. S-layers exist at the interface between the cell and its environment and probably serve as molecular sieves that exclude destructive macromolecules while allowing passage of small nutrients and secreted proteins. Some S-layers are refractory to ingestion by macrophages and, generally, bacteria are more virulent when S-layers are present.When grown in rich medium under aerobic conditions, B. anthracis strain Delta Sterne-1 secretes large amounts of a proteinaceous extractable antigen 1 (EA1) into the growth medium. Immunocytochemistry with rabbit polyclonal anti-EAl antibody made against the secreted protein and gold-conjugated goat anti-rabbit IgG showed that EAI was localized at the cell surface (fig 1), which suggests its role as an S-layer protein.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

scholarly journals Predictive modelling of soils’ hydraulic conductivity using artificial neural network and multiple linear regression

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Charles Gbenga Williams ◽  
Oluwapelumi O. Ojuri
Keyword(s):  
Neural Network ◽  
Artificial Neural Network ◽  
Hydraulic Conductivity ◽  
Linear Regression ◽  
Multiple Linear Regression ◽  
Coarse Grained ◽  
Soil Types ◽  
Wide Range ◽  
Artificial Neural ◽  
Input Variables

AbstractAs a result of heterogeneity nature of soils and variation in its hydraulic conductivity over several orders of magnitude for various soil types from fine-grained to coarse-grained soils, predictive methods to estimate hydraulic conductivity of soils from properties considered more easily obtainable have now been given an appropriate consideration. This study evaluates the performance of artificial neural network (ANN) being one of the popular computational intelligence techniques in predicting hydraulic conductivity of wide range of soil types and compared with the traditional multiple linear regression (MLR). ANN and MLR models were developed using six input variables. Results revealed that only three input variables were statistically significant in MLR model development. Performance evaluations of the developed models using determination coefficient and mean square error show that the prediction capability of ANN is far better than MLR. In addition, comparative study with available existing models shows that the developed ANN and MLR in this study performed relatively better.

scholarly journals Adjustment models for multivariate geodetic time series with vector-autoregressive errors

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Boris Kargoll ◽  
Alexander Dorndorf ◽  
Mohammad Omidalizarandi ◽  
Jens-André Paffenholz ◽  
Hamza Alkhatib
Keyword(s):  
Least Squares Method ◽  
Functional Model ◽  
Expectation Maximization Algorithm ◽  
Two Dimensions ◽  
Vector Autoregressive ◽  
Wide Range ◽  
Engineering Geodesy ◽  
Cross Correlations ◽  
T Distribution ◽  
Multivariate T

Abstract In this contribution, a vector-autoregressive (VAR) process with multivariate t-distributed random deviations is incorporated into the Gauss-Helmert model (GHM), resulting in an innovative adjustment model. This model is versatile since it allows for a wide range of functional models, unknown forms of auto- and cross-correlations, and outlier patterns. Subsequently, a computationally convenient iteratively reweighted least squares method based on an expectation maximization algorithm is derived in order to estimate the parameters of the functional model, the unknown coefficients of the VAR process, the cofactor matrix, and the degree of freedom of the t-distribution. The proposed method is validated in terms of its estimation bias and convergence behavior by means of a Monte Carlo simulation based on a GHM of a circle in two dimensions. The methodology is applied in two different fields of application within engineering geodesy: In the first scenario, the offset and linear drift of a noisy accelerometer are estimated based on a Gauss-Markov model with VAR and multivariate t-distributed errors, as a special case of the proposed GHM. In the second scenario real laser tracker measurements with outliers are adjusted to estimate the parameters of a sphere employing the proposed GHM with VAR and multivariate t-distributed errors. For both scenarios the estimated parameters of the fitted VAR model and multivariate t-distribution are analyzed for evidence of auto- or cross-correlations and deviation from a normal distribution regarding the measurement noise.

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