Sortases and the art of anchoring proteins to the envelopes of gram-positive bacteria

Strain-Dependent Adhesion Variations of Shouchella clausii Isolated from Healthy Human Volunteers: A Study on Cell Surface Properties and Potential Probiotic Benefits

The probiotic potential of Shouchella clausii is widely recognized, but little is known about its adhesive properties. Hence, this study aims to investigate the adhesion potential and cell surface properties of four human-origin S. clausii strains (B619/R, B603/Nb, B106, and B637/Nm). We evaluated epithelial adhesion, Extracellular Matrix (ECM) binding, aggregation ability, and cell surface hydrophobicity and used genome analysis for validation. Our results demonstrate that adhesion capability is a strain-specific attribute, with significant variations observed among the four strains. B619/R, B603/Nb, and B106 displayed stronger adhesion properties than B637/Nm. Supplementary adhesion assays showed that B637/Nm displayed high hydrophobicity, significant auto-aggregation, and significant mucin-binding abilities. Conversely, B619/R, B603/Nb, and B106 had mildly hydrophobic surfaces and low aggregation abilities. Genome annotation revealed the presence of various adhesion proteins in four strains. Notably, the reduced adhesion potential of B637/Nm was supported by the absence of the cell wall surface anchor family protein (LPxTG motif), which is crucial for interactions with intestinal epithelial cells or mucus components. Further, docking studies provided insights into the interaction of adhesion proteins with gut mucins. These findings contribute to a better understanding of how S. clausii strains interact with the gut environment, facilitating the development of probiotic formulations tailored for improved gut health and well-being.

Signal peptidase SpsB coordinates staphylococcal cell cycle, surface protein septal trafficking and LTA synthesis

Many cell wall anchored surface proteins of Gram-positive bacteria harbor a highly conserved YSIRK/G-S signal peptide (SPYSIRK+), which deposits surface protein precursors at the cell division septum where they are subsequently anchored to septal peptidoglycan. Previously we identified that LtaS-mediated lipoteichoic acid (LTA) synthesis regulates septal trafficking of YSIRK+ proteins in S. aureus. Interestingly, both LtaS and SPYSIRK+ are cleaved by the signal peptidase SpsB, but the biological implications remain unclear. Here we show that SpsB is required for cleaving SPSpA(YSIRK+) of staphylococcal surface protein A (SpA). Depletion of spsB not only diminished SPSpA processing but also abolished SpA septal localization. The mis-localization is attributed to the cleavage activity of SpsB, as an A37P mutation of SPSpA that disrupted SpsB cleavage also abrogated SpA septal localization. Strikingly, depletion of spsB led to aberrant cell morphology, cell cycle arrest and daughter cell separation defects. Localization studies showed that SpsB predominantly localized at the septum of dividing staphylococcal cells. Finally, we show that SpsB spatially regulates LtaS as spsB depletion enriched LtaS at the septum. Collectively, the data suggest a new dual-mechanism model mediated by SpsB: the abundant YSIRK+ proteins are efficiently processed by septal localized SpsB; SpsB cleaves LtaS at the septum, which spatially regulates LtaS activity contributing to YSIRK+ proteins septal trafficking. The study identifies SpsB as a novel and key regulator orchestrating protein secretion, cell cycle and cell envelope biogenesis.

Exploring Plant-Based Compounds as Alternatives for Targeting Enterococcus faecalis in Endodontic Therapy: A Molecular Docking Approach

Endodontic infections pose significant challenges in dental practice due to their persistence and potential complications. Among the causative agents, Enterococcus faecalis stands out for its ability to form biofilms and develop resistance to conventional antibiotics, leading to treatment failures and recurrent infections. The urgent need for alternative treatments arises from the growing concern over antibiotic resistance and the limitations of current therapeutic options in combating E. faecalis-associated endodontic infections. Plant-based natural compounds offer a promising avenue for exploration, given their diverse bioactive properties and potential as sources of novel antimicrobial agents. In this study, molecular docking and dynamics simulations are employed to explore the interactions between SrtA, a key enzyme in E. faecalis, and plant-based natural compounds. Analysis of phytocompounds through molecular docking unveiled several candidates with binding energies surpassing that of the control drug, ampicillin, with pinocembrin emerging as the lead compound due to its strong interactions with key residues of SrtA. Comparative analysis with ampicillin underscored varying degrees of structural similarity among the study compounds. Molecular dynamics simulations provided deeper insights into the dynamic behavior and stability of protein-ligand complexes, with pinocembrin demonstrating minimal conformational changes and effective stabilization of the N-terminal region. Free energy landscape analysis supported pinocembrin's stabilizing effects, further corroborated by hydrogen bond analysis. Additionally, physicochemical properties analysis highlighted the drug-likeness of pinocembrin and glabridin. Overall, this study elucidates the potential anti-bacterial properties of selected phytocompounds against E. faecalis infections, with pinocembrin emerging as a promising lead compound for further drug development efforts, offering new avenues for combating bacterial infections and advancing therapeutic interventions in endodontic practice.

Structural and functional insights of sortases and their interactions with antivirulence compounds

Sortase proteins play a crucial role as integral membrane proteins in anchoring bacterial surface proteins by recognizing them through a Cell-Wall Sorting (CWS) motif and cleaving them at specific sites before initiating pilus assembly. Both sortases and their substrate proteins are major virulence factors in numerous Gram-positive pathogens, making them attractive targets for antimicrobial intervention. Recognizing the significance of virulence proteins, a comprehensive exploration of their structural and functional characteristics is essential to enhance our understanding of pilus assembly in diverse Gram-positive bacteria. Therefore, this review article discusses the structural features of different classes of sortases and pilin proteins, primarily serving as substrates for sortase-assembled pili. Moreover, it thoroughly examines the molecular-level interactions between sortases and their inhibitors, providing insights from both structural and functional perspectives. In essence, this review article will provide a contemporary and complete understanding of both sortase pathways and various strategies to target them effectively to counteract the virulence.

Halenaquinol Blocks Staphylococcal Protein A Anchoring on Cell Wall Surface by Inhibiting Sortase A in Staphylococcus aureus

Sortase A (SrtA) is a cysteine transpeptidase that binds to the periplasmic membrane and plays a crucial role in attaching surface proteins, including staphylococcal protein A (SpA), to the peptidoglycan cell wall. Six pentacyclic polyketides (1-6) were isolated from the marine sponge Xestospongia sp., and their structures were elucidated using spectroscopic techniques and by comparing them to previously reported data. Among them, halenaquinol (2) was found to be the most potent SrtA inhibitor, with an IC50 of 13.94 μM (4.66 μg/mL). Semi-quantitative reverse transcription PCR data suggest that halenaquinol does not inhibit the transcription of srtA and spA, while Western blot analysis and immunofluorescence microscopy images suggest that it blocks the cell wall surface anchoring of SpA by inhibiting the activity of SrtA. The onset and magnitude of the inhibition of SpA anchoring on the cell wall surface in S. aureus that has been treated with halenaquinol at a value 8× that of the IC50 of SrtA are comparable to those for an srtA-deletion mutant. These findings contribute to the understanding of the mechanism by which marine-derived pentacyclic polyketides inhibit SrtA, highlighting their potential as anti-infective agents targeting S. aureus virulence.

Harnessing the combined effect of antivirulence agent trans-chalcone with bactericidal curcumin against sortase A enzyme to tackle Gram-positive bacterial infections

Gram-positive bacteria are responsible for a wide range of infections in humans. In most Gram-positive bacteria, sortase A plays a significant role in attaching virulence factors to the bacteria's cell wall. These cell surface proteins play a significant role in virulence and pathogenesis. Even though antibiotics are available to treat these infections, there is a continuous search for an alternative strategy due to an increase in antibiotic resistance. Thus, using anti-sortase drugs to combat these bacterial infections may be a promising approach. Here, we describe a method for targeting Gram-positive bacterial infection by combining curcumin and trans-chalcone as sortase A inhibitors. We have used curcumin and trans-chalcone alone and in combination as a sortase A inhibitor. We have seen ~78%, ~43%, and ~94% inhibition when treated with curcumin, trans-chalcone, and a combination of both compounds, respectively. The compounds have also shown a significant effect on biofilm formation, IgG binding, protein A recruitment, and IgG deposition. We discovered that combining curcumin and trans-chalcone is more effective against Gram-positive bacteria than either compound alone. The present work demonstrated that a combination of these natural compounds could be used as an antivirulence therapy against Gram-positive bacterial infection.

