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The Streptococcal C5a peptidase (ScpA) specifically inactivates the human complement factor hC5a, a potent anaphylatoxin recently identified as a therapeutic target for treatment of COVID-19 infections. Engineering of ScpA to enhance its potential as a therapeutic will require detailed examination of the basis for its highly selective activity. The emerging view of ScpA and related subtilases is that selection of their substrates is a dynamic two-step process involving flexibility in the domains around the active site and in the C-ter of the substrate. Surface plasmon resonance (SPR) analyses of the ScpA-hC5a interaction have shown that high affinity binding of the substrate is driven by electrostatic interactions between an exosite on the Fn2 domain of the enzyme and the bulky N-ter cleavage product (P

Graphical abstract, The Streptococcal C5a peptidase (ScpA) specifically inactivates the human complement factor hC5a, a potent anaphylatoxin recently identified as a therapeutic target for treatment of COVID-19 infections. Biologics used to modulate hC5a are predominantly monoclonal antibodies. Here we present data to support an alternative therapeutic approach based on the specific inactivation of hC5a by ScpA in studies using recombinant hC5a (rhC5a). Initial characterization of ScpA confirmed activity in human serum and against rhC5a desArg (rhC5adR), the predominant hC5a form in blood. A new FRET based enzyme assay showed that ScpA cleaved rhC5a at near physiological concentrations (Km 185 nM). Surface Plasmon Resonance (SPR) and Isothermal Titration Calorimetry (ITC) studies established a high affinity ScpA-rhC5a interaction (KD 34 nM, KDITC 30.8 nM). SPR analyses also showed that substrate binding is dominated (89% of ΔG°bind) by interactions with the bulky N-ter cleavage product (PN, ’core’ residues 1-67) with interactions involving the C-ter R74 contributing most of the remaining ΔG°bind. Furthermore, reduced binding affinity following mutation of a subset of positively charged Arginine residues of PN and in the presence of higher salt concentrations, highlighted the importance of electrostatic interactions. These data provide the first in-depth study of the ScpA-C5a interaction and indicate that ScpA’s ability to efficiently cleave physiological concentrations of C5a is driven by electrostatic interactions between an exosite on the enzyme and the ‘core’ of C5a. The results and methods described herein will facilitate engineering of ScpA to enhance its potential as a therapeutic for excessive immune response to infectious disease.

Nickel and cobalt cyclam modified mesocellular foam (MCF) materials were prepared and characterised. The metal cyclam modified materials displayed reduced surface areas and pore diameters in comparison to MCF. The modified materials were used to specifically anchor a histidine tagged form of the enzyme, alanine racemase (HT-AlaR). Non-specific adsorption was predominantly hydrophobic//hydrophilic in nature and could be significantly reduced in the presence of 2% polyethylene glycol. The activity of HT-AlaR immobilised on Ni and Co-MCF was essentially the same as that of the free enzyme, demonstrating that enzymes can be specifically immobilised within the pores of mesoporous materials in a stable and catalytically active manner.

The marketplace for probiotic foods is burgeoning, measured in billions of euro per annum. It is imperative, however, that all bacterial strains are fully assessed for human safety. The ability to bind fibrinogen is considered a potential pathogenicity trait that can lead to platelet aggregation, serious medical complications, and in some instances, death. Here we examined strains from species frequently used as probiotics for their ability to bind human fibrinogen. Only one strain (CCUG 47825), a Lactobacillus salivarius isolate from a case of septicaemia, was found to strongly adhere to fibrinogen. Furthermore, this strain was found to aggregate human platelets at a level comparable to the human pathogen Staphylococcus aureus. By sequencing the genome of CCUG 47825, we were able to identify candidate genes responsible for fibrinogen binding. Complementing the genetic analysis with traditional molecular microbiological techniques enabled the identification of the novel fibrinogen receptor, CCUG_2371. Although only strain CCUG 47825 bound fibrinogen under laboratory conditions, homologues of the novel fibrinogen binding gene CCUG_2371 are widespread among L. salivarius strains, maintaining their potential to bind fibrinogen if expressed. We highlight the fact that without a full genetic analysis of strains for human consumption, potential pathogenicity traits may go undetected. © 2012 Blackwell Publishing Ltd. (Less)

