Cyclic Peptides that Govern Signal Transduction Pathways: From Prokaryotes to Multi-Cellular Organisms

Characterization of Genomic, Physiological, and Probiotic Features of Lactiplantibacillus plantarum JS21 Strain Isolated from Traditional Fermented Jiangshui

This study aimed to understand the genetic and metabolic traits of a Lactiplantibacillus plantarum JS21 strain and its probiotic abilities through laboratory tests and computer analysis. L. plantarum JS21 was isolated from a traditional fermented food known as "Jiangshui" in Hanzhong city. In this research, the complete genetic makeup of JS21 was determined using Illumina and PacBio technologies. The JS21 genome consisted of a 3.423 Mb circular chromosome and five plasmids. It was found to contain 3023 protein-coding genes, 16 tRNA genes, 64 rRNA operons, 40 non-coding RNA genes, 264 pseudogenes, and six CRISPR array regions. The GC content of the genome was 44.53%. Additionally, the genome harbored three complete prophages. The evolutionary relationship and the genome collinearity of JS21 were compared with other L. plantarum strains. The resistance genes identified in JS21 were inherent. Enzyme genes involved in the Embden-Meyerhof-Parnas (EMP) and phosphoketolase (PK) pathways were detected, indicating potential for facultative heterofermentative pathways. JS21 possessed bacteriocins plnE/plnF genes and genes for polyketide and terpenoid assembly, possibly contributing to its antibacterial properties against Escherichia coli (ATCC 25922), Escherichia coli (K88), Staphylococcus aureus (CMCC 26003), and Listeria monocytogenes (CICC 21635). Furthermore, JS21 carried genes for Na+/H+ antiporters, F0F1 ATPase, and other stress resistance genes, which may account for its ability to withstand simulated conditions of the human gastrointestinal tract in vitro. The high hydrophobicity of its cell surface suggested the potential for intestinal colonization. Overall, L. plantarum JS21 exhibited probiotic traits as evidenced by laboratory experiments and computational analysis, suggesting its suitability as a dietary supplement.

Genomic and phenotypic analyses reveal Paenibacillus polymyxa PJH16 is a potential biocontrol agent against cucumber fusarium wilt

In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain Paenibacillus polymyxa PJH16 in preventing Fusarium oxysporum f. sp. cucumerinum (Foc). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of β-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as P. polymyxa PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of P. polymyxa PJH16 with four closely related P. polymyxa strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in P. polymyxa PJH16. Therefore, P. polymyxa PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future.

Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species

BACKGROUND

The gut microbiota is considered a rich source for potential novel probiotics. Enterococcus genus is a normal component of a healthy gut microbiota, suggesting its vital role. Nosocomial infections caused mainly by E. facalis and E. faecium have been attributed to the plasticity of the Enterococcus genomes. In this study, we assessed the probiotic and safety characteristics of two E. lactis strains isolated from the human gut microbiota using in-vitro and in silico approaches. Additionally, the safety of the E. lactis species was evaluated using comparative genomics analysis.

RESULTS

The two E. lactis strains 10NA and 50NA showed resistance to bile salts and acid tolerance with antibacterial activity against Escherichia coli, Salmonella typhi, and Clostridioides difficile. For safety assays, the two strains did not display any type of hemolysis on blood agar, and the survival of Caco-2 cells was not significantly different (P-value > 0.05) compared to the control using cell free supernatants at 100% (v/v), 50% (v/v), 10% (v/v), and 5% (v/v) concentrations. Regarding antibiotic susceptibility, both strains were sensitive to vancomycin, tetracycline, and chloramphenicol. Comprehensive whole-genome analysis revealed no concerning associations between virulence or antibiotic resistance genes and any of the identified mobile genetic elements. Comparative genome analysis with closely related E. faecium species genomes revealed the distinctive genomic safety of the E. lactis species.

CONCLUSIONS

Our two E. lactis strains showed promising probiotic properties in-vitro. Their genomes were devoid of any transferable antibiotic resistance genes. In silico comparative analysis confirmed the safety of the E. lactis species. These results suggest that E. lactis species could be a potential source for safer Enterococcus probiotic supplements.