The Transpeptidase Sortase A Binds Nucleic Acids and Mediates Mammalian Cell Labeling

Wild-type sortase A is an important virulence factor displaying a diverse array of proteins on the surface of bacteria. This protein display relies on the transpeptidase activity of sortase A, which is widely engineered to allow protein ligation and protein engineering based on the interaction between sortase A and peptides. Here an unknown interaction is found between sortase A from Staphylococcus aureus and nucleic acids, in which exogenously expressed engineered sortase A binds oligonucleotides in vitro and is independent of its canonical transpeptidase activity. When incubated with mammalian cells, engineered sortase A further mediates oligonucleotide labeling to the cell surface, where sortase A attaches itself and is part of the labeled moiety. The labeling reaction can also be mediated by many classes of wild-type sortases as well. Cell surface GAG appears involved in sortase-mediated oligonucleotide cell labeling, as demonstrated by CRISPR screening. This interaction property is utilized to develop a technique called CellID to facilitate sample multiplexing for scRNA-seq and shows the potential of using sortases to label cells with diverse oligonucleotides. Together, the binding between sortase A and nucleic acids opens a new avenue to understanding the virulence of wild-type sortases and exploring the application of sortases in biotechnology.

Antibacterial activities of Miang extracts against selected pathogens and the potential of the tannin-free extracts in the growth inhibition of Streptococcus mutans

Bacterial pathogens have remained a major public health concern for several decades. This study investigated the antibacterial activities of Miang extracts (at non-neutral and neutral pH) against Bacillus cereus TISTR 747, Escherichia coli ATCC 22595, Salmonella enterica serovar Typhimurium TISTR 292 and Streptococcus mutans DMST 18777. The potential of Polyvinylpolypyrrolidone (PVPP)-precipitated tannin-free Miang extracts in growth-inhibition of the cariogenic Streptococcus mutans DMST 18777 and its biofilms was also evaluated. The tannin-rich fermented extracts had the best bacterial growth inhibition against S. mutans DMST 18777 with an MIC of 0.29 and 0.72 mg/mL for nonfilamentous fungi (NFP) Miang and filamentous-fungi-processed (FFP) Miang respectively. This observed anti-streptococcal activity still remained after PVPP-mediated precipitation of bioactive tannins especially, in NFP and FFP Miang. Characterization of the PVPP-treated extracts using High performance liquid chromatography quadrupole-time of flight-mass spectrometry (HPLC-QToF-MS) analysis, also offered an insight into probable compound classes responsible for the activities. In addition, Crystal violet-staining also showed better IC50 values for NFP Miang (4.30 ± 0.66 mg/mL) and FFP Miang (12.73 ± 0.11 mg/mL) against S. mutans DMST 18777 biofilms in vitro. Homology modeling and molecular docking analysis using HPLC-MS identified ligands in tannin-free Miang supernatants, was performed against modelled S. mutans DMST 18777 sortase A enzyme. The in silico analysis suggested that the inhibition by NFP and FFP Miang might be attributed to the presence of ellagic acid, flavonoid aglycones, and glycosides. Thus, these Miang extracts could be optimized and explored as natural active pharmaceutical ingredients (NAPIs) for applications in oral hygienic products.

Sortase-encoding genes, srtA and srtC, mediate Enterococcus faecalis OG1RF persistence in the Helicoverpa zea gastrointestinal tract

Enterococcus faecalis is a commensal and opportunistic pathogen in the gastrointestinal (GI) tract of mammals and insects. To investigate mechanisms of bacterial persistence in the gastrointestinal tract (GIT), we developed a non-destructive sampling model using Helicoverpa zea, a destructive agricultural pest, as host to study the role of bacterial sortase enzymes in mitigating persistence in the gastrointestinal tract. E. faecalis OG1RF ΔsrtA and E. faecalis OG1RF ΔsrtC, isogenic E. faecalis OG1RF sortase mutants grew similarly under planktonic growth conditions relative to a streptomycin-resistant E. faecalis OG1RFS WT in vitro but displayed impaired biofilm formation under, both, physiological and alkaline conditions. In the H. zea GI model, both mutants displayed impaired persistence relative to the WT. This represents one of the initial reports in which a non-destructive insect model has been used to characterize mechanisms of bacterial persistence in the Lepidopteran midgut and, furthermore, sheds light on new molecular mechanisms employed by diverse microorganisms to associate with invertebrate hosts.

Empowering Site-Specific Bioconjugations In Vitro and In Vivo: Advances in Sortase Engineering and Sortase-Mediated Ligation

Sortase-mediated ligation (SML) has emerged as a powerful and versatile methodology for site-specific protein conjugation, functionalization/labeling, immobilization, and design of biohybrid molecules and systems. However, the broader application of SML faces several challenges, such as limited activity and stability, dependence on calcium ions, and reversible reactions caused by nucleophilic side-products. Over the past decade, protein engineering campaigns and particularly directed evolution, have been extensively employed to overcome sortase limitations, thereby expanding the potential application of SML in multiple directions, including therapeutics, biorthogonal chemistry, biomaterials, and biosensors. This review provides an overview of achieved advancements in sortase engineering and highlights recent progress in utilizing SML in combination with other state-of-the-art chemical and biological methodologies. The aim is to encourage scientists to employ sortases in their conjugation experiments.

Pan-genome analysis of Streptococcus suis serotype 2 highlights genes associated with virulence and antibiotic resistance

Streptococcus suis serotype 2 (SS2) is a Gram-positive bacterium. It is a common and significant pathogen in pigs and a common cause of zoonotic meningitis in humans. It can lead to sepsis, endocarditis, arthritis, and pneumonia. If not diagnosed and treated promptly, it has a high mortality rate. The pan-genome of SS2 is open, and with an increasing number of genes, the core genome and accessory genome may exhibit more pronounced differences. Due to the diversity of SS2, the genes related to its virulence and resistance are still unclear. In this study, a strain of SS2 was isolated from a pig farm in Sichuan Province, China, and subjected to whole-genome sequencing and characterization. Subsequently, we conducted a Pan-Genome-Wide Association Study (Pan-GWAS) on 230 strains of SS2. Our analysis indicates that the core genome is composed of 1,458 genes related to the basic life processes of the bacterium. The accessory genome, consisting of 4,337 genes, is highly variable and a major contributor to the genetic diversity of SS2. Furthermore, we identified important virulence and resistance genes in SS2 through pan-GWAS. The virulence genes of SS2 are mainly associated with bacterial adhesion. In addition, resistance genes in the core genome may confer natural resistance of SS2 to fluoroquinolone and glycopeptide antibiotics. This study lays the foundation for further research on the virulence and resistance of SS2, providing potential new drug and vaccine targets against SS2.

Structure-based virtual screening and molecular dynamics approaches to identify new inhibitors of Staphylococcus aureus sortase A

Staphylococcus aureus is a prevalent Gram-positive bacteria leading cause of a wide range of human pathologies. Moreover, antibiotic résistance of pathogenesis bacteria is one of the worldwide health problems. In Gram-positive bacteria, the enzyme of SrtA, is responsible for the anchoring of surface-exposed proteins to the cell wall peptidoglycan. Because of its critical role in Gram-positive bacterial pathogenesis, SrtA is an attractive target for anti-virulence during drug development. To date, some SrtA inhibitors have been discovered most of them being derived from flavonoid compounds, like Myricetin. In order to provide potential hit molecules against SrtA for clinical use, we obtained a total of 293 compounds by performing in silico shape-based screening of compound libraries against Myristin as a reference structure. Employing molecular docking and scoring functions, the top 3 compounds Apigenin, Efloxate, and Compound 8261032 were screened by comparing their docking scores with Myricetin. Furthermore, MD simulations and MM-PBSA binding energy calculation studies revealed that only Compound 8261032 strongly binds to the catalytic core of the SrtA enzyme than Myricetin, and stable behavior was consistently observed in the docking complex. Compound 8261032 showed a good number of hydrogen bonds with SrtA and higher MM-PBSA binding energy when compared to all three molecules. Also, it makes strength interactions with Arg139 and His62, which are critical for SrtA biological activity. This study showed that the development of this inhibitor could be a fundamental strategy against resistant bacteria, but further studies in vitro are needed to confirm this claim.Communicated by Ramaswamy H. Sarma.

Berberine disrupts staphylococcal proton motive force to cause potent anti-staphylococcal effects in vitro

The presence of antibiotic resistance has increased the urgency for more effective treatments of bacterial infections. Biofilm formation has complicated this issue as biofilm bacteria become tolerant to antibiotics due to environmental factors such as nutrient deprivation and adhesion. In septic arthritis, a disease with an 11% mortality rate, bacteria in synovial fluid organize into floating, protein-rich, bacterial aggregates (mm-cm) that display depressed metabolism and antibiotic tolerance. In this study, Staphylococcus aureus (S. aureus), which is the most common pathogen in septic arthritis, was tested against different inhibitors that modulate bacterial surface protein availability and that should decrease bacterial aggregation. One of these, berberine, a quaternary ammonium compound, was found to reduce bacterial counts by 3-7 logs in human synovial fluid (aggregating medium) with no effect in tryptic soy broth (TSB, non-aggregating). Unlike traditional antibiotics, the bactericidal activity of berberine appeared to be independent of bacterial metabolism. To elucidate the mechanism, we used synovial fluid fractionation, targeted MRSA transposon insertion mutants, dyes to assess changes in membrane potential (DiSC3(5)) and membrane permeability (propidium iodide (PI)), colony counting, and fluorescence spectroscopy. We showed that berberine's activity was dependent on an alkaline pH and berberine killed both methicillin-sensitive S. aureus and MRSA in alkaline media (pH 8.5-9.0; p < 0.0001 vs. same pH controls). Under these alkaline conditions, berberine localized to S. aureus where berberine was isolated in cytoplasmic (∼95%) and DNA (∼5%) fractions. Importantly, berberine increased bacterial cell membrane permeability, and disrupted the proton motive force, suggesting a mechanism whereby it may be able to synergize with other antibacterial compounds under less harsh conditions. We suggest that berberine, which is cheap and readily available, can be made into an effective treatment.

Functional genome analysis and anti-Helicobacter pylori activity of a novel bacteriocinogenic Lactococcus sp. NH2-7C from Thai fermented pork (Nham)

Helicobacter pylori, linked to gastric diseases, is targeted for probiotic treatment through bacteriocin production. Bacteriocins have gained recognition for their non-toxic effects on host cells and their ability to combat a wide range of pathogens. This study aimed to taxonomically characterize and evaluate the safety and probiotic properties of the novel species of Lactococcus sp. NH2-7C isolated from fermented pork, as well as its bacteriocin NH2-7C, both in vitro and in silico. Comparative genotypic analysis revealed an average nucleotide identity of 94.96%, an average amino acid identity of 94.29%, and a digital DNA-DNA hybridization value of 63.80% when compared to Lactococcus lactis subsp. lactis JCM 5805T. These findings suggest that strain NH2-7C represents a novel species within the genus Lactococcus. In silico assessments confirmed the non-pathogenic nature of strain NH2-7C and the absence of genes associated with virulence and biogenic amine formation. Whole-genome analysis revealed the presence of the nisA gene responsible for nisin A production, indicating its potential as a beneficial compound with anti-Helicobacter pylori activity and non-toxic characteristics. Probiotic assessments indicated bile salt hydrolase and cholesterol assimilation activities, along with the modulation of interleukin-6 and tumour necrosis factor-α secretion. Strain NH2-7C demonstrated gastrointestinal tolerance and the ability to adhere to Caco-2 cells, affirming its safety and probiotic potential. Additionally, its ability to produce bacteriocins supports its suitability as a functional probiotic strain with therapeutic potential. However, further in vitro and in vivo investigations are crucial to ensure its safety and explore potential applications for Lactococcus sp. NH2-7C as a probiotic agent.

Domain structure and cross-linking in a giant adhesin from the Mobiluncus mulieris bacterium

Cell-surface proteins known as adhesins enable bacteria to colonize particular environments, and in Gram-positive bacteria often contain autocatalytically formed covalent intramolecular cross-links. While investigating the prevalence of such cross-links, a remarkable example was discovered in Mobiluncus mulieris, a pathogen associated with bacterial vaginosis. This organism encodes a putative adhesin of 7651 residues. Crystallography and mass spectrometry of two selected domains, and AlphaFold structure prediction of the remainder of the protein, were used to show that this adhesin belongs to the family of thioester, isopeptide and ester-bond-containing proteins (TIE proteins). It has an N-terminal domain homologous to thioester adhesion domains, followed by 51 immunoglobulin (Ig)-like domains containing ester- or isopeptide-bond cross-links. The energetic cost to the M. mulieris bacterium in retaining such a large adhesin as a single gene or protein construct suggests a critical role in pathogenicity and/or persistence.

Synergy of Antibiotics and Antibiofilm Agents against Methicillin-Resistant Staphylococcus aureus Biofilms

Methicillin-resistant Staphylococcus aureus (MRSA) infections are some of the most common antibiotic-resistant infections, often exacerbated by the formation of biofilms. Here, we evaluated six compounds, three common antibiotics used against MRSA and three antibiofilm compounds, in nine combinations to investigate the mechanisms of synergistic eradication of MRSA biofilms. Using metabolic assessment, colony enumeration, confocal fluorescence microscopy, and scanning electron microscopy, we identified two promising combinations of antibiotics with antibiofilm agents against preformed MRSA biofilms. The broad-spectrum protease, proteinase K, and membrane-targeting antibiotic, daptomycin, worked in synergy against MRSA biofilms by manipulating the protein content, increasing access to the cell membrane of biofilm bacteria. We also found that the combination of cationic peptide, IDR-1018, with the cell wall cross-linking inhibitor, vancomycin, exhibited synergy against MRSA biofilms by causing bacterial damage and preventing repair. Our findings identify synergistic combinations of antibiotics and antibiofilm agents, providing insight into mechanisms that may be explored further for the development of effective treatments against MRSA biofilm.

Comparative Structure Analysis of the Multi-Domain, Cell Envelope Proteases of Lactic Acid Bacteria

Lactic acid bacteria (LAB) have an extracellular proteolytic system that includes a multi-domain, cell envelope protease (CEP) with a subtilisin homologous protease domain. These CEPs have different proteolytic activities despite having similar protein sequences. Structural characterization has previously been limited to CEP homologs of dairy- and human-derived LAB strains, excluding CEPs of plant-derived LAB strains. CEP structures are a challenge to determine experimentally due to their large size and attachment to the cell envelope. This study aims to clarify the prevalence and structural diversity of CEPs by using the structure prediction software AlphaFold 2. Domain boundaries are clarified based on a comparative analysis of 21 three-dimensional structures, revealing novel domain architectures of CEP homologs that are not necessarily restricted to specific LAB species or ecological niches. The C-terminal flanking region of the protease domain is divided into fibronectin type-III-like domains with various structural traits. The analysis also emphasizes the existence of two distinct domains for cell envelope attachment that are preceded by an intrinsically disordered cell wall spanning domain. The domain variants and their combinations provide CEPs with different stability, proteolytic activity, and potentially adhesive properties, making CEPs targets for steering proteolytic activity with relevance for both food development and human health.

Integrated regulation of tubulin tyrosination and microtubule stability by human α-tubulin isotypes

Tubulin isotypes are critical for the functions of cellular microtubules, which exhibit different stability and harbor various post-translational modifications. However, how tubulin isotypes determine the activities of regulators for microtubule stability and modifications remains unknown. Here, we show that human α4A-tubulin, a conserved genetically detyrosinated α-tubulin isotype, is a poor substrate for enzymatic tyrosination. To examine the stability of microtubules reconstituted with defined tubulin compositions, we develop a strategy to site-specifically label recombinant human tubulin for single-molecule TIRF microscopy-based in vitro assays. The incorporation of α4A-tubulin into the microtubule lattice stabilizes the polymers from passive and MCAK-stimulated depolymerization. Further characterization reveals that the compositions of α-tubulin isotypes and tyrosination/detyrosination states allow graded control for the microtubule binding and the depolymerization activities of MCAK. Together, our results uncover the tubulin isotype-dependent enzyme activity for an integrated regulation of α-tubulin tyrosination/detyrosination states and microtubule stability, two well-correlated features of cellular microtubules.

The crystal structure of sortase C from an early colonizer of dental plaque, Streptococcus sanguinis, reveals an active open-lid conformation

Dental plaque is a complex microbial biofilm community of many species and a major cause of oral infections and infectious endocarditis. Plaque development begins when primary colonizers attach to oral tissues and undergo coaggregation. Primary colonizers facilitate cellular attachment and inter-bacterial interactions through sortase-dependent pili (or fimbriae) extending out from their cell surface. Consequently, the sortase enzyme is viewed as a potential drug target for controlling biofilm formation and avoiding infection. Streptococcus sanguinis is a primary colonizing bacterium whose pili consist of three different pilin subunits that are assembled together by the pilus-specific (C-type) SsaSrtC sortase. Here, we report on the crystal structure determination of the recombinant wild-type and active-site mutant forms of SsaSrtC. Interestingly, the SsaSrtC structure exhibits an open-lid conformation, although a conserved DPX motif is lacking in the lid. Based on molecular docking and structural analysis, we identified the substrate-binding residues essential for pilin recognition and pilus assembly. We also demonstrated that while recombinant SsaSrtC is enzymatically active toward the five-residue LPNTG sorting motif peptide of the pilins, this activity is significantly reduced by the presence of zinc. We further showed that rutin and α-crocin are potential candidate inhibitors of the SsaSrtC sortase via structure-based virtual screening and inhibition assays. The structural knowledge gained from our study will provide the means to develop new approaches that target pilus-mediated attachment, thereby preventing oral biofilm growth and infection.

Förster Resonance Energy Transfer Assay for Investigating the Reactivity of Thioesters in Biochemistry and Native Chemical Ligation

Thioesters are considered to be "energy-rich" functional groups that are susceptible to attack by thiolate and amine nucleophiles while remaining hydrolytically stable at neutral pH, which enables thioester chemistry to take place in an aqueous medium. Thus, the inherent reactivity of thioesters enables their fundamental roles in biology and unique applications in chemical synthesis. Here, we investigate the reactivity of thioesters that mimic acyl-coenzyme A (CoA) species and S-acylcysteine modifications as well as aryl thioesters applied in chemical protein synthesis by native chemical ligation (NCL). We developed a fluorogenic assay format for the direct and continuous investigation of the rate of reaction between thioesters and nucleophiles (hydroxide, thiolate, and amines) under various conditions and were able to recapitulate previously reported reactivity of thioesters. Further, chromatography-based analyses of acetyl- and succinyl-CoA mimics revealed striking differences in their ability to acylate lysine side chains, providing insight into nonenzymatic protein acylation. Finally, we investigated key aspects of native chemical ligation reaction conditions. Our data revealed a profound effect of the tris-(2-carboxyethyl)phosphine (TCEP) commonly used in systems where thiol-thioester exchange occurs, including a potentially harmful hydrolysis side reaction. These data provide insight into the potential optimization of native chemical ligation chemistry.

Probiotic characteristics and whole-genome sequence analysis of Pediococcus acidilactici isolated from the feces of adult beagles

The beneficial effects of lactic acid bacteria are well known and recognized as functional foods that are health benefits for companion animals. This study, for the first time, reports the probiotic properties, safety, and whole-genome sequence of Pediococcus acidilactici GLP06 isolated from feces of beagles. In this study, candidate probiotic bacteria P. acidilactici GLP02 and GLP06 were morphologically characterized and tested for their antimicrobial capacity, tolerance to different conditions (low pH, bile salts, an artificial gastrointestinal model, and high temperature), antibiotic sensitivity, hemolytic activity, cell surface hydrophobicity, autoaggregation activity, and adhesion to Caco-2 cells. P. acidilactici GLP06 showed better probiotic potential. Therefore, P. acidilactici GLP06 was evaluated for in vivo safety in mice and whole-genome sequencing. The results showed, that the supplemented MG06 group (1010 cfu/mL), GLP06 was not only nontoxic to mice, but also promoted the development of the immune system, improved resistance to oxidative stress, and increased the diversity of intestinal microorganisms and the abundance of Lactobacillus. Whole-genome sequencing showed that P. acidilactici GLP06 was 2,014,515 bp and contained 1,976 coding sequences, accounting for 86.12% of the genome, with no drug resistance genes and eight CRISPR sequences. In conclusion, the newly isolated canine-derived P. acidilactici GLP06 had good probiotic potential, was nontoxic to mice and promoted the development of immune organs, improved the biodiversity of the intestinal flora, and had no risk of drug-resistant gene transfer, indicating that P. acidilactici GLP06 can be used as a potential probiotic for the prevention and treatment of gastrointestinal diseases in companion animals.

Whole genome sequence analysis enabled affirmation of the probiotic potential of marine sporulater Bacillus amyloliquefaciens BTSS3 isolated from Centroscyllium fabricii

Probiotics are microorganisms when administered in adequate amounts, confer health benefits on the host. Many probiotics find application in various industries however, probiotic bacteria linked to marine environments are less explored.Although Bifidobacteria, Lactobacilli, and Streptococcus thermophilus are the most frequently used probiotics, Bacillus spp. have acquired much acceptance in human functional foods due to their increased tolerance and enduring competence in harsh environments like the gastrointestinal (GI) tract. In this study, the 4 Mbp genome sequence of Bacillus amyloliquefaciens strain BTSS3, a marine spore former isolated from deep-sea shark Centroscyllium fabricii, with antimicrobial and probiotic properties was sequenced, assembled, and annotated. Analysis revealed the presence of numerous genes presenting probiotic traits like production of vitamins, secondary metabolites, amino acids, secretory proteins, enzymes and other proteins that allow survival in GI tract as well as adhesion to intestinal mucosa. Adhesion by colonization in the gut was studied in vivo in zebrafish (Danio rerio) using FITC labelled B.amyloliquefaciens BTSS3. Preliminary study revealed the ability of the marine Bacillus to attach to the intestinal mucosa of the fish gut. The genomic data and the in vivo experiment affirms that this marine spore former is a promising probiotic candidate with potential biotechnological applications.

Insights into the synthesis strategies of plant-derived cyclotides

Cyclotides are plant peptides characterized with a head-to-tail cyclized backbone and three interlocking disulfide bonds, known as a cyclic cysteine knot. Despite the variations in cyclotides peptide sequences, this core structure is conserved, underlying their most useful feature: stability against thermal and chemical breakdown. Cyclotides are the only natural peptides known to date that are orally bioavailable and able to cross cell membranes. Cyclotides also display bioactivities that have been exploited and expanded to develop as potential therapeutic reagents for a wide range of conditions (e.g., HIV, inflammatory conditions, multiple sclerosis, etc.). As such, in vitro production of cyclotides is of the utmost importance since it could assist further research on this peptide class, specifically the structure-activity relationship and its mechanism of action. The information obtained could be utilized to assist drug development and optimization. Here, we discuss several strategies for the synthesis of cyclotides using both chemical and biological routes.

Harnessing sortase A transpeptidation for advanced targeted therapeutics and vaccine engineering

The engineering of potent prophylactic and therapeutic complexes has always required careful protein modification techniques with seamless capabilities. In this light, methods that favor unobstructed multivalent targeting and correct antigen presentations remain essential and very demanding. Sortase A (SrtA) transpeptidation has exhibited these attributes in various settings over the years. However, its applications for engineering avidity-inspired therapeutics and potent vaccines have yet to be significantly noticed, especially in this era where active targeting and multivalent nanomedications are in great demand. This review briefly presents the SrtA enzyme and its associated transpeptidation activity and describes interesting sortase-mediated protein engineering and chemistry approaches for achieving multivalent therapeutic and antigenic responses. The review further highlights advanced applications in targeted delivery systems, multivalent therapeutics, adoptive cellular therapy, and vaccine engineering. These innovations show the potential of sortase-mediated techniques in facilitating the development of simple plug-and-play nanomedicine technologies against recalcitrant diseases and pandemics such as cancer and viral infections.

Integrating in Silico and In Vitro Studies to Screen Anti-Staphylococcus aureus Activity From Vietnamese Ganoderma multiplicatum and Ganoderma sinense

Background: Staphylococcus aureus is a nosocomial pathogen responsible for many serious infectious diseases in humans. Finding the anti- S. aureus agents is a time-consuming and costly process. Recently, computational methods have provided a better understanding of the interactions between herbal medicine drug targets to help clinical practitioners rationally design herbal formulae. Methods: In this study, molecular docking simulation was applied to screen a list of natural secondary metabolites from Ganoderma sp. on the protein target S. aureus sortase A. Molecular dynamics models were used to assess the stability of protein–ligand complexes during the first 100 ns. To validate the computational results, 2 Ganoderma species, G. multiplicatum VNKKK1901 and G. sinense VNKKK1902, were tested for antibacterial activity against S. aureus using the disk diffusion method. Results: The results showed that, among the selected compounds, ganosinensin B and ganosinoside A generated the highest binding energy on S. aureus sortase A, and demonstrated strong and stable binding capacity to proteins. In addition, the extracts of G. sinense VNKKK1902 and G. multiplicatum VNKKK1901 were bactericidal, with minimum bactericidal concentration (MBC)/minimum inhibitory concentration (MIC) ratios of 2. Conclusion: Our findings provide the first scientific report on the antibacterial activity of Ganoderma sp., which contain 2 promising compounds, ganosinensin B and ganosinoside A, as potential hits for developing novel drugs capable of supporting treatment of S. aureus infection.

Structural and functional characterization of the catalytic domain of a cell-wall anchored bacterial lytic polysaccharide monooxygenase from Streptomyces coelicolor

Bacterial lytic polysaccharide monooxygenases (LPMOs) are known to oxidize the most abundant and recalcitrant polymers in Nature, namely cellulose and chitin. The genome of the model actinomycete Streptomyces coelicolor A3(2) encodes seven putative LPMOs, of which, upon phylogenetic analysis, four group with typical chitin-oxidizing LPMOs, two with typical cellulose-active LPMOs, and one which stands out by being part of a subclade of non-characterized enzymes. The latter enzyme, called ScLPMO10D, and most of the enzymes found in this subclade are unique, not only because of variation in the catalytic domain, but also as their C-terminus contains a cell wall sorting signal (CWSS), which flags the LPMO for covalent anchoring to the cell wall. Here, we have produced a truncated version of ScLPMO10D without the CWSS and determined its crystal structure, EPR spectrum, and various functional properties. While showing several structural and functional features typical for bacterial cellulose active LPMOs, ScLPMO10D is only active on chitin. Comparison with two known chitin-oxidizing LPMOs of different taxa revealed interesting functional differences related to copper reactivity. This study contributes to our understanding of the biological roles of LPMOs and provides a foundation for structural and functional comparison of phylogenetically distant LPMOs with similar substrate specificities.

GPApred: The first computational predictor for identifying proteins with LPXTG-like motif using sequence-based optimal features

The cell surface proteins of gram-positive bacteria are involved in many important biological functions, including the infection of host cells. Owing to their virulent nature, these proteins are also considered strong candidates for potential drug or vaccine targets. Among the various cell surface proteins of gram-positive bacteria, LPXTG-like proteins form a major class. These proteins have a highly conserved C-terminal cell wall sorting signal, which consists of an LPXTG sequence motif, a hydrophobic domain, and a positively charged tail. These surface proteins are targeted to the cell envelope by a sortase enzyme via transpeptidation. A variety of LPXTG-like proteins have been experimentally characterized; however, their number in public databases has increased owing to extensive bacterial genome sequencing without proper annotation. In the absence of experimental characterization, identifying and annotating these sequences is extremely challenging. Therefore, in this study, we developed the first machine learning-based predictor called GPApred, which can identify LPXTG-like proteins from their primary sequences. Using a newly constructed benchmark dataset, we explored different classifiers and five feature encodings and their hybrids. Optimal features were derived using the recursive feature elimination method, and these features were then trained using a support vector machine algorithm. The performance of different models was evaluated using independent datasets, and a final model (GPApred) was selected based on consistency during cross-validation and independent assessment. GPApred can be an effective tool for predicting LPXTG-like sequences and can be further employed for functional characterization or drug targeting. Availability: https://procarb.org/gpapred/.

Sortase A Inhibitor Protein Nanoparticle Formulations Demonstrate Antibacterial Synergy When Combined with Antimicrobial Peptides

Sortase A (SrtA) is an enzyme which attaches proteins, including virulence factors, to bacterial cell walls. It is a potential target for developing anti-virulence agents against pathogenic and antimicrobial resistant bacteria. This study aimed to engineer 𝛽-lactoglobulin protein nanoparticles (PNPs) for encapsulating safe and inexpensive natural SrtA inhibitors (SrtAIs; trans-chalcone (TC), curcumin (CUR), quercetin (QC), and berberine (BR)) to improve their poor aqueous dispersibility, to screen for synergy with antimicrobial peptides (AMPs), and to reduce the cost, dose, and toxicity of AMPs. Minimum inhibitory concentration (MIC), checkerboard synergy, and cell viability assays were performed for SrtAI PNPs against Gram-positive (methicillin-sensitive and -resistant S. aureus) and Gram-negative (E. coli, P. aeruginosa) bacteria alone and combined with leading AMPs (pexiganan, indolicidin, and a mastoparan derivative). Each SrtAI PNP inhibited Gram-positive (MIC: 62.5-125 µg/mL) and Gram-negative (MIC: 31.3-500 µg/mL) bacterial growth. TC PNPs with pexiganan demonstrated synergy against each bacteria, while BR PNPs with pexiganan or indolicidin provided synergy towards S. aureus. Each SrtAI PNP inhibited SrtA (IC₅₀: 25.0-81.8 µg/mL), and did not affect HEK-293 cell viability at their MIC or optimal synergistic concentrations with AMPs. Overall, this study provides a safe nanoplatform for enhancing antimicrobial synergy to develop treatments for superbug infections.

Spatial and temporal localization of cell wall associated pili in Enterococcus faecalis

Enterococcus faecalis virulence requires cell wall-associated proteins, including the sortase-assembled endocarditis and biofilm associated pilus (Ebp), important for biofilm formation in vitro and in vivo. The current paradigm for sortase-assembled pilus biogenesis in Gram-positive bacteria is that sortases attach substrates to lipid II peptidoglycan (PG) precursors, prior to their incorporation into the growing cell wall. Contrary to prevailing dogma, by following the distribution of Ebp and PG throughout the E. faecalis cell cycle, we found that cell surface Ebp do not co-localize with newly synthesized PG. Instead, surface-exposed Ebp are localized to the older cell hemisphere and excluded from sites of new PG synthesis at the septum. Moreover, Ebp deposition on the younger hemisphere of the E. faecalis diplococcus appear as foci adjacent to the nascent septum. We propose a new model whereby sortase substrate deposition can occur on older PG rather than at sites of new cell wall synthesis. Consistent with this model, we demonstrate that sequestering lipid II to block PG synthesis via ramoplanin, does not impact new Ebp deposition at the cell surface. These data support an alternative paradigm for sortase substrate deposition in E. faecalis, in which Ebp are anchored directly onto uncrosslinked cell wall, independent of new PG synthesis.

Adhesive Virulence Factors of Staphylococcus aureus Resist Digestion by Coagulation Proteases Thrombin and Plasmin

Staphylococcus aureus (S. aureus) is an invasive and life-threatening pathogen that has undergone extensive coevolution with its mammalian hosts. Its molecular adaptations include elaborate mechanisms for immune escape and hijacking of the coagulation and fibrinolytic pathways. These capabilities are enacted by virulence factors including microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) and the plasminogen-activating enzyme staphylokinase (SAK). Despite the ability of S. aureus to modulate coagulation, until now the sensitivity of S. aureus virulence factors to digestion by proteases of the coagulation system was unknown. Here, we used protein engineering, biophysical assays, and mass spectrometry to study the susceptibility of S. aureus MSCRAMMs to proteolytic digestion by human thrombin, plasmin, and plasmin/SAK complexes. We found that MSCRAMMs were highly resistant to proteolysis, and that SAK binding to plasmin enhanced this resistance. We mapped thrombin, plasmin, and plasmin/SAK cleavage sites of nine MSCRAMMs and performed biophysical, bioinformatic, and stability analysis to understand structural and sequence features common to protease-susceptible sites. Overall, our study offers comprehensive digestion patterns of S. aureus MSCRAMMs by thrombin, plasmin, and plasmin/SAK complexes and paves the way for new studies into this resistance and virulence mechanism.

A review on pilus assembly mechanisms in Gram-positive and Gram-negative bacteria

The surface of Gram-positive and Gram-negative bacteria contains long hair-like proteinaceous protrusion known as pili or fimbriae. Historically, pilin proteins were considered to play a major role in the transfer of genetic material during bacterial conjugation. Recent findings however elucidate their importance in virulence, biofilm formation, phage transduction, and motility. Therefore, it is crucial to gain mechanistic insights on the subcellular assembly of pili and the localization patterns of their subunit proteins (major and minor pilins) that aid the macromolecular pilus assembly at the bacterial surface. In this article, we review the current knowledge of pilus assembly mechanisms in a wide range of Gram-positive and Gram-negative bacteria, including subcellular localization patterns of a few pilin subunit proteins and their role in virulence and pathogenesis.

Isovitexin Protects Mice from Methicillin-Resistant Staphylococcus aureus-Induced Pneumonia by Targeting Sortase A

The rise of methicillin-resistant Staphylococcus aureus (MRSA) has resulted in significant morbidity and mortality, and clinical treatment of MRSA infections has become extremely difficult. Sortase A (SrtA), a virulence determinant that anchors numerous virulence-related proteins to the cell wall, is a prime druggable target against S. aureus infection due to its crucial role in the pathogenicity of S. aureus. Here, we demonstrate that isovitexin, an active ingredient derived from a variety of traditional Chinese medicines, can reversibly inhibit SrtA activity in vitro with a low dose (IC₅₀=24.72 μg/ml). Fluorescence quenching and molecular simulations proved the interaction between isovitexin and SrtA. Subsequent point mutation experiments further confirmed that the critical amino acid positions for SrtA binding to isovitexin were Ala-92, Ile-182, and Trp-197. In addition, isovitexin treatment dramatically reduced S. aureus invasion of A549 cells. This study shows that treatment with isovitexin could alleviate pathological injury and prolong the life span of mice in an S. aureus pneumonia model. According to our research, isovitexin represents a promising lead molecule for the creation of anti-S. aureus medicines or adjuncts.

Host–Pathogen Interactions of Marine Gram-Positive Bacteria

Simple Summary

Complex interactions between marine Gram-positive pathogens and fish hosts in the marine environment can result in diseases of economically important finfish, which cause economic losses in the aquaculture industry. Understanding how these pathogens interact with the fish host and generate disease will contribute to efficient prophylactic measures and treatments. To our knowledge, there are no systematic reviews on marine Gram-positive pathogens. Therefore, here we reviewed the host–pathogen interactions of marine Gram-positive pathogens from the pathogen-centric and host-centric points of view.

Abstract

Marine Gram-positive bacterial pathogens, including Renibacterium salmoninarum, Mycobacterium marinum, Nocardia seriolae, Lactococcus garvieae, and Streptococcus spp. cause economic losses in marine fish aquaculture worldwide. Comprehensive information on these pathogens and their dynamic interactions with their respective fish–host systems are critical to developing effective prophylactic measures and treatments. While much is known about bacterial virulence and fish immune response, it is necessary to synthesize the knowledge in terms of host–pathogen interactions as a centerpiece to establish a crucial connection between the intricate details of marine Gram-positive pathogens and their fish hosts. Therefore, this review provides a holistic view and discusses the different stages of the host–pathogen interactions of marine Gram-positive pathogens. Gram-positive pathogens can invade fish tissues, evade the fish defenses, proliferate in the host system, and modulate the fish immune response. Marine Gram-positive pathogens have a unique set of virulence factors that facilitate adhesion (e.g., adhesins, hemagglutination activity, sortase, and capsules), invasion (e.g., toxins, hemolysins/cytolysins, the type VII secretion system, and immune-suppressive proteins), evasion (e.g., free radical quenching, actin-based motility, and the inhibition of phagolysosomal fusion), and proliferation and survival (e.g., heme utilization and siderophore-mediated iron acquisition systems) in the fish host. After infection, the fish host initiates specific innate and adaptive immune responses according to the extracellular or intracellular mechanism of infection. Although efforts have continued to be made in understanding the complex interplay at the host–pathogen interface, integrated omics-based investigations targeting host–pathogen–marine environment interactions hold promise for future research.

Structures of Streptococcus pyogenes Class A sortase in complex with substrate and product mimics provide key details of target recognition

The cell wall is a critical extracellular barrier for bacteria and many other organisms. In bacteria, this structural layer consists of peptidoglycan, which maintains cell shape and structural integrity and provides a scaffold for displaying various protein factors. To attach proteins to the cell wall, Gram-positive bacteria utilize sortase enzymes, which are cysteine transpeptidases that recognize and cleave a specific sorting signal, followed by ligation of the sorting signal–containing protein to the peptidoglycan precursor lipid II (LII). This mechanism is the subject of considerable interest as a target for therapeutic intervention and as a tool for protein engineering, where sortases have enabled sortase-mediated ligation or sortagging strategies. Despite these uses, there remains an incomplete understanding of the stereochemistry of substrate recognition and ligation product formation. Here, we solved the first structures of sortase A from Streptococcus pyogenes bound to two substrate sequences, LPATA and LPATS. In addition, we synthesized a mimetic of the product of sortase-mediated ligation involving LII (LPAT-LII) and solved the complex structure in two ligand conformations. These structures were further used as the basis for molecular dynamics simulations to probe sortase A-ligand dynamics and to construct a model of the acyl–enzyme intermediate, thus providing a structural view of multiple key states in the catalytic mechanism. Overall, this structural information provides new insights into the recognition of the sortase substrate motif and LII ligation partner and will support the continued development of sortases for protein engineering applications.

Streptococcus mutans PrsA mediates AtlA secretion contributing to extracellular DNA release and biofilm formation in the pathogenesis of infective endocarditis

The role of secretion chaperone-regulated virulence proteins in the pathogenesis of infective endocarditis (IE) induced by viridans streptococci such as Streptococcus mutans is unclear. In this study, we investigated the contribution of the foldase protein PrsA, a putative parvulin-type peptidyl-prolyl isomerase, to the pathogenesis of S. mutans-induced IE. We found that a prsA-deficient strain had reduced virulence in terms of formation of vegetation on damaged heart valves, as well as reduced autolysis activity, eDNA release and biofilm formation capacity. The secretion and surface exposure of AtlA in vitro was reduced in the prsA-deficient mutant strain, and complementation of recombinant AtlA in the culture medium restored a wild type biofilm phenotype of the prsA-deficient mutant strain. This result suggests that secretion and surface localization of AtlA is regulated by PrsA during biofilm formation. Together, these results demonstrate that S. mutans PrsA could regulate AtlA-mediated eDNA release to contribute to biofilm formation in the pathogenesis of IE.

A conserved signal-peptidase antagonist modulates membrane homeostasis of actinobacterial sortase critical for surface morphogenesis

Cell wall anchoring of surface proteins in Gram-positive bacteria requires a sortase enzyme. Here, we unveiled the hitherto unknown function of an evolutionarily conserved small transmembrane protein, named SafA, genetically linked to the housekeeping sortase in Actinobacteria. We show that Actinomyces oris SafA interacts with the housekeeping sortase SrtA via the conserved FPW motif and prevents SrtA cleavage by the signal peptidase LepB2, hence maintaining membrane homeostasis of SrtA. This function is conserved as ectopic expression of SafA from Corynebacterium diphtheriae and Corynebacterium matruchotii in the A. oris safA mutant rescues its defects in cell morphology, pilus assembly, surface protein localization, and polymicrobial interactions. Thus, SafA represents an archetypal antagonist of signal peptidase that modulates surface assembly in Actinobacteria.

Most Actinobacteria encode a small transmembrane protein, whose gene lies immediately downstream of the housekeeping sortase coding for a transpeptidase that anchors many extracellular proteins to the Gram-positive bacterial cell wall. Here, we uncover the hitherto unknown function of this class of conserved proteins, which we name SafA, as a topological modulator of sortase in the oral Actinobacterium Actinomyces oris. Genetic deletion of safA induces cleavage and excretion of the otherwise predominantly membrane-bound SrtA in wild-type cells. Strikingly, the safA mutant, although viable, exhibits severe abnormalities in cell morphology, pilus assembly, surface protein localization, and polymicrobial interactions—the phenotypes that are mirrored by srtA depletion. The pleiotropic defect of the safA mutant is rescued by ectopic expression of safA from not only A. oris, but also Corynebacterium diphtheriae or Corynebacterium matruchotii. Importantly, the SrtA N terminus harbors a tripartite-domain feature typical of a bacterial signal peptide, including a cleavage motif AXA, mutations in which prevent SrtA cleavage mediated by the signal peptidase LepB2. Bacterial two-hybrid analysis demonstrates that SafA and SrtA directly interact. This interaction involves a conserved motif FPW within the exoplasmic face of SafA, since mutations of this motif abrogate SafA-SrtA interaction and induce SrtA cleavage and excretion as observed in the safA mutant. Evidently, SafA is a membrane-imbedded antagonist of signal peptidase that safeguards and maintains membrane homeostasis of the housekeeping sortase SrtA, a central player of cell surface assembly.

Intramolecular covalent bonds in Gram-positive bacterial surface proteins

Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.

Identification and prioritization of promising lead molecules from Syzygium aromaticum against Sortase C from Streptococcus pyogenes: an in silico investigation

Sortases are extracellular transpeptidases that play an essential role in the adhesion of secreted proteins to the peptidoglycan layer of the cell wall of Gram-negative bacteria. Sortases are an important drug target protein due to their involvement in synthesizing the peptidoglycan cell wall of Streptococcus pyogenes, and these are not found in Homo sapiens. In this study, initially, we have performed protein sequence analysis to understand the sequential properties of Sortase C. Next, a comparative protein modeling approach was used to predict the three-dimensional model of Sortase C based on the crystal structure of Sortase C from Streptococcus pneumoniae. Virtual screening with an in-house library of phytochemicals from Syzygium aromaticum and molecular docking studies were performed to identify the promising lead molecules. These compounds were also analyzed for their drug-like and pharmacokinetic properties. Subsequently, the protein-ligand complexes of the selected ligands were subjected to molecular dynamics (MD) simulations to investigate their dynamic behavior in physiological conditions. The global and essential dynamics analyses result implied that the Sortase C complexes of the proposed three lead candidates exhibited adequate stability during the MD simulations. Additionally, the three proposed molecules showed favorable MM/PBSA binding free energy values ranging from -13.8 +/- 9.41 to -56.6 +/- 8.82 kcal/mol. After an extensive computational investigation, we have identified three promising lead candidates (CID:13888122, CID:3694932 and CID:102445430) against Sortase C from S. pyogenes. The result obtained from these computational studies can be used to screen and develop the inhibitors against Sortase C from S. pyogenes. Communicated by Ramaswamy H. Sarma.

Deciphering the substrate specificity of housekeeping sortase A and pilus-specific sortase C of probiotic bacterium Lactococcus lactis

Several strains and species of lactic acid bacteria (LAB) are widely used in fermented foods, including dairy products and also as probiotics, because of their contribution to various health benefits in humans. Sortase enzymes decorate the bacterial cell wall with different surface proteins and pili for facilitating the interactions with host and environment for the colonization and beneficial effects. While the sortases and sortase anchored proteins from pathogens have been the prime focus of the research in the past, sortases from many non-pathogenic bacteria, including LAB strains, have attracted attention for their potential applications in vaccine delivery and other clinical interventions. Here, we report the purification and functional characterization of two sortases (housekeeping SrtA and pilus-specific SrtC) from a probiotic Lactococcus lactis. The purified sortases were found to be active against the putative LPXTG motif-based peptide substrates, albeit with differences. The in-silico analysis provides insights into the residues involved in substrate binding and specificity. Overall, this study sheds new light on the aspects of structure, substrate specificity, and function of sortases from non-pathogenic bacteria, which may have physiological ramifications as well as their applications in sortase-mediated protein bioconjugation.

Chemically Modified Bacterial Sacculi as a Vaccine Microparticle Scaffold

Vaccine scaffolds and carrier proteins increase the immunogenicity of subunit vaccines. Here, we developed, characterized, and demonstrated the efficacy of a novel microparticle vaccine scaffold comprised of bacterial peptidoglycan (PGN), isolated as an entire sacculi. The PGN microparticles contain bio-orthogonal chemical handles allowing for site-specific attachment of immunogens. We first evaluated the purification, integrity, and immunogenicity of PGN microparticles derived from a variety of bacterial species. We then optimized PGN microparticle modification conditions; Staphylococcus aureus PGN microparticles containing azido-d-alanine yielded robust conjugation to immunogens. We then demonstrated that this vaccine scaffold elicits comparable immunostimulation to the conventional carrier protein, keyhole limpet hemocyanin (KLH). We further modified the S. aureus PGN microparticle to contain the SARS-CoV-2 receptor-binding domain (RBD)—this conjugate vaccine elicited neutralizing antibody titers comparable to those elicited by the KLH-conjugated RBD. Collectively, these findings suggest that chemically modified bacterial PGN microparticles are a conjugatable and biodegradable microparticle scaffold capable of eliciting a robust immune response toward an antigen of interest.

Challenges in the use of sortase and other peptide ligases for site-specific protein modification

Site-specific protein modification is a widely-used biochemical tool. However, there are many challenges associated with the development of protein modification techniques, in particular, achieving site-specificity, reaction efficiency and versatility. The engineering of peptide ligases and their substrates has been used to address these challenges. This review will focus on sortase, peptidyl asparaginyl ligases (PALs) and variants of subtilisin; detailing how their inherent specificity has been utilised for site-specific protein modification. The review will explore how the engineering of these enzymes and substrates has led to increased reaction efficiency mainly due to enhanced catalytic activity and reduction of reversibility. It will also describe how engineering peptide ligases to broaden their substrate scope is opening up new opportunities to expand the biochemical toolkit, particularly through the development of techniques to conjugate multiple substrates site-specifically onto a protein using orthogonal peptide ligases.

We highlight chemical and biochemical strategies taken to optimise peptide and protein modification using peptide ligases.

Mutations of the brpR and brpS genes affect biofilm formation in Staphylococcus aureus

BACKGROUND

In the United States, Staphylococcus aureus (S. aureus) kills tens of thousands of individuals each year and the formation of a biofilm contributes to lethality. Biofilm-associated infections are hard to treat once the biofilm has formed. A new stilbene drug, labeled SK-03-92, was shown to kill S. aureus and affected transcription of two genes tied to a putative two-component system (TCS) we have named brpR (biofilm regulating protein regulator) and brpS (biofilm regulating protein sensor).

AIM

To determine if BrpR and BrpS regulate biofilm formation, brpR and brpS mutants were assessed using biofilm assays compared to wild-type S. aureus.

METHODS

A combination of biofilm and quantitative real-time-polymerase chain reaction assays were used. In addition, bioinformatic software tools were also utilized.

RESULTS

Significantly more biofilm was created in the brpR and brpS mutants vs wild-type cells. Quantitative real-time polymerase chain reactions showed the brpS mutant had differences in transcription of biofilm associated genes that were eight-fold higher for srtA, two-fold lower for lrgA, and 1.6-fold higher for cidA compared to wild-type. Bioinformatic analysis demonstrated that the S. aureus brpR/brpS TCS had homology to streptococcal late-stage competence proteins involved in cell-death, increased biofilm production, and the development of persister cells.

CONCLUSION

Our study suggests that brpR/brpS is a TCS that may repress S. aureus biofilm production and be linked to late-stage competence in S. aureus.

Identification of novel small-molecular inhibitors of Staphylococcus aureus sortase A using hybrid virtual screening

Staphylococcus aureus is one of the most dangerous pathogens commonly associated with high levels of morbidity and mortality. Sortase A is considered as a promising molecular target for the development of antistaphylococcal agents. Using hybrid virtual screening approach and FRET analysis, we have identified five compounds able to decrease the activity of sortase A by more than 50% at the concentration of 200 µM. The most promising compound was 2-(2-amino-3-chloro-benzoylamino)-benzoic acid which was able to inhibit S. aureus sortase A at the IC₅₀ value of 59.7 µM. This compound was selective toward sortase A compared to other four cysteine proteases - cathepsin L, cathepsin B, rhodesain, and the SARS-CoV2 main protease. Microscale thermophoresis experiments confirmed that this compound bound sortase A with K_D value of 189 µM. Antibacterial and antibiofilm assays also confirmed high specificity of the hit compound against two standard and three wild-type, S. aureus hospital infection isolates. The effect of the compound on biofilms produced by two S. aureus ATCC strains was also observed suggesting that the compound reduced biofilm formation by changing the biofilm structure and thickness.

Engineering nanobodies for next-generation molecular imaging

In recent years, nanobodies have emerged as ideal imaging agents for molecular imaging. Molecular nanobody imaging combines the specificity of nanobodies with the sensitivity of state-of-the-art molecular imaging modalities, such as positron emission tomography (PET). Given that modifications of nanobodies alter their pharmacokinetics (PK), the engineering strategies that combine nanobodies with radionuclides determine the effectiveness, reliability, and safety of the molecular imaging probes. In this review, we introduce conjugation strategies that have been applied to nanobodies, including random conjugation, ^99mTc tricarbonyl chemistry, sortase A-mediated site-specific conjugation, maleimide-cysteine chemistry, and click chemistries. We also summarize the latest advances in nanobody tracers, emphasizing their preclinical and clinical use. In addition, we elaborate on nanobody-based near-infrared fluorescence (NIRF) imaging and image-guided surgery.

Versatile Supramolecular Complex for Targeted Antimicrobial Photodynamic Inactivation

We report the development of a supramolecular structure endowed with photosensitizing properties and targeting capability for antimicrobial photodynamic inactivation. Our synthetic strategy uses the tetrameric bacterial protein streptavidin, labeled with the photosensitizer eosin, as the main building block. Biotinylated immunoglobulin G (IgG) from human serum, known to associate with Staphylococcus aureus protein A, was bound to the complex streptavidin-eosin. Fluorescence correlation spectroscopy and fluorescence microscopy demonstrate binding of the complex to S. aureus. Efficient photoinactivation is observed for S. aureus suspensions treated with IgG-streptavidin-eosin at concentrations higher than 0.5 μM and exposed to green light. The proposed strategy offers a flexible platform for targeting a variety of molecules and microbial species.

Exploration of Bacterial Re-Growth as In Vitro Phenomenon Affecting Methods for Analysis of the Antimicrobial Activity of Chimeric Bacteriophage Endolysins

Drug alternatives to combat methicillin-resistant Staphylococcus aureus (MRSA) in human and animal healthcare are urgently needed. Recently, the recombinant bacteriophage endolysins, PRF-119 and its successor substance HY-133, have proven to be highly active against various S. aureus clonal lineages and to exhibit a very rapid bactericidal effect when standard methods for susceptibility testing are applied. Along with subsequent growth curve experiments, a re-growth phenomenon was observed in vitro necessitating its clarification for the assessment of the agent’s stability and activity as well as for methodological aspects of endolysin testing in general. Distinct in vitro parameters were comparatively examined applying also scanning electron microscopy, fluorescence assays and SDS-PAGE analysis. The shape and material of the culture vessels as well as the shaking conditions were identified as factors influencing the in vitro stability and activity of HY-133. The highest function maintenance was observed in plain centrifuge tubes. Based on this, the conditions and parameters of assays for testing the antimicrobial activities of phage endolysins were determined and adjusted. In particular, shear forces should be kept to a minimum. Our results form the basis for both future test standardization and re-growth-independent experiments as prerequisites for exact determination of the antimicrobial activities of engineered endolysins.

Peptide ligases: A Novel and potential enzyme toolbox for catalytic cross-linking of protein/peptide-based biomaterial scaffolds for tissue engineering

The fabrication of novel biomaterial scaffolds with improved biological interactions and mechanical properties is an important aspect of tissue engineering. The three-dimensional (3D) protein/peptide-based polymeric scaffolds are promising in vitro biomaterials to replicate the in vivo microenvironment mimicking the extracellular matrix (ECM) for cell differentiation and subsequent tissue formation. Among different strategies in the fabrication of scaffolds, bioorthogonal enzymatic reactions for rapid in situ zero-length cross-linking are advantageous. Peptide ligases as a novel toolbox have the potentiality to enzymatically cross-link natural/synthetic protein/peptide-based polymeric chains for a wide range of biomedical applications. Although natural peptide ligases, such as sortases and butelase 1 are known cysteine proteases with ligase activity, some serine proteases, such as trypsin and subtilisin, are protein engineered to form trypsiligase and subtiligase, respectively, which exhibited efficient ligase activity by linking proteins/peptides with a great variety of molecules. Peptide ligase activity by these engineered proteases is more efficient than the hydrolysis of peptide bonds (peptidase activity). Peptide esters form acyl-enzyme intermediate with serine/cysteine residues of these proteases, with subsequent aminolysis forming covalent peptide bond with N-terminal residue of another polymeric chain. In addition, peptide ligases have the potential to conjugate with cell-adhesive ECM proteins or motifs and growth factors to (bio)polymeric networks to enhance cell attachment, growth, and differentiation. Here, we review the potential and limitations of natural and engineered peptide ligases as an enzyme toolbox with a focus on sortases (classes A-D), butelase 1, trypsiligase, and subtilisin variants, and the mechanisms for their zero-length cross-linking of (bio)polymeric scaffolds for various tissue engineering and regenerative applications.

Comparative genomics and proteomics of Eubacterium maltosivorans: functional identification of trimethylamine methyltransferases and bacterial microcompartments in a human intestinal bacterium with a versatile lifestyle

Eubacterium maltosivorans YI^T is a human intestinal isolate capable of acetogenic, propionogenic and butyrogenic growth. Its 4.3-Mb genome sequence contains coding sequences for 4227 proteins, including 41 different methyltransferases. Comparative proteomics of strain YI^T showed the Wood-Ljungdahl pathway proteins to be actively produced during homoacetogenic growth on H₂ and CO₂ while butyrogenic growth on a mixture of lactate and acetate significantly upregulated the production of proteins encoded by the recently identified lctABCDEF cluster and accessory proteins. Growth on H₂ and CO₂ unexpectedly induced the production of two related trimethylamine methyltransferases. Moreover, a set of 16 different trimethylamine methyltransferases together with proteins for bacterial microcompartments were produced during growth and deamination of the quaternary amines, betaine, carnitine and choline. Growth of strain YI^T on 1,2-propanediol generated propionate with propanol and induced the formation of bacterial microcompartments that were also prominently visible in betaine-grown cells. The present study demonstrates that E. maltosivorans is highly versatile in converting low-energy fermentation end-products in the human gut into butyrate and propionate whilst being capable of preventing the formation of the undesired trimethylamine by converting betaine and other quaternary amines in bacterial microcompartments into acetate and butyrate.

Prevalence and conservation of ebp genes in Enterococcus faecalis originated from animals

AIMS

The study aimed to investigate the prevalence and conservation of endocarditis and biofilm-associated pili (ebp) genes in Enterococcus faecalis originated from animals and the potential of developing Ebp into serological diagnostic and vaccine targets.

METHODS AND RESULTS

In this work, we investigated the prevalence and conservation of ebp genes in 116 strains of E. faecalis originated from animals by using PCR and sequencing methods. The results demonstrated the presence of ebp genes (ebpA, ebpB and ebpC) in all 116 strains of E. faecalis, and their amino acid homology ranges from 96.6% to 100.0%. Moreover, the phylogenetic analysis of ebp genes in all 164 E. faecalis strains (including 48 reference strains) revealed that ebp genes show no significant correlation with species origins and regions of E. faecalis, indicating that ebp genes are conserved features in E. faecalis, even though it evolved under environmental pressures from various regions and origins. Given that EbpA1 as a part of the adhesion protein EbpA has immunogenicity, we further determined whether amino acid mutations have effects on the function and 3D structure of EbpA1. The results showed that two of the 26 mutations, at amino acids positions 178 and 387, had deleterious effects on the biological function of EbpA1 protein, while all mutations had no effect on the 3D structure or binding pockets of EbpA1 protein.

CONCLUSIONS

This study suggests that ebp genes are prevalent and conserved in E. faecalis originated from diverse animal origins and regions. EbpA1 could be a potential target for serological diagnosis and vaccine development to prevent E. faecalis infection.

SIGNIFICANCE AND IMPACT OF STUDY

The current study provides data to support further research on Ebp as a serological diagnostic and vaccine target against E. faecalis infection.