Many bacterial pathogens interfere with the contact system (kallikrein–kinin system) in human plasma. Activation of this system has two consequences: cleavage of high-molecular-mass kininogen (HK) resulting in release of the potent proinflammatory peptide bradykinin, and initiation of the intrinsic pathway of coagulation. In this study, two species of the Gram-negative anaerobic commensal organismBacteroides, namelyBacteroides fragilisandBacteroides thetaiotaomicron, were found to bind HK and fibrinogen, the major clotting protein, from human plasma as shown by immunoelectron microscopy and Western blot analysis. In addition, theseBacteroidesspecies were capable of activating the contact system at its surface leading to a significant prolongation of the intrinsic coagulation time and also to the release of bradykinin. Members of the genusBacteroideshave been known to act as opportunistic pathogens outside the gut, withB. fragilisbeing the most common isolate from clinical infections, such as intra-abdominal abscesses and bacteraemia. The present results thus provide more insight into howBacteroidesspecies cause infection.

The aim of this study was to use comparative modeling to predict the three-dimensional structure of the CHAP(K) protein (cysteine, histidine-dependent amidohydrolase/peptidase domain of the LysK endolysin, derived from bacteriophage K). Iterative PSI-BLAST searches against the Protein Data Bank (PDB) and nonredundant (nr) databases were used to populate a multiple alignment for analysis using the T-Coffee Expresso server. A consensus Maximum Parsimony phylogenetic tree with a bootstrap analysis setting of 1,000 replicates was constructed using MEGA4. Structural templates relevant to our target (CHAP(K)) were identified, processed in Expresso and used to generate a 3D model in the alignment mode of SWISS-MODEL. These templates were also processed in the I-TASSER web server. A Staphylococcus saprophyticus CHAP domain protein, 2K3A, was identified as the structural template in both servers. The I-TASSER server generated the CHAP(K) model with the best bond geometries when analyzed using PROCHECK and the most logical organization of the structure. The predicted 3D model indicates that CHAP(K) has a papain-like fold. Circular dichroism spectropolarimetry also indicated that CHAP(K) has an αβ fold, which is consistent with the model presented. The putative active site maintained a highly conserved Cys54-His117-Glu134 charge relay and an oxyanion hole residue Asn136. The residue triplet, Cys-His-Glu, is known to be a viable proteolytic triad in which we predict the Cys residue is used in a nucleophilic attack on peptide bonds at a specific site in the pentaglycine cross bridge of staphylococcal cell wall peptidoglycan. Use of comparative modeling has allowed approximation of the 3D structure of CHAP(K) giving information on the structure and an insight into the binding and active site of the catalytic domain. This may facilitate its development as an alternative antibacterial agent.

Primary deep infection following joint replacement surgery accounts for 7% of all revisions. Glass polyalkenoate cements (GPCs) have previously been shown to exhibit antibacterial properties. The present study had two objectives. The first was to determine if addition of tri-sodium citrate (TSC) to the powder phase of an Al-free GPC (0.04 SrO-0.12 CaO-0.36 ZnO-0.48 SiO2, by mole fraction) enhanced the resultant cement's antibacterial properties against three strains of bacteria that are commonly found in periprosthetic sites following total joint replacements (TJRs); namely, E. coli, B. fragilis, and S. epidermidis. Four cement sets were prepared, which contained 0 wt% TSC (control), 5 wt% TSC, 10 wt% TSC, and 15 wt% TSC. All the TSC-modified cements were found to exhibit large inhibition zones against all the bacterial strains, especially the cement containing 15 wt% TSC against E. coli. The antibacterial properties of the TSC containing GPCs are attributed to the release of Zn and Na ions from the cements and the presence of the TSC. The second objective was to investigate if, when a modified GPC is embedded in a bovine bone model, ionic transfer occurs. It was found that Zn ions migrated from the cement to the surrounding bone, particularly at the cement-bone interface. This is a desirable outcome as Zn ions are known to play a vital role in both bone metabolism and the regeneration of healthy bone. The present results point to the potential clinical benefits of using TSC-modified GPCs in TJRs.