Assessing the efficacy of probiotics in augmenting bovine reproductive health: an integrated in vitro, in silico, and in vivo study

The aim of this study was to isolate and characterize bovine-vaginal probiotics genotypically and phenotypically using in silico and evaluate their in vivo performance in buffaloes with endometritis. For the in vitro isolation and characterization, vaginal swabs were collected from 34 cows and 17 buffaloes, and 709 primary bacterial isolates with probiotic activity were obtained using MRS agar media. Two isolates Lactiplantibacillus plantarum KUGBRC (LPKUGBRC) and Pediococcus pentosaceus GBRCKU (PPGBRCKU) demonstrated optimum in vitro probiotic activities as compared to Lacticaseibacillus rhamnosus GG including, acid production, secretion of fatty acids and exopolysaccharide, cell surface hydrophobicity, self-aggregating and co-aggregating capacity with pathogens, anti-microbial activity and bacteriocin-like compounds against pathogens Escherichia coli and Staphylococcus aureus in cell-free supernatant and absence of hemolytic activity. Their phenotypic capacity was confirmed by analyzing the whole genome sequencing data and identifying genes and pathways associated with probiotic properties. These probiotic isolates have shown no virulence genes were discovered in their genomic study. In vivo study of 92 buffaloes suffering from clinical endometritis with purulent cervico-vaginal mucus (CVM) were randomly allocated 40 × 10⁸ CFU/ml LPKUGBRC and PPGBRCKU and 40 ml Normal saline. The LPKUGBRC reduced the duration between administration of probiotic to induction of healthy estrus significantly. However, no effect was observed on pregnancy rate. These results suggest that LPKUGBRC and PPGBRCKU probiotic bacteria demonstrate probiotic efficiency and adaptability. Further sourced from the same niche as the targeted infection, they offer a distinct advantage in targeting the specific microbial population associated with endometritis. The findings of this study highlight the potential of LPKUGBRC and PPGBRCKU probiotics in treating endometritis and suggest further exploration of their clinical applications.

Targeting Peptide-Based Quorum Sensing Systems for the Treatment of Gram-Positive Bacterial Infections

Bacteria utilize a cell density-dependent communication system called quorum sensing (QS) to coordinate group behaviors. In Gram-positive bacteria, QS involves the production of and response to auto-inducing peptide (AIP) signaling molecules to modulate group phenotypes, including pathogenicity. As such, this bacterial communication system has been identified as a potential therapeutic target against bacterial infections. More specifically, developing synthetic modulators derived from the native peptide signal paves a new way to selectively block the pathogenic behaviors associated with this signaling system. Moreover, rational design and development of potent synthetic peptide modulators allows in depth understanding of the molecular mechanisms that drive QS circuits in diverse bacterial species. Overall, studies aimed at understanding the role of QS in microbial social behavior could result in the accumulation of significant knowledge of microbial interactions, and consequently lead to the development of alternative therapeutic agents to treat bacterial infectivity. In this review, we discuss recent advances in the development of peptide-based modulators to target QS systems in Gram-positive pathogens, with a focus on evaluating the therapeutic potential associated with these bacterial signaling pathways.

A Novel and Efficient Platform for Discovering Noncanonical Quorum-Quenching Proteins

Quorum sensing (QS) is a well-known chemical signaling system responsible for intercellular communication that is widespread in bacteria. Acyl-homoserine lactone (AHL) is the most-studied QS signal. Previously, bacterially encoded AHL-degrading enzymes were considered to be canonical quorum-quenching proteins that have been widely used to control pathogenic infections. Here, we report a novel platform that enabled the efficient discovery of noncanonical AHL quorum-quenching proteins. This platform initially asked bacteriologists to carry out comparative genomic analyses between phylogenetically related AHL-producing and non-AHL-producing members to identify genes that are conservatively shared by non-AHL-producing members but absent in AHL-producing species. These candidate genes were then introduced into recombinant AHL-producing E. coli to screen for target proteins with the ability to block AHL production. Via this platform, we found that non-AHL-producing Lysobacter containing numerous environmentally ubiquitous members encoded a conserved glycosyltransferase-like protein Le4759, which was experimentally shown to be a noncanonical AHL-quenching protein. Le4759 could not directly degrade exogenous AHL but rather recognized and altered the activities of multiple AHL synthases through protein-protein interactions. This versatile capability enabled Le4759 to block specific AHL synthase such as CarI from Pectobacterium carotovorum to reduce its protein abundance to suppress AHL synthesis, thereby impairing bacterial infection. Thus, this study provided bacteriologists with a unique platform to discover noncanonical quorum-quenching proteins that could be developed as promising next-generation drug candidates to overcome emerging bacterial antibiotic resistance. IMPORTANCE Targeting and blocking bacterial quorum sensing (QS), the process known as quorum quenching (QQ) is an effective mean to control bacterial infection and overcome the emerging antibiotic resistance. Previously, diverse QS signal-degradation enzymes are identified as canonical QQ proteins. Here, we provided a novel and universal platform that enabled to discover previously unidentified noncanonical QQ proteins that were unable to degrade acyl-homoserine lactone (AHL) but could block AHL generation by recognizing multiple AHL synthases via direct protein-protein interactions. Our findings are believed to trigger broad interest for bacteriologists to identify potentially widely distributed noncanonical QQ proteins that have great potential for developing next-generation anti-infectious drugs.

