Antibacterial mechanism of daptomycin antibiotic against Staphylococcus aureus based on a quantitative bacterial proteome analysis

Comparative Proteomics of Bacteria Under Stress Conditions

Bacteria are unicellular organisms with the ability to exist in the harshest of climate and cope with sub-optimal fluctuating environmental conditions. They accomplish this by modification of their internal cellular environment. When external conditions are varied, change in the cell is triggered at the transcriptional level, which usually leads to proteolysis and rewiring of the proteome. Changes in cellular homeostasis, modifications in proteome, and dynamics of such survival mechanisms can be studied using various scientific techniques. Our focus in this chapter would be on comparative proteomics of bacteria under stress conditions using approaches like 2D electrophoresis accompanied by N-terminal sequencing and recently, mass spectrometry. More than 170 such studies on bacteria have been accomplished till to date and involve analysis of whole cells as well as that of cellular fractions, i.e., outer membrane, inner membrane, cell envelope, cytoplasm, thylakoid, lipid bodies, etc. Similar studies conducted on gram-negative and gram-positive model organism, i.e., Escherichia coli and Bacillus subtilis, respectively, have been summarized. Vital information, hypothesis about conservation of stress-specific proteome, and conclusions are also presented in the light of research conducted over the last decades.

Antibiotics daptomycin interacts with S protein of SARS-CoV-2 to promote cell invasion of Omicron (B1.1.529) pseudovirus

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed enormous challenges to global public health. The use of antibiotics has greatly increased during the SARS-CoV-2 epidemic owing to the presence of bacterial co-infection and secondary bacterial infections. The antibiotics daptomycin (DAP) is widely used in the treatment of infectious diseases caused by gram-positive bacteria owing to its highly efficient antibacterial activity. It is pivotal to study the antibiotics usage options for patients of coronavirus infectious disease (COVID-19) with pneumonia those need admission to receive antibiotics treatment for bacterial co-infection in managing COVID-19 disease. Herein, we have revealed the interactions of DAP with the S protein of SARS-CoV-2 and the variant Omicron (B1.1.529) using the molecular docking approach and Omicron (B1.1.529) pseudovirus (PsV) mimic invasion. Molecular docking analysis shows that DAP has a certain degree of binding ability to the S protein of SARS-CoV-2 and several derived virus variants, and co-incubation of 1-100 μM DAP with cells promotes the entry of the PsV into human angiotensin-converting enzyme 2 (hACE2)-expressing HEK-293T cells (HEK-293T-hACE2), and this effect is related to the concentration of extracellular calcium ions (Ca2+). The PsV invasion rate in the HEK-293T-hACE2 cells concurrently with DAP incubation was 1.7 times of PsV infection alone. In general, our findings demonstrate that DAP promotes the infection of PsV into cells, which provides certain reference of antibiotics selection and usage optimization for clinicians to treat bacterial coinfection or secondary infection during SARS-CoV-2 infection.

Caspofungin enhances the potency of rifampin against Gram-negative bacteria

Introduction

Developing antibiotic adjuvants is an effective strategy to combat antimicrobial resistance (AMR). The envelope of Gram-negative bacteria (GNB) is a barrier to prevent the entry of antibiotics, making it an attractive target for novel antibiotic and adjuvant development.

Methods and Results

In this study, we identified Caspofungin acetate (CAS) as an antibiotic adjuvant against GNB in the repurposing screen of 3,158 FDA-approved drugs. Checkerboard assays suggested that CAS could enhance the antimicrobial activity of rifampin or colistin against various GNB strains in vitro, Moreover, Galleria mellonella larvae infection model also indicated that CAS significantly potentiated the efficacy of rifampin against multidrug-resistant Escherichia coli 72 strain in vivo. Most importantly, resistance development assay showed that CAS was less susceptible to accelerating the resistance development of drug-sensitive strain E. coli MG1655. Functional studies and RNA-seq analysis confirmed that the mechanisms by which CAS enhanced the antimicrobial activities of antibiotics were involved in permeabilizing the bacterial cell envelope, disrupting proton motive force and inhibiting bacterial biofilm formation. Additionally, it has been found that PgaC is the CAS target and enzymatic assay has confirmed the inhibition activity.