Myoglobin has been immobilized onto different ordered mesoporous silicates. The effect of the pH on the adsorption, leaching and activity was studied. The results showed that the maximum amount of protein was adsorbed at a pH 6.5, just below the protein isoelectric point (7–7.3). There was no effect of increasing ionic strength on the adsorption profile at different pH values. The adsorption is rationalized in terms of local electrostatic forces acting between the enzyme and the silica surface as well as hydrophobic interactions close to the protein isoelectric point, whereas at low pH the global charges give rise to protein–protein repulsion and at high pH enzyme–silica repulsion. Higher amounts of immobilized myoglobin were leached at a pH 4, while lower amounts were leached at pH 6.5. The catalytic activity of myoglobin immobilized onto SBA-15 showed optimal activity at a pH 6.5 in comparison to a pH of 5 for the free form.

Background: The Helicobacter pylori protein HorB (encoded by HP0127) is a member of a paralogous family that includes the adhesins BabA, AlpA, AlpB, and HopZ, which contribute to adhesion to gastric epithelial cells. Of the verified H. pylori porins, the HorB sequence is most similar to that of HopE, but the function of HorB is unknown. The aim of our study was to investigate the role of HorB in H. pylori gastric epithelial cell adhesion. Materials and methods: We disrupted the horB gene in H. pylori and measured the adhesion to gastric epithelial cells (AGS cells). We then assessed the effect that HorB disruption had on lipopolysaccharide (LPS) O-chain production and Lewis x and Lewis y antigen expression. A HorB mutant in the mouse-adapted strain H. pylori SS1 was created by marker exchange and mouse stomach colonization was quantified. Using reverse transcription polymerase chain reaction, human gastric biopsy material from H. pylori-infected patients was then examined for expression of the horB gene. Results: Disruption of the horB gene reduced H. pylori adhesion by more than twofold. Adhesion in the horB knockout strain was restored to wild-type levels by re-introduction of HorB into the chromosome. Disruption of HorB reduced production of LPS O-chains and lowered the level of expression of Lewis x and Lewis y antigens. Insertional mutagenesis of the horB gene in H. pylori SS1 reduced mouse stomach colonization threefold. Finally, expression of the horB gene was detected in human gastric biopsy material from H. pylori-infected patients. Conclusions: From these data we conclude that HorB has a role in H. pylori adhesion during infection.

Six mesoporous materials functionalized with amine groups were developed and screened as potential supports for chloroperoxidase (CPO). A periodic mesoporous organosilane (PMO PA-40) with pore entrances large enough to allow the enzyme entry inside the pores was found to be the best support. When CPO was immobilized onto this material, it could be reused 20 times with retention of activity. On materials with little mesoporous structure and/or pore entrances too narrow to allow the enzyme entry to the channels, immobilized CPO rapidly lost activity upon reuse. Similarly, postsynthetic amino functionalization of a pure silica mesoporous material did not yield a stable biocatalyst.

Mesoporous silicates (MPS) materials are attractive materials for immobilizing proteins/enzymes because of their well ordered structures, large surface areas (up to 1000 m(2) g(-1)), narrow pore size distributions, large pore diameters, and pore volumes. MPS with average pore diameters ranging from 28 to 300 Angstroms were prepared using cationic and nonionic surfactants. The influence of water content, pH, storage, and thermal treatment on the activity of trypsin immobilized onto MPS was investigated. In a range of solvents, the amidolytic activity of immobilized trypsin was higher than that of the lyophilized preparation. Significant increases in k(cat)/K(M) occurred in propanol, ethanol, methanol, and formamide of 90, 62, 45 and 26, respectively. The observed increases were primarily a result of substantial increases in k(cat).