Association of CRISPR-Cas System with the Antibiotic Resistance and Virulence Genes in Nosocomial Isolates of Enterococcus

PURPOSE

This study aimed to investigate the prevalence of the CRISPR-Cas system in nosocomial isolates of Enterococcus and their possible association with antibiotic resistance and virulence genes.

MATERIALS AND METHODS

Identification and antimicrobial susceptibility of the microorganism were performed by the automatized VITEK 2 Compact system (bioMerieux, France). A total of 100 Enterococcus isolates were collected and identified by VITEK 2 Compact automatic microbial identification drug susceptibility analyzer. The prevalence of various CRISPR-Cas systems, antibiotic resistance genes and virulence genes were investigated by polymerase chain reaction (PCR). The prevalence of CRISPR-Cas systems associated with antibiotic resistance and virulence genes was performed by appropriate statistical tests.

RESULTS

A total of 100 isolates of Enterococcus were identified and there were 62/100(62.0%) Enterococcus faecalis isolates and 38/100(38.0%) Enterococcus faecalis isolates. In total, 46 (46.0%) of 100 isolates had at least one CRISPR-Cas locus. CRISPR elements were more prevalent in Enterococcus faecalis isolates. The results of PCR demonstrated that CRISPR1-Cas, orphan CRISPR2, and CRISPR3-Cas were present in 23 (23.0%), 42 (42.0%) and 5 (5.0%) Enterococcus isolates, respectively. Compared with CRISPR-Casnegative isolates, the CRISPR-Cas positive isolates showed significant lower resistance rates against ampicillin, erythromycin, levofloxacin, tetracycline, vancomycin, gentamicin, streptomycin, and rifampicin. Presumably consistent with drug susceptibility, fewer CRISPR loci were identified in vanA, tetM, ermB, aac6'-aph(2"), aadE, and ant(6) positive isolates. There was a significant negative correlation between the CRISPR-Cas locus and the enterococcal virulence factors enterococcal surface protein (esp) gene.

CONCLUSION

In conclusion, the results indicated that the absence of the CRISPR-Cas system was negatively associated with some antibiotic resistance in clinical isolates of Enterococcus faecalis and Enterococcus faecium. Also, there was a negative correlation with the carriage of antibiotic resistance genes. Furthermore, CRISPR-Cas may prevent some isolates from acquiring certain virulence factors.

Functional Annotation of Lactiplantibacillus plantarum 13-3 as a Potential Starter Probiotic Involved in the Food Safety of Fermented Products

The important role of Lactiplantibacillus plantarum strains in improving the human mucosal and systemic immunity, preventing non-steroidal anti-provocative drug-induced reduction in T-regulatory cells, and as probiotic starter cultures in food processing has motivated in-depth molecular and genomic research of these strains. The current study, building on this research concept, reveals the importance of Lactiplantibacillus plantarum 13-3 as a potential probiotic and bacteriocin-producing strain that helps in improving the condition of the human digestive system and thus enhances the immunity of the living beings via various extracellular proteins and exopolysaccharides. We have assessed the stability and quality of the L. plantarum 13-3 genome through de novo assembly and annotation through FAST-QC and RAST, respectively. The probiotic-producing components, secondary metabolites, phage prediction sites, pathogenicity and carbohydrate-producing enzymes in the genome of L. plantarum 13-3 have also been analyzed computationally. This study reveals that L. plantarum 13-3 is nonpathogenic with 218 subsystems and 32,918 qualities and five classes of sugars with several important functions. Two phage hit sites have been identified in the strain. Cyclic lactone autoinducer, terpenes, T3PKS, and RiPP-like gene clusters have also been identified in the strain evidencing its role in food processing. Combined, the non-pathogenicity and the food-processing ability of this strain have rendered this strain industrially important. The subsystem and qualities characterization provides a starting point to investigate the strain’s healthcare-related applications as well.