Discussion

Our results illustrate the feasibility of CAS as an antibiotic adjuvant against GNB, which is an alternative strategy of anti-infection.

A new understanding on the prerequisite of antibiotic biodegradation in wastewater treatment: Adhesive behavior between antibiotic-degrading bacteria and ciprofloxacin

The extensive exploration of antibiotic biodegradation by antibiotic-degrading bacteria in biological wastewater treatment processes has left a notable gap in understanding the behavior of these bacteria when exposed to antibiotics and the initiation of biodegradation processes. This study, therefore, delves into the adhesive behavior of Paraclostridium bifermentans, isolated from a bioreactor treating ciprofloxacin-laden wastewater, towards ciprofloxacin molecules. For the first time, this behavior is observed and characterized through quartz crystal microbalance with dissipation (QCM-D) and atomic force microscopy. The investigation further extends to identify key regulatory factors and mechanisms governing this adhesive behavior through a comparative proteomics analysis. The results reveal the dominance of extracellular proteins, particularly those involved in nucleotide binding, hydrolase, and transferase, in the adhesion process. These proteins play pivotal roles through direct chemical binding and the regulation of signaling molecule. Furthermore, QCM-D measurements provide evidence that transferase-related signaling molecules, especially tyrosine, augment the binding between ciprofloxacin and transferases, resulting in enhance ciprofloxacin removal by P. bifermentans (increased by ∼1.2-fold). This suggests a role for transferase-related signaling molecules in manipulating the adhesive behavior of P. bifermentans towards ciprofloxacin. These findings contribute to a new understanding of the prerequisites for antibiotic biodegradation and offer potential strategies for improving the application of antibiotic-degrading bacteria in the treatment of antibiotics-laden wastewater.

Oxidized pullulan exhibits potent antibacterial activity against S. aureus by disrupting its membrane integrity

The capability of bacteria to withstand the misuse of antibiotics leads to the generation of multi-drug resistant strains, posing a new challenge to curb wound infections. The biological macromolecules, due to their biocompatibility, biodegradability, and antimicrobial properties, have been explored for a variety of antimicrobial and therapeutic purposes. This work reports that a single-step oxidation of pullulan polymer leads to the formation of oxidized pullulan (o-pullulan), which shows striking antibacterial and antibiofilm activities against the Gram-positive bacteria, Staphylococcus aureus, implicated in wound-related infections. Oxidation of pullulan generates 28 % aldehyde groups (3.462 mmol/g) which exerted 97 % bactericidal activity against S. aureus by targeting cell wall-associated membrane protein SpA (Staphylococcal protein A). The molecular docking, gene silencing, and fluorescence quenching studies revealed a direct binding of o-pullulan with the B and C domains of SpA, which alters the membrane potential and inhibits Ca2+-Mg2+-ATPase pumps. O-pullulan also exhibited scavenging activity against intracellular reactive oxygen species (ROS), and non-immunotoxic activity and was found to be non-toxic to mammalian cells. Thus, o-pullulan shows great promise as an antimicrobial polymer against S. aureus for chronic wound management.

Dissecting LuxS/AI-2 quorum sensing system-mediated phenyllactic acid production mechanisms of Lactiplantibacillus plantarum L3