Cytochrome c and xylanase were adsorbed onto two mesoporous materials, SBA-15 (a pure silicate) and MSE (an organosilicate), with very similar physical properties but differing chemical compositions. A methodical order was developed whereby the influences of surface area, pore size, extent of order, particle size, surface potentials, isoelectric points, pH, and ionic strength on immobilization were explored. In silico studies of cytochrome c and xylanase were conducted before any immobilization experiments were carried out in order to select compatible materials and probe the interactions between the adsorbents and the mesoporous silicates. The stabilities of the mesoporous materials at different pH values and their isoelectric points and zeta potentials were determined. Electrostatic attraction dominated protein interactions with SBA-15, while weaker hydrophobic interactions are more prominent with MSE for both cytochrome c and xylanase. The ability of the immobilized protein/enzyme to withstand leaching was measured, and activity tests and thermostability experiments were conducted. Cytochrome c immobilized onto SBA-15 showed resistance to leaching and an enhanced activity compared to free protein. The immobilized cytochrome c was shown to have higher intrinsic activity but lower thermostability than free cytochrome c. From an extensive characterization of the surface properties of the silicates and proteins, we describe a systematic methodology for the adsorption of proteins onto mesoporous silicates. This approach can be utilized in the design of a solid support for any protein.

This study presents evidence for a novel protease-protease inhibitor couple, SpeB-Spi, in the human pathogen Streptococcus pyogenes. The gene for the inhibitor Spi is located directly downstream of the gene for the streptococcal cysteine protease SpeB. Spi is 37% identical and 70% similar to the sequence of the SpeB propeptide, suggesting that Spi and the SpeB propeptide might bind to SpeB in an analogous manner. Secondary structure predictions and molecular modelling suggested that Spi would adopt a structure similar to the SpeB propeptide. The spi gene was co-transcribed with speB on the 1.7 knt and 2.2 knt transcripts previously identified for speB. The Spi protein was purified by SpeB-affinity chromatography from the S. pyogenes cytoplasm. Recombinant Spi was produced and purified, and shown to bind to SpeB and to inhibit its protease activity. Although a similar genetic arrangement of protease and inhibitor is present in staphylococci, this is the first example of an inhibitor molecule that is a structural homologue of the cognate propeptide, and which is genetically linked to the protease gene. Thus, this represents a novel system whereby bacteria may control the intracellular activity of their proteases.

The immobilization of the hydrolytic enzyme trypsin onto various mesoporous silicates (MPS) was studied. MPS were prepared using cationic or non-ionic surfactants (average pore diameters were in the range of 28–300 A). All MPS were characterised by X-ray diffraction, scanning electron microscopy and nitrogen porosimetry. Enzyme purity strongly influenced loading. Trypsin adsorbed on MPS was found to be desorbed more readily by polyethylene glycol than by ammonium sulphate, suggesting that hydrophobic–hydrophilic interactions were important. Immobilized trypsin showed 10–20 times higher activity than the free trypsin and was stable for 4–6 weeks when stored at 4 or 25 °C. The trypsin–MPS catalyst was successfully reused for up to 6 cycles

Trypsin supported on MCM-41 is demonstrated as a stable catalyst for the transesterfication of N-acetyl-L-tyrosine ethyl ester with propan-1-ol. An enzyme loading of 5 micromoles of trypsin per gram of silicate was readily achieved. The ultimate enzyme loading was shown to depend strongly on enzyme purity. The adsorbed enzyme exhibited the same turnover frequency for the transesterification reaction as native trypsin, the catalyst could be reused without loss of activity following separation by centrifuging and the enzyme did not leach during testing.

Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species., Lactobacillus is a lactic acid bacteria and has a wide range of application from use in probiotic food production to biotherapeutics. Here, the authors sequence and compare the genomes of 213 different Lactobacillus strains and related genera, and provide new insight into phylogenomic organization and adaptive immunity elements in this bacteria family.

peer-reviewed The specific binding of streptavidin to biotinylated protein A was demonstrated using a microwave detection system. In control experiments, the degree of non-specific binding was negligible. The method of detection was used to monitor the adsorption of two other proteins, cytochrome c and glucose oxidase, on to the IDE microwave sensor surface. The response of the sensor was also examined on different substrate materials, with detection of protein binding observed obtained on both smooth, conductive (gold) and on rough, insulating (hydroxyapatite) surfaces.

peer-reviewed The specific immobilisation of a histidine-tagged protein, Spi, onto mono-anchored nickel(II)-cyclam functionalised SBA-15 is reported. ACCEPTED peer-reviewed

Pathogenic bacteria secrete protein toxins that weaken or disable their host, and thereby act as virulence factors. We have determined the crystal structure of streptococcal pyrogenic exotoxin B (SpeB), a cysteine protease that is a major virulence factor of the human pathogen Streptococcus pyogenes and participates in invasive disease episodes, including necrotizing fasciitis. The structure, determined for the 40-kDa precursor form of SpeB at 1.6-Å resolution, reveals that the protein is a distant homologue of the papain superfamily that includes the mammalian cathepsins B, K, L, and S. Despite negligible sequence identity, the protease portion has the canonical papain fold, albeit with major loop insertions and deletions. The catalytic site differs from most other cysteine proteases in that it lacks the Asn residue of the Cys-His-Asn triad. The prosegment has a unique fold and inactivation mechanism that involves displacement of the catalytically essential His residue by a loop inserted into the active site. The structure also reveals the surface location of an integrin-binding Arg-Gly-Asp (RGD) motif that is a feature unique to SpeB among cysteine proteases and is linked to the pathogenesis of the most invasive strains of S. pyogenes .

Background Streptococcus equi ssp. equi is the causative agent of ‘Strangles’ in horses. This is a debilitating condition leading to economic loss, yard closures and cancellation of equestrian events. There are multiple genotypes of S. equi ssp. equi which can cause disease, but to date there has been no systematic study of strains which are prevalent in Ireland. This study identified and classified Streptococcus equi ssp. equi strains isolated from within the Irish equine industry. Results Two hundred veterinary isolates were subjected to SLST (single locus sequence typing) based on an internal sequence from the seM gene of Streptococcus equi ssp equi. Of the 171 samples which successfully gave an amplicon, 162 samples (137 Irish and 24 UK strains) gave robust DNA sequence information. Analysis of the sequences allowed division of the isolates into 19 groups, 13 of which contain at least 2 isolates and 6 groups containing single isolates. There were 19 positions where a DNA SNP (single nucleotide polymorphism) occurs, and one 3 bp insertion. All groups had multiple (2–8) SNPs. Of the SNPs 17 would result in an amino acid change in the encoded protein. Interestingly, the single isolate EI8, which has 6 SNPs, has the three base pair insertion which is not seen in any other isolate, this would result in the insertion of an Ile residue at position 62 in that protein sequence. Comparison of the relevant region in the determined sequences with the UK Streptococcus equi seM MLST database showed that Group B (15 isolates) and Group I (2 isolates), as well as the individual isolates EI3 and EI8, are unique to Ireland, and some groups are most likely of UK origin (Groups F and M), but many more probably passed back and forth between the two countries. Conclusions The strains occurring in Ireland are not clonal and there is a considerable degree of sequence variation seen in the seM gene. There are two major clades causing infection in Ireland and these strains are also common in the UK.