Microbiomics for enhancing electron transfer in an electrochemical system

In microbial electrochemical systems, microorganisms catalyze chemical reactions converting chemical energy present in organic and inorganic molecules into electrical energy. The concept of microbial electrochemistry has been gaining tremendous attention for the past two decades, mainly due to its numerous applications. This technology offers a wide range of applications in areas such as the environment, industries, and sensors. The biocatalysts governing the reactions could be cell secretion, cell component, or a whole cell. The electroactive bacteria can interact with insoluble materials such as electrodes for exchanging electrons through colonization and biofilm formation. Though biofilm formation is one of the major modes for extracellular electron transfer with the electrode, there are other few mechanisms through which the process can occur. Apart from biofilm formation electron exchange can take place through flavins, cytochromes, cell surface appendages, and other metabolites. The present article targets the various mechanisms of electron exchange for microbiome-induced electron transfer activity, proteins, and secretory molecules involved in the electron transfer. This review also focuses on various proteomics and genetics strategies implemented and developed to enhance the exo-electron transfer process in electroactive bacteria. Recent progress and reports on synthetic biology and genetic engineering in exploring the direct and indirect electron transfer phenomenon have also been emphasized.

Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria

Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.

Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory

The present work describes the genome sequencing and characterization of a novel Lactiplantibacillus plantarum strain assigned UTNGt21A isolated from wild Solanum quitoense (L.) fruits. In silico analysis has led to identifying a wide range of biosynthetic gene clusters (BGCs) and metabolic compounds. The genome had a total of 3,558,611 bp with GC of 43.96%, harboring 3,449 protein-coding genes, among which 3,209 were assigned by the EggNOG database, and 240 hypothetical proteins have no match in the BLASTN database. It also contains 68 tRNAs, 1 23S rRNA, 1 16S rRNA, 6 5S rRNA, and 1 tmRNA. In addition, no acquired resistance genes nor virulence and pathogenic factors were predicted, indicating that UTNGt21A is a safe strain. Three areas of interest (AOI) consisting of multiple genes encoding for bacteriocins and ABC transporters were predicted with BAGEL4, while eight secondary metabolite regions were predicted with the antiSMASH web tool. GutSMASH analysis predicted one metabolic gene cluster (MGC) type pyruvate to acetate-formate, a primary metabolite region essential for anaerobe growth. Several lanthipeptides and non-ribosomal peptide synthetase (NRPS) clusters were detected in the UTNGt21A but not the reference genomes, suggesting that their genome diversity might be linked to its niche-specific lineage and adaptation to a specific environment. Moreover, the application of a targeted genome mining tool (RiPPMiner) uncovered a diverse arsenal of important antimicrobial molecules such as lanthipeptides. Furthermore, in vitro analysis indicated that the crude extract (CE) of UTNGt21A exerted a wide spectrum of inhibition against several pathogens. The results indicated that the possible peptide-protein extract (PC) from UTNGt21A induces morphological and ultrastructural changes of Salmonella enterica subsp. enterica ATCC51741, compatible with its inhibitory potential. Genome characterization is the basis for further in vitro and in vivo studies to explore their use as antimicrobial producers or probiotic strains.

Elucidating the Role and Structure-Activity Relationships of the Streptococcus oligofermentans Competence-Stimulating Peptide

Streptococcus oligofermentans is an early colonizer of the oral microbiome with documented bactericidal activity against the oral pathogen Streptococcus mutans. S. oligofermentans has been observed to possess the typical comABCDE competence regulon found within most oral streptococci; however, the competence-stimulating peptide (CSP) responsible for QS activation and the regulatory role of the competence regulon is yet to be explored. Herein, we have both confirmed the identity of the S. oligofermentans CSP and utilized a wide range of phenotypic assays to characterize its regulatory role in competence, biofilm formation, and hydrogen peroxide formation. To determine the importance of each amino acid residue in CSP/ComD binding, we performed systematic replacement of amino acid residues within the S. oligofermentans CSP and developed a luciferase-based reporter system to assess the ability of these mutated analogues to modulate the competence regulon. Additionally, we performed CD analysis on mutated CSP analogues to determine the correlation between the peptide secondary structure and QS activation. To further explore S. oligofermentans' potential as a biotherapeutic against S. mutans infection, lead QS activators and inhibitors were used in interspecies competition assays to assess the effect of QS modulation on interactions between these two species. Lastly, we have documented a lack of S. oligofermentans-induced cytotoxicity, highlighting the potential of this native flora as a biotherapeutic with minimal health risks.