The phenyllactic acid (PLA) produced by lactic acid bacteria (LAB) inhibits fungi and facilitates the quality control of fermented milk. A strain of Lactiplantibacillus plantarum L3 (L. plantarum L3) with high PLA production was screened in the pre-laboratory, but the mechanism of its PLA formation is unclear. The amount of autoinducer-2 (AI-2) increased with increasing culture time, as did cell density and PLA. The results in this study suggest that PLA production in L. plantarum L3 may be regulated by the LuxS/AI-2 Quorum Sensing (QS) system. Tandem mass tag (TMT) quantitative proteomics analysis showed that a total of 1291 differentially expressed proteins (DEPs) were quantified in the incubated for 24 h compared with the incubated for 2 h, of which 516 DEPs were up-regulated and 775 DEPs were down-regulated. Among them, S-ribosomal homocysteine lyase (luxS), aminotransferase (araT), and lactate dehydrogenase (ldh) are the key proteins for PLA formation. The DEPs were mainly involved in the QS pathway and the core pathway of PLA synthesis. Furanone effectively inhibited the production of L. plantarum L3 PLA. In addition, Western blot analysis demonstrated that luxS, araT, and ldh were the key proteins regulating PLA production. This study reveals the regulatory mechanism of PLA based on the LuxS/AI-2 QS system, which provides a theoretical basis for the efficient and large-scale production of PLA in industries in the future.

Antioxidant and antimicrobial characteristics of ethyl acetate polar fractions from walnut green husk

Walnut green husk (WGH) is rich in natural compounds and is valued as a potential source of antioxidant and antimicrobial properties. In this study, the antioxidant and antimicrobial activities of petroleum ether polar fraction, dichloromethane polar fraction, ethyl acetate polar fraction (EAPF), and n-butanol polar fraction from WGH were analyzed. The results showed that EAPF exhibited the highest total flavonoid content (65.74 ± 1.01 mg rutin equivalents [RE]/g dry weight [DW]) and total phenol content (48.73 ± 1.09 mg gallic acid equivalent [GAE]/g DW), with the highest 2,2-diphenyl-1-picrylhydrazyl, hydroxyl radical (•OH), and 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonate scavenging activity compared with other fractions. EAPF also showed good antibacterial activity against Escherichia coli and Bacillus cereus vegetative cells, with a diameter of inhibition zones of 33.5 and 37.6 mm, respectively, a minimum inhibitory concentration of 31.25 mg/ml and a minimum bactericidal concentration of 62.5 mg/ml, which inhibited the growth of both bacteria. Analysis of the antibacterial mechanism demonstrated that EAPF damaged the integrity of the cell membrane, increased the membrane permeability, and triggered the leakage of intracellular material. In addition, ultrahigh performance liquid chromatography-tandem with mass spectrometry analysis revealed that 8 polyphenols and 14 flavonoids were mainly present in EAPF, such as chlorogenic acid (C₁₆ H₁₈ O₉ ), gallic acid (C₇ H₆ O₅ ), vanillic acid (C₈ H₈ O₄ ), ferulic acid (C₁₀ H₁₀ O₄ ), epicatechin (C₁₅ H₁₄ O₆ ), catechin (C₁₅ H₁₄ O₆ ), hesperetin (C₁₆ H₁₄ O₆ ), naringenin (C₁₅ H₁₂ O₅ ), hyperin (C₂₁ H₂₀ O₁₂ ), luteolin (C1₅ H₁₀ O₆ ), and so on. Therefore, WGH had the potential to be developed as a natural antioxidant and antibacterial material. PRACTICAL APPLICATION: Our work indicates that WGH contains abundant flavonoids and polyphenols compounds. Therefore, the plant byproducts like WGH may have a promising application as a source of antimicrobial and antioxidant additives.

A review of potential antibacterial activities of nisin against Listeria monocytogenes: the combined use of nisin shows more advantages than single use

Listeria monocytogenes is a foodborne pathogen causing serious public health problems. Nisin is a natural antimicrobial agent produced by Lactococcus lactis and widely used in the food industry. However, the anti-L. monocytogenes efficiency of nisin might be decreased due to natural or acquired resistance of L. monocytogenes to nisin, or complexity of the food environment. The limitation of nisin as a bacteriostatic agent in food could be improved using a combination of methods. In this review, the physiochemical characteristics, species, bioengineered mutants, and antimicrobial mechanism of nisin are reviewed. Strategies of nisin combined with other antibacterial methods, including physical, chemical, and natural substances, and nanotechnology to enhance antibacterial effect are highlighted and discussed. Additionally, the antibacterial efficiency of nisin applied in real meat, dairy, and aquatic products is evaluated and analyzed. Among the various binding treatments, the combination with natural substances is more effective than the combination with physical and chemical methods. However, the combination of nisin and nanotechnology has more potential in terms of the impact on food quality.