The marketplace for probiotic foods is burgeoning, measured in billions of euro per annum. It is imperative, however, that all bacterial strains are fully assessed for human safety. The ability to bind fibrinogen is considered a potential pathogenicity trait that can lead to platelet aggregation, serious medical complications, and in some instances, death. Here we examined strains from species frequently used as probiotics for their ability to bind human fibrinogen. Only one strain (CCUG 47825), a Lactobacillus salivarius isolate from a case of septicaemia, was found to strongly adhere to fibrinogen. Furthermore, this strain was found to aggregate human platelets at a level comparable to the human pathogen Staphylococcus aureus. By sequencing the genome of CCUG 47825, we were able to identify candidate genes responsible for fibrinogen binding. Complementing the genetic analysis with traditional molecular microbiological techniques enabled the identification of the novel fibrinogen receptor, CCUG_2371. Although only strain CCUG 47825 bound fibrinogen under laboratory conditions, homologues of the novel fibrinogen binding gene CCUG_2371 are widespread among L. salivarius strains, maintaining their potential to bind fibrinogen if expressed. We highlight the fact that without a full genetic analysis of strains for human consumption, potential pathogenicity traits may go undetected.

peer-reviewed Mesoporous silicates (MPS) possess ordered pore structures with pore diameters sufficiently large to accommodate a range of enzymes. The successful immobilization of an enzyme on MPS usually requires modification of the surface of MPS to optimize the interactions between the support and the enzyme. Recent developments on the functionalization of MPS for the immobilization of enzymes are described in this review. ACCEPTED peer-reviewed

Background Bacteroides fragilis and Bacteroides thetaiotaomicron are members of the normal human intestinal microbiota. However, both organisms are capable of causing opportunistic infections, during which the environmental conditions to which the bacteria are exposed change dramatically. To further explore their potential for contributing to infection, we have characterized the expression in B. thetaiotaomicron of four homologues of the gene encoding the C10 cysteine protease SpeB, a potent extracellular virulence factor produced by Streptococcus pyogenes. Results We identified a paralogous set of genes (btp genes) in the B. thetaiotaomicron genome, that were related to C10 protease genes we recently identified in B. fragilis. Similar to C10 proteases found in B. fragilis, three of the B. thetaiotaomicron homologues were transcriptionally coupled to genes encoding small proteins that are similar in structural architecture to Staphostatins, protease inhibitors associated with Staphopains in Staphylococcus aureus. The expression of genes for these C10 proteases in both B. fragilis and B. thetaiotaomicron was found to be regulated by environmental stimuli, in particular by exposure to oxygen, which may be important for their contribution to the development of opportunistic infections. Conclusions Genes encoding C10 proteases are increasingly identified in operons which also contain genes encoding proteins homologous to protease inhibitors. The Bacteroides C10 protease gene expression levels are responsive to different environmental stimuli suggesting they may have distinct roles in the bacterial-host interaction.

Infection following surgery can result in significant pain and morbidity for patients undergoing vertebroplasty/kyphoplasty, and often results in revision surgery. This study focuses on the development of Al-free glass polyalkenoate cements (GPCs) based on 0.04SrO—0.12CaO—0.36ZnO—0.48SiO 2 glass, with the intent of optimizing their antibacterial efficacy by incorporating low—molecular-weight polyacrylic acids (PAA) and trisodium citrate (TSC), and evaluating the resultant GPCs against bacteria relevant to spinal infections, P. aeruginosa and E. coli. Ion-release profiles were determined for the GPC formulation containing E6 PAA (Cement A) and E7 PAA (Cement B), and Zn, Na, and Sr release was recorded over 1, 7, and 30 days. Inhibition was found in E. coli at each time period (0—30 days) and this generally decreased with exposure time in water. The largest GPC inhibition zones were produced by Cement A (6 mm); however the control material Simplex P + tobramycin produced much higher inhibition zones (11 mm). When testing the GPC against P. aeruginosa, inhibition was only present at the 0-day time period. Simplex P + tobramycin was found to produce inhibition at each time frame. Analysis of the agar from the inhibition zone of the E. coli test revealed that there is a significant change in Zn concentration as compared to a control agar specimen, which suggests that Zn release is responsible for the antibacterial effect of the GPCs.