Structure-based design of a Cortistatin analogue with immunomodulatory activity in models of inflammatory bowel disease

Ulcerative colitis and Crohn’s disease are forms of inflammatory bowel disease whose incidence and prevalence are increasing worldwide. These diseases lead to chronic inflammation of the gastrointestinal tract as a result of an abnormal response of the immune system. Recent studies positioned Cortistatin, which shows low stability in plasma, as a candidate for IBD treatment. Here, using NMR structural information, we design five Cortistatin analogues adopting selected native Cortistatin conformations in solution. One of them, A5, preserves the anti-inflammatory and immunomodulatory activities of Cortistatin in vitro and in mouse models of the disease. Additionally, A5 displays an increased half-life in serum and a unique receptor binding profile, thereby overcoming the limitations of the native Cortistatin as a therapeutic agent. This study provides an efficient approach to the rational design of Cortistatin analogues and opens up new possibilities for the treatment of patients that fail to respond to other therapies.

Inflammatory bowel disease is caused by chronic inflammation of the gastrointestinal tract and disturbed immune responses. Here the authors present examination of Cortistatin analogues that display enhanced half-life stability whilst maintaining immunomodulatory functionality.

Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations

Protein-protein interactions are vital to biological processes, but the shape and size of their interfaces make them hard to target using small molecules. Cyclic peptides have shown promise as protein-protein interaction modulators, as they can bind protein surfaces with high affinity and specificity. Dozens of cyclic peptides are already FDA approved, and many more are in various stages of development as immunosuppressants, antibiotics, antivirals, or anticancer drugs. However, most cyclic peptide drugs so far have been natural products or derivatives thereof, with de novo design having proven challenging. A key obstacle is structural characterization: cyclic peptides frequently adopt multiple conformations in solution, which are difficult to resolve using techniques like NMR spectroscopy. The lack of solution structural information prevents a thorough understanding of cyclic peptides' sequence-structure-function relationship. Here we review recent development and application of molecular dynamics simulations with enhanced sampling to studying the solution structures of cyclic peptides. We describe novel computational methods capable of sampling cyclic peptides' conformational space and provide examples of computational studies that relate peptides' sequence and structure to biological activity. We demonstrate that molecular dynamics simulations have grown from an explanatory technique to a full-fledged tool for systematic studies at the forefront of cyclic peptide therapeutic design.

177Lu-DOTATATE Peptide Receptor Radionuclide Therapy: Indigenously Developed Freeze Dried Cold Kit and Biological Response in In-Vitro and In-Vivo Models

Somatostatin receptors (SStR) based ¹⁷⁷Lu-DOTATATE therapy is known as one of the highly effective neuroendocrine tumors (NETs) treatment strategy. Development of DOTATATE freeze-dried kit for imaging and therapy of SStR positive NETs is a prime goal in neuroendocrine cancer research. The present work describes the development of ¹⁷⁷Lu-DOTATATE freeze dried cold kit for indigenous needs, through technology development fund (TDF) program offered by Higher Education Commission (HEC) Pakistan. The parameters for freeze dried kit production was optimized and tested the stored lyophilized cold kits for different time intervals after labeling with ¹⁷⁷Lu radioisotope. The effect of ligand to radionuclide ratio, pH and reaction time at 90°C was recorded. Five times greater molar concentration of ligand, pH 5 and 30 min reaction time were the effective reaction conditions for maximum radiochemical yield. The radiolabeling yield at 1 day, 1-week and 4-week post storing period showed ∼100% radiochemical yield. The biodistribution study using rat model depicted the absence of non-targeted accumulation while glomerular filtration rate also explains the rapid renal washout. Cytotoxicity study showed quite favorable results for subjecting the radiopharmaceutical to clinical practice in Pakistan.