Molecular docking and proteomics reveals the synergistic antibacterial mechanism of theaflavin with β-lactam antibiotics against MRSA

Recurrent epidemics of methicillin-resistant Staphylococcus aureus (S. aureus) (MRSA) have illustrated that the effectiveness of antibiotics in clinical application is rapidly fading. A feasible approach is to combine natural products with existing antibiotics to achieve an antibacterial effect. In this molecular docking study, we found that theaflavin (TF) preferentially binds the allosteric site of penicillin-binding protein 2a (PBP2a), inducing the PBP2a active site to open, which is convenient for β-lactam antibiotics to treat MRSA infection, instead of directly exerting antibacterial activity at the active site. Subsequent TMT-labeled proteomics analysis showed that TF treatment did not significantly change the landscape of the S. aureus USA300 proteome. Checkerboard dilution tests and kill curve assays were performed to validate the synergistic effect of TF and ceftiofur, and the fractional inhibitory concentration index (FICI) was 0.1875. The antibacterial effect of TF combined with ceftiofur was better than that of single-drug treatment in vitro. In addition, TF effectively enhanced the activity of ceftiofur in a mouse model of MRSA-induced pneumonia. Our findings provide a potential therapeutic strategy to combine existing antibiotics with natural products to resolve the prevalent infections of multidrug-resistant pathogens.

Breaking the Bottleneck in Anticancer Drug Development: Efficient Utilization of Synthetic Biology

Natural products have multifarious bioactivities against bacteria, fungi, viruses, cancers and other diseases due to their diverse structures. Nearly 65% of anticancer drugs are natural products or their derivatives. Thus, natural products play significant roles in clinical cancer therapy. With the development of biosynthetic technologies, an increasing number of natural products have been discovered and developed as candidates for clinical cancer therapy. Here, we aim to summarize the anticancer natural products approved from 1950 to 2021 and discuss their molecular mechanisms. We also describe the available synthetic biology tools and highlight their applications in the development of natural products.

Proteome profiling of evolved methicillin-resistant Staphylococcus aureus strains with distinct daptomycin tolerance and resistance phenotypes

Methicillin-resistant Staphylococcus aureus (MRSA) is a highly dangerous pathogen, and daptomycin has been increasingly used to treat its infections in clinics. Recently, several groups have shown that tolerance and resistance of microbes can evolve rapidly under cyclic antibiotic exposure. We have previously shown that the same tolerance and resistance development occurs in MRSA treated with daptomycin in an adaptive laboratory evolution (ALE) experiment. In the present study, we performed proteomic analysis to compare six daptomycin-tolerant and resistant MRSA strains that were evolved from the same ancestral strain. The strain with a higher tolerance level than the others had the most different proteome and response to antibiotic treatment, resembling those observed in persister cells, which are small subpopulations of bacteria that survive lethal antibiotics treatment. By comparing the proteome changes across strains with similar phenotypes, we identified the key proteins that play important roles in daptomycin tolerance and resistance in MRSA. We selected two candidates to be confirmed by gene overexpression analysis. Overexpression of EcsA1 and FabG, which were up-regulated in all of the tolerant evolved strains, led to increased daptomycin tolerance in wild-type MRSA. The proteomics data also suggested that cell wall modulations were implicated in both resistance and tolerance, but in different ways. While the resistant strains had peptidoglycan changes and a more positive surface charge to directly repel daptomycin, the tolerant strains possessed different cell wall changes that do not involve the peptidoglycan nor alterations of the surface charge. Overall, our study showed the differential proteome profiles among multiple tolerant and resistant strains, pinpointed the key proteins for the two phenotypes and revealed the differences in cell wall modulations between the daptomycin-tolerant/resistant strains.

Mutation in the Two-Component System Regulator YycH Leads to Daptomycin Tolerance in Methicillin-Resistant Staphylococcus aureus upon Evolution with a Population Bottleneck

Adaptive laboratory evolution (ALE) is a useful tool to study the evolution of antibiotic tolerance in bacterial populations under diverse environmental conditions. The role of population bottlenecks in the evolution of tolerance has been investigated in Escherichia coli, but not in a more clinically relevant pathogen, methicillin-resistant Staphylococcus aureus (MRSA). In this study, we used ALE to evolve MRSA under repetitive daptomycin treatment and incorporated population bottlenecks following antibiotic exposure. We observed that the populations finally attained a tolerance mutation in the yycH gene after 2 weeks of evolution with population bottlenecks, and additional mutations in yycI and several other genes further increased the tolerance level. The tolerant populations also became resistant to another glycopeptide antibiotic, vancomycin. Through proteomics, we showed that yycH and yycI mutations led to the loss of function of the proteins and downregulated the WalKR two-component system and the downstream players, including the autolysin Atl and amidase Sle1, which are important for cell wall metabolism. Overall, our study offers new insights into the evolution of daptomycin tolerance under population bottlenecking conditions, which are commonly faced by pathogens during infection; the study also identified new mutations conferring daptomycin tolerance and revealed the proteome alterations in the evolved tolerant populations. IMPORTANCE Although population bottlenecks are known to influence the evolutionary dynamics of microbial populations, how such bottlenecks affect the evolution of tolerance to antibiotics in a clinically relevant methicillin-resistant S. aureus (MRSA) pathogen are still unclear. Here, we performed in vitro evolution of MRSA under cyclic daptomycin treatment and applied population bottlenecks following the treatment. We showed that under these experimental conditions, MRSA populations finally attained mutations in yycH, yycI, and several other genes that led to daptomycin tolerance. The discovered yycH and yycI mutations caused early termination of the genes and loss of function of the proteins, and they subsequently downregulated the expression of proteins controlled by the WalKR two-component system, such as Atl and Sle1. In addition, we compared our proteomics data with multiple studies on distinct daptomycin-tolerant MRSA mutants to identify proteins with a consistent expression pattern that could serve as biological markers for daptomycin tolerance in MRSA.

iTRAQ-Based Quantitative Proteomic Analysis of Antibacterial Mechanism of Milk-Derived Peptide BCp12 against Escherichia coli

BCp12 is a novel casein-derived antibacterial peptide with a broad-spectrum antibacterial effect. However, its action mechanism against E. coli is unknown. In this study, the growth curve showed that BCp12 had excellent antibacterial activity against E. coli. Red (propidium iodide staining) and green (fluorescein isothiocyanate staining) fluorescence signals were detected at the edges of the E. coli cells treated with BCp12. scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images showed that E. coli cells became rough and shrunken, and part of the cell contents leaked to form a cavity. Furthermore, the iTRAQ proteome analysis showed that 193 and 174 proteins were significantly up-regulated and down-regulated, respectively, after BCp12 treatment. Four enzymes involved in fatty acid degradation of E. coli were down-regulated, disrupting the synthesis of cell membranes. Molecular docking and gel retardation assays showed that BCp12 could bind to genes encoding four key enzymes involved in the fatty acid degradation pathway through hydrogen bonding and hydrophobic interactions, thus significantly inhibiting their activities. Overall, the results indicate that BCp12 inhibits the growth of E. coli, causing metabolic disorders, thus destroying the structure of cell membranes.

Antibacterial Activity and Multi-Targeting Mechanism of Dehydrocorydaline From Corydalis turtschaninovii Bess. Against Listeria monocytogenes

Listeria monocytogenes is a foodborne pathogen, with relatively low incidence but high case-fatality. Phytochemicals have been recognized as a promising antimicrobial agent as an alternative to synthetic chemicals due to their safety and high efficacy with multi-target sites. This study identified and characterized a novel antibacterial agent, dehydrocorydaline, in the Corydalis turschaninovii rhizome using HPLC-LTQ-Orbitrap-HRMS, and its antibacterial effect with lowest MIC (1 mg/mL) and MBC (2 mg/mL) values. In addition, an in vitro growth kinetic assay, cytoplasmic nucleic acid and protein leakage assay, and observation of morphological changes in bacterial cells supported the strong antibacterial activity. Dehydrocorydaline also displayed effective inhibitory effects on biofilm formation and bacterial motility. In order to investigate the potential antibacterial mechanism of action of dehydrocorydaline against L. monocytogenes, label-free quantitative proteomics was used, demonstrating that dehydrocorydaline has multiple targets for combating L. monocytogenes including dysregulation of carbohydrate metabolism, suppression of cell wall synthesis, and inhibition of bacterial motility. Overall, this study demonstrated that dehydrocorydaline has potential as a natural and effective antibacterial agent with multi-target sites in pathogenic bacteria, and provides the basis for development of a new class of antibacterial agent.

Global Proteomic Analysis of Listeria monocytogenes' Response to Linalool

Listeria monocytogenes (LM) is one of the most serious foodborne pathogens. Listeriosis, the disease caused by LM infection, has drawn attention worldwide because of its high hospitalization and mortality rates. Linalool is a vital constituent found in many essential oils; our previous studies have proved that linalool exhibits strong anti-Listeria activity. In this study, iTRAQ-based quantitative proteomics analysis was performed to explore the response of LM exposed to linalool, and to unravel the mode of action and drug targets of linalool against LM. A total of 445 differentially expressed proteins (DEPs) were screened out, including 211 up-regulated and 234 down-regulated proteins which participated in different biological functions and pathways. Thirty-one significantly enriched gene ontology (GO) functional categories were obtained, including 12 categories in “Biological Process”, 10 categories in “Cell Component”, and 9 categories in “Molecular Function”. Sixty significantly enriched biological pathways were classified, including 6 pathways in “Cell Process”, 6 pathways in “Environmental Information Processing”, 3 pathways in “Human Disease”, 40 pathways in “Metabolism”, and 2 pathways in “Organic System”. GO and Kyoto Encyclopedia of Genes (KEGG) enrichment analysis together with flow cytometry data implied that cell membranes, cell walls, nucleoids, and ribosomes might be the targets of linalool against LM. Our study provides good evidence for the proteomic analysis of bacteria, especially LM, exposed to antibacterial agents. Further, those drug targets discovered by proteomic analysis can provide theoretical support for the development of new drugs against LM.

Comparative proteomic investigation of multiple methicillin-resistant Staphylococcus aureus strains generated through adaptive laboratory evolution

Recent discoveries indicate that tolerance and resistance could rapidly evolve in bacterial populations under intermittent antibiotic treatment. In the present study, we applied antibiotic combinations in laboratory experiments to generate novel methicillin-resistant Staphylococcus aureus strains with distinct phenotypes (tolerance, resistance, and suppressed tolerance), and compared their proteome profiles to uncover the adaptation mechanisms. While the tolerant strains have very different proteomes than the susceptible ancestral strain, the resistant strain largely resembles the ancestral in terms of their proteomes. Our proteomics data and other assays support the connection between the detected mutations to the observed phenotypes, confirming the general understanding of tolerance and resistance mechanisms. While resistance directly counteracts the action mechanism of the antibiotic, tolerance involves complex substantial changes in the cells' biological process to achieve survival advantages. Overall, this study provides insights into the existence of diverse evolutionary pathways for tolerance and resistance development under different treatment scenarios.

Fast identification of off-target liabilities in early antibiotic discovery with Fourier-transform infrared spectroscopy

Structural modifications of known antibiotic scaffolds have kept the upper hand on resistance, but we are on the verge of not having antibiotics for many common infections. Mechanism-based discovery assays reveal novelty, exclude off-target liabilities, and guide lead optimization. For that, we developed a fast and automatable protocol using high-throughput Fourier-transform infrared spectroscopy (FTIRS). Metabolic fingerprints of Staphylococcus aureus and Escherichia coli exposed to 35 compounds, dissolved in dimethyl sulfoxide (DMSO) or water, were acquired. Our data analysis pipeline identified biomarkers of off-target effects, optimized spectral preprocessing, and identified the top-performing machine learning algorithms for off-target liabilities and mechanism of action (MOA) identification. Spectral bands with known biochemical associations more often yielded more significant biomarkers of off-target liabilities when bacteria were exposed to compounds dissolved in water than DMSO. Highly discriminative models distinguished compounds with predominant off-target effects from antibiotics with well-defined MOA (AUROC > 0.87, AUPR > 0.79, F1 > 0.81), and from the latter predicted their MOA (AUROC > 0.88, AUPR > 0.70, F1 > 0.70). The compound solvent did not affect predictive models. FTIRS is fast, simple, inexpensive, automatable, and highly effective at predicting MOA and off-target liabilities. As such, FTIRS mechanism-based screening assays can be applied for hit discovery and to guide lead optimization during the early stages of antibiotic discovery.

Plasmon-Enhanced Antibacterial Activity of Chiral Gold Nanoparticles and In Vivo Therapeutic Effect

d-cysteine (d-cys) has been demonstrated to possess an extraordinary antibacterial activity because of its unique steric configuration. However, inefficient antibacterial properties seriously hinder its wide applications. Here, cysteine-functionalized gold nanoparticles (d-/l-Au NPs) were prepared by loading d-/l-cysteine on the surface of gold nanoparticles for the effective inhibition of Escherichia coli (E. coli) in vitro and in vivo, and the effects on the intestinal microflora in mice were explored during the treatment of E. coli infection in the gut. We found that the antibacterial activity of d-/l-Au NPs was more than 2-3 times higher than pure d-cysteine, l-cysteine and Au NPs. Compared with l-Au NPs, d-Au NPs showed the stronger antibacterial activity, which was related to its unique steric configuration. Chiral Au NPs showed stronger destructive effects on cell membrane compared to other groups, which further leads to the leakage of the cytoplasm and bacterial cell death. The in vivo antibacterial experiment illustrated that d-Au NPs displayed impressive antibacterial activity in the treatment of E. coli-infected mice comparable to kanamycin, whereas they could not affect the balance of intestinal microflora. This work is of great significance in the development of an effective chiral antibacterial agent.

Technologies for High-Throughput Identification of Antibiotic Mechanism of Action

There are two main strategies for antibiotic discovery: target-based and phenotypic screening. The latter has been much more successful in delivering first-in-class antibiotics, despite the major bottleneck of delayed Mechanism-of-Action (MOA) identification. Although finding new antimicrobial compounds is a very challenging task, identifying their MOA has proven equally challenging. MOA identification is important because it is a great facilitator of lead optimization and improves the chances of commercialization. Moreover, the ability to rapidly detect MOA could enable a shift from an activity-based discovery paradigm towards a mechanism-based approach. This would allow to probe the grey chemical matter, an underexplored source of structural novelty. In this study we review techniques with throughput suitable to screen large libraries and sufficient sensitivity to distinguish MOA. In particular, the techniques used in chemical genetics (e.g., based on overexpression and knockout/knockdown collections), promoter-reporter libraries, transcriptomics (e.g., using microarrays and RNA sequencing), proteomics (e.g., either gel-based or gel-free techniques), metabolomics (e.g., resourcing to nuclear magnetic resonance or mass spectrometry techniques), bacterial cytological profiling, and vibrational spectroscopy (e.g., Fourier-transform infrared or Raman scattering spectroscopy) were discussed. Ultimately, new and reinvigorated phenotypic assays bring renewed hope in the discovery of a new generation of antibiotics.

Antibacterial mechanism of ultrasound against Escherichia coli: Alterations in membrane microstructures and properties

This study was aimed at providing new insights on the response of bacterial cell membranes to ultrasound exposure. Escherichia coli (E. coli) O157:H7 cells were exposed to different ultrasound treatments (power intensities of 64, 191, 372, and 573 W/cm², frequency of 20 kHz, pulsed mode of 2 sec: 2 sec) and the dynamic changes in cell viability within 27 min were assessed. With an increase in ultrasonic intensity and prolonged duration, a 0.76-3.52 log CFU/mL reduction in E. coli populations was attained. The alterations in the sensitivity of ultrasound-treated cells to antimicrobial compounds were evaluated by exposure to thyme essential oil nanoemulsion (TEON). The treatment reduced the E. coli population by 2.16-7.10 log CFU/mL, indicating the effects of ultrasonic field on facilitating the antibacterial efficacy of TEON. Ultrasonic-treated E. coli cells also displayed remarkable morphological and ultrastructural damages with destroyed membrane integrity and misshaped cell structures, which was observed by electron microscopy analysis. Significant increase in outer and inner membrane permeability, along with the cytoplasmic leakage and membrane depolarization were assessed utilizing spectrophotometry. For the first time, significant reduction in the membrane fluidity in response to ultrasound exposure were investigated. Additional efforts in exploring the effect of ultrasonic field on some bacterial membrane compositions were performed with infrared spectroscopy. In this study, multiple lines of evidence effectively served to elucidate the alterations on cellular membrane structure and property during exposure to sonication that could extend our understanding of the antimicrobial molecular mechanisms of ultrasound.

A mutation in the glycosyltransferase gene lafB causes daptomycin hypersusceptibility in Enterococcus faecium

OBJECTIVES

To verify dissemination of daptomycin-non-susceptible Enterococcus faecium in a hospital where daptomycin was not in use and to understand the evolutionary pathways connecting daptomycin hypersusceptibility to non-susceptibility.

METHODS

Clonality of 26 E. faecium was assessed by PFGE and the STs of these isolates were determined. The most daptomycin-susceptible isolate was evolved in vitro by stepwise daptomycin selection, generating isolates for genome comparisons.

RESULTS

The spread of a high-risk daptomycin-non-susceptible VRE clone was detected, as was the occurrence of an unusual daptomycin-hypersusceptible strain (HBSJRP18). To determine the basis for daptomycin hypersusceptibility, we evolved HBSJRP18 in vitro and identified candidate genetic alterations potentially related to daptomycin susceptibility. Both lafB, encoding glycosyltransferase, which is putatively involved in lipoteichoic acid (LTA) biosynthesis, and dak, encoding a dihydroxyacetone kinase likely involved in fatty acid metabolism, were mutated in multiple independent experiments. Trans-complementation showed that the lafB polymorphism naturally occurring in HBSJRP18 caused its daptomycin hypersusceptibility. Fourier-transform infrared spectroscopy identified differences between the extracted LTA spectra from the hypersusceptible isolate and its revertant, as well as other non-susceptible variants, supporting a role for LafB in E. faecium LTA biosynthesis. Zeta potential difference was detected in one evolved dak mutant derivative. While much more susceptible to daptomycin, HBSJRP18 showed enhanced growth in the presence of piperacillin, suggesting that this, or another cell wall-targeting antibiotic, may have selected for the daptomycin-hypersusceptible phenotype.

CONCLUSIONS

Our findings provide new information on the basis for daptomycin susceptibility in E. faecium, with implications for limiting the development and spread of daptomycin resistance.

Simultaneous elucidation of antibiotic mechanism of action and potency with high-throughput Fourier-transform infrared (FTIR) spectroscopy and machine learning

The low rate of discovery and rapid spread of resistant pathogens have made antibiotic discovery a worldwide priority. In cell-based screening, the mechanism of action (MOA) is identified after antimicrobial activity. This increases rediscovery, impairs low potency candidate detection, and does not guide lead optimization. In this study, high-throughput Fourier-transform infrared (FTIR) spectroscopy was used to discriminate the MOA of 14 antibiotics at pathway, class, and individual antibiotic level. For that, the optimal combinations and parametrizations of spectral preprocessing were selected with cross-validated partial least squares discriminant analysis, to which various machine learning algorithms were applied. This coherently resulted in very good