Commensal lactobacilli frequently produce bile salt hydrolase (Bsh) enzymes whose roles in intestinal survival are unclear. Twenty-six Lactobacillus salivarius strains from different sources all harbored a bsh1 allele on their respective megaplasmids. This allele was related to the plasmid-borne bsh1 gene of the probiotic strain UCC118. A second locus ( bsh2 ) was found in the chromosomes of two strains that had higher bile resistance levels. Four Bsh1-encoding allele groups were identified, defined by truncations or deletions involving a conserved residue. In vitro analyses showed that this allelic variation was correlated with widely varying bile deconjugation phenotypes. Despite very low activity of the UCC118 Bsh1 enzyme, a mutant lacking this protein had significantly lower bile resistance, both in vitro and during intestinal transit in mice. However, the overall bile resistance phenotype of this and other strains was independent of the bsh1 allele type. Analysis of the L. salivarius transcriptome upon exposure to bile and cholate identified a multiplicity of stress response proteins and putative efflux proteins that appear to broadly compensate for, or mask, the effects of allelic variation of bsh genes. Bsh enzymes with different bile-degrading kinetics, though apparently not the primary determinants of bile resistance in L. salivarius , may have additional biological importance because of varying effects upon bile as a signaling molecule in the host.

Mesoporous silicates (MPS) have an ordered pore structure with dimensions comparable to many biological molecules. They have been extensively explored as supports for proteins and enzymes in biocatalytic applications. Since their initial discovery, novel syntheses methods have led to precise control over pore size and structure, particle size, chemical composition, and stability, thus allowing the adsorption of a wide variety of biological macromolecules, such as heme proteins, lipases, antibody fragments, and proteases, into their structures. This Review discusses the application of ordered, large-pore, functionalized mesoporous silicates to immobilize proteins for biocatalysis.

A truncated derivative of the phage endolysin LysK containing only the CHAP (cysteine- and histidine-dependent amidohydrolase/peptidase) domain exhibited lytic activity against live clinical staphylococcal isolates, including methicillin-resistant Staphylococcus aureus . This is the first known report of a truncated phage lysin which retains high lytic activity against live staphylococcal cells.

Probiotics have a range of proposed health benefits for the consumer, which may include modulating the levels of beneficial elements in the microbiota. Recent investigations using molecular approaches have revealed a human intestinal microbiota comprising over 1000 phylotypes. Mechanisms whereby probiotics impact on the intestinal microbiota include competition for substrates, direct antagonism by inhibitory substances, competitive exclusion, and potentially host-mediated effects such as improved barrier function and altered immune response. We now have the microbial inventories and genetic blueprints to begin tackling intestinal microbial ecology at an unprecedented level of detail, aided by the understanding that dietary components may be utilized differentially by individual phylotypes. Controlled intervention studies in humans, utilizing latest molecular technologies, are required to consolidate evidence for bacterial species that impact on the microbiota. Mechanistic insights should be provided by metabolomics and other analytical techniques for small molecules. Rigorous characterization of interactions between the diet, microbiota, and probiotic bacteria will provide new opportunities for modulating the microbiota towards improving human health.

Mesoporous silicates (MPS) have an ordered pore structure with dimensions comparable to many biological molecules. They have been extensively explored as supports for proteins and enzymes in biocatalytic applications. Since their initial discovery, novel syntheses methods have led to precise control over pore size and structure, particle size, chemical composition, and stability, thus allowing the adsorption of a wide variety of biological macromolecules, such as heme proteins, lipases, antibody fragments, and proteases, into their structures. This Review discusses the application of ordered, large-pore, functionalized mesoporous silicates to immobilize proteins for biocatalysis.

The crystal structure of an active form of ScpA has been solved to 1.9 A resolution. ScpA is a multidomain cell-envelope subtilase from Streptococcus pyogenes that cleaves complement component C5a. The catalytic triad of ScpA is geometrically consistent with other subtilases, clearly demonstrating that the additional activation mechanism proposed for the Streptococcus agalactiae homologue (ScpB) is not required for ScpA. The ScpA structure revealed that access to the catalytic site is restricted by variable regions in the catalytic domain (vr7, vr9, and vr11) and by the presence of the inserted protease-associated (PA) domain and the second fibronectin type III domains (Fn2). Modeling of the ScpA-C5a complex indicates that the substrate binds with carboxyl-terminal residues (65-74) extended through the active site and core residues (1-64) forming exosite-type interactions with the Fn2 domain. This is reminiscent of the two-site mechanism proposed for C5a binding to its receptor. In the nonprime region of the active site, interactions with the substrate backbone are predicted to be more similar to those observed in kexins, involving a single beta-strand in the peptidase. However, in contrast to kexins, there would be diminished emphasis on side-chain interactions, with little charged character in the S3-S1 and S6-S4 subsites occupied by the side chains of residues in vr7 and vr9. Substrate binding is anticipated to be dominated by ionic interactions in two distinct regions of ScpA. On the prime side of the active site, salt bridges are predicted between P1', P2', and P7' residues, and residues in the catalytic and PA domains. Remote to the active site, a larger number of ionic interactions between residues in the C5a core and the Fn2 domain are observed in the model. Thus, both PA and Fn2 domains are expected to play significant roles in substrate recognition.

This study presents evidence for a novel protease-protease inhibitor couple, SpeB-Spi, in the human pathogen Streptococcus pyogenes. The gene for the inhibitor Spi is located directly downstream of the gene for the streptococcal cysteine protease SpeB. Spi is 37% identical and 70% similar to the sequence of the SpeB propeptide, suggesting that Spi and the SpeB propeptide might bind to SpeB in an analogous manner. Secondary structure predictions and molecular modelling suggested that Spi would adopt a structure similar to the SpeB propeptide. The spi gene was co-transcribed with speB on the 1.7 knt and 2.2 knt transcripts previously identified for speB. The Spi protein was purified by SpeB-affinity chromatography from the S. pyogenes cytoplasm. Recombinant Spi was produced and purified, and shown to bind to SpeB and to inhibit its protease activity. Although a similar genetic arrangement of protease and inhibitor is present in staphylococci, this is the first example of an inhibitor molecule that is a structural homologue of the cognate propeptide, and which is genetically linked to the protease gene. Thus, this represents a novel system whereby bacteria may control the intracellular activity of their proteases.

Mesoporous silicates (MPS) provide a means of immobilizing proteins and enzymes in a stable environment while retaining physiological function. A systematic methodology of assessing the potential of immobilising a given protein on to MPS has been developed from extensive characterization of the surface properties of the silicates and proteins. This approach can be potentially utilised in the design of a solid support for any protein.

Background The C10 family of cysteine proteases includes enzymes that contribute to the virulence of bacterial pathogens, such as SpeB in Streptococcus pyogenes. The presence of homologues of cysteine protease genes in human commensal organisms has not been examined. Bacteroides fragilis is a member of the dominant Bacteroidetes phylum of the human intestinal microbiota, and is a significant opportunistic pathogen. Results Four homologues of the streptococcal virulence factor SpeB were identified in the B. fragilis genome. These four protease genes, two were directly contiguous to open reading frames predicted to encode staphostatin-like inhibitors, with which the protease genes were co-transcribed. Two of these protease genes are unique to B. fragilis 638R and are associated with two large genomic insertions. Gene annotation indicated that one of these insertions was a conjugative Tn-like element and the other was a prophage-like element, which was shown to be capable of excision. Homologues of the B. fragilis C10 protease genes were present in a panel of clinical isolates, and in DNA extracted from normal human faecal microbiota. Conclusions This study suggests a mechanism for the evolution and dissemination of an important class of protease in major members of the normal human microbiota.