Progress Overview of Bacterial Two-Component Regulatory Systems as Potential Targets for Antimicrobial Chemotherapy

Bacteria adapt to changes in their environment using a mechanism known as the two-component regulatory system (TCS) (also called “two-component signal transduction system” or “two-component system”). It comprises a pair of at least two proteins, namely the sensor kinase and the response regulator. The former senses external stimuli while the latter alters the expression profile of bacterial genes for survival and adaptation. Although the first TCS was discovered and characterized in a non-pathogenic laboratory strain of Escherichia coli, it has been recognized that all bacteria, including pathogens, use this mechanism. Some TCSs are essential for cell growth and fitness, while others are associated with the induction of virulence and drug resistance/tolerance. Therefore, the TCS is proposed as a potential target for antimicrobial chemotherapy. This concept is based on the inhibition of bacterial growth with the substances acting like conventional antibiotics in some cases. Alternatively, TCS targeting may reduce the burden of bacterial virulence and drug resistance/tolerance, without causing cell death. Therefore, this approach may aid in the development of antimicrobial therapeutic strategies for refractory infections caused by multi-drug resistant (MDR) pathogens. Herein, we review the progress of TCS inhibitors based on natural and synthetic compounds.

Biological Evaluation of Native Streptococcal Competence Stimulating Peptides Reveal Potential Crosstalk Between Streptococcus mitis and Streptococcus pneumoniae and a New Scaffold for the Development of S. pneumoniae Quorum Sensing Modulators

Streptococcus pneumoniae, an opportunistic human pathogen, acquires genes from its neighboring species of the mitis group of streptococci that confer antibiotic resistances and allow it to produce diverse virulence factors. Most species of the mitis group are naturally competent, and they utilize the competence stimulating peptide (CSP) and the CSP-dependent competence regulon, a conserved quorum sensing (QS) circuit, to regulate their competence behavior. The dependence of the mitis group on this communication pathway makes QS a potential target to control their behavior. In this work, we sought to evaluate the impact of native pheromones of the adjacent species of S. pneumoniae to modulate the activity of the S. pneumoniae competence regulon. Our results revealed the potential role of S. mitis as a modulator of QS in S. pneumoniae. Most importantly, our analysis also revealed that by using the native pheromone of S. mitis as a template, highly potent pan-group agonists and antagonists of the pneumococcal competence regulon could be developed. The newly developed QS modulators may have therapeutic utility in treating pneumococcus infections.

Designing cyclic competence-stimulating peptide (CSP) analogs with pan-group quorum-sensing inhibition activity in Streptococcus pneumoniae

Streptococcus pneumoniae is an opportunistic human pathogen that utilizes the competence regulon, a quorum-sensing circuitry, to acquire antibiotic resistance genes and initiate its attack on the human host. Interception of the competence regulon can therefore be utilized to study S. pneumoniae cell-cell communication and behavioral changes, as well as attenuate S. pneumoniae infectivity. Herein we report the design and synthesis of cyclic dominant negative competence-stimulating peptide (dnCSP) analogs capable of intercepting the competence regulon in both S. pneumoniae specificity groups with activities at the low nanomolar range. Structural analysis of lead analogs provided important insights as to the molecular mechanism that drives CSP receptor binding and revealed that the pan-group cyclic CSPs exhibit a chimeric hydrophobic patch conformation that resembles the hydrophobic patches required for both ComD1 and ComD2 binding. Moreover, the lead cyclic dnCSP, CSP1-E1A-cyc(Dap6E10), was found to possess superior pharmacological properties, including improved resistance to enzymatic degradation, while remaining nontoxic. Lastly, CSP1-E1A-cyc(Dap6E10) was capable of attenuating mouse mortality during acute pneumonia caused by both group 1 and group 2 S. pneumoniae strains. This cyclic pan-group dnCSP is therefore a promising drug lead scaffold against S. pneumoniae infections that could be administered individually or utilized in combination therapy to augment the effects of current antimicrobial agents.

Development and utilization of peptide-based quorum sensing modulators in Gram-positive bacteria

Quorum sensing (QS) is a mechanism by which bacteria regulate cell density-dependent group behaviors. Gram-positive bacteria generally rely on auto-inducing peptide (AIP)-based QS signaling to regulate their group behaviors. To develop synthetic modulators of these behaviors, the natural peptide needs to be identified and its structure-activity relationships (SARs) with its cognate receptor (either membrane-bound or cytosolic) need to be understood. SAR information allows for the rational design of peptides or peptide mimics with enhanced characteristics, which in turn can be utilized in studies to understand species-specific QS mechanisms and as lead scaffolds for the development of therapeutic candidates that target QS. In this review, we discuss recent work associated with the approaches used towards forwarding each of these steps in Gram-positive bacteria, with a focus on species that have received less attention.

Ribosomal Peptides and Small Proteins on the Rise

Genetically encoded and ribosomally synthesised peptides and small proteins act as important regulators in fundamental cellular processes, including gene expression, development, signalling and metabolism. Moreover, they also play a crucial role in eukaryotic and prokaryotic defence against microorganisms. Extremely diverse in size and structure, they are often subject to extensive post-translational modification. Recent technological advances are now allowing the analysis of the whole cellular transcriptome and proteome, revealing the presence of hundreds of long-overlooked alternative and short open reading frames (short ORFs, or sORFs) in mRNA and supposedly noncoding RNAs. However, in many instances the biological roles of their translational products remain to be elucidated. Here we provide an overview on the intriguing structural and functional diversity of ribosomally synthesised peptides and newly discovered peptides and small proteins.

Development of a Dominant Negative Competence-Stimulating Peptide (dnCSP) that Attenuates Streptococcus pneumoniae Infectivity in a Mouse Model of Acute Pneumonia

Streptococcus pneumoniae (pneumococcus) is a prevalent human pathogen responsible for a variety of diseases, including pneumonia, bacteremia, sepsis, meningitis and otitis media, with a death toll of >22 000 a year in the United States alone. Pneumococcus uses the competence regulon and its associated signaling peptide, the competence stimulating peptide (CSP), to initiate its attack on the host and establish an infection. In this work, we set out to: 1) develop a pan-group quorum sensing inhibitor that could effectively interact with both the pneumococcus ComD1 and ComD2 receptors; and 2) evaluate the utility of dominant-negative CSPs (dnCSPs) in attenuating pneumococcus infectivity. Our results highlight the potential of inhibiting the competence regulon as a therapeutic approach to combat pneumococcus infections.

Rational Design of Potent Activators and Inhibitors of the Enterococcus faecalis Fsr Quorum Sensing Circuit

The increasing rate of resistance development to conventional antibiotics by bacteria necessitates the identification of alternative treatment possibilities that can reduce the ability of bacteria to adapt. Enterococcus faecalis remains the leading cause of clinical enterococci infections and has exhibited quorum sensing (QS)-dependent pathogenicity. Here, we report the development of macrocyclic peptide-based activators and inhibitors of the E. faecalis Fsr QS circuitry. To this end, we developed, optimized, and compared three synthetic routes for lactone-containing macrocyclic peptide scaffolds. We then utilized previous and current structure-activity relationship (SAR) insights of the native QS signaling peptide to rationally design the most potent activators and inhibitors of the Fsr QS circuitry identified to date. The application of these peptides could provide a means to attenuate the pathogenicity of E. faecalis without introducing significant selective pressure on the bacteria to develop resistance.

Structural Characterization of Competence-Stimulating Peptide Analogues Reveals Key Features for ComD1 and ComD2 Receptor Binding in Streptococcus pneumoniae

Streptococcus pneumoniae is an important pathogen that utilizes quorum sensing (QS) to regulate genetic transformation, virulence, and biofilm formation. The competence-stimulating peptide (CSP) is a 17-amino acid signal peptide that is used by S. pneumoniae to trigger QS. S. pneumoniae strains can be divided into two main specificity groups based on the CSP signal they produce (CSP1 or CSP2) and their compatible receptors (ComD1 or ComD2, respectively). Modulation of QS in S. pneumoniae can be achieved by targeting the CSP:ComD interaction using synthetic CSP analogues. However, to rationally design CSP-based QS modulators with enhanced activities, an in-depth understanding of the structural features that are required for receptor binding is needed. Herein, we report a comprehensive in-solution three-dimensional structural characterization of eight CSP1 and CSP2 analogues with varied biological activities using nuclear magnetic resonance spectroscopy. Analysis of these structures revealed two distinct hydrophobic patches required for effective ComD1 and ComD2 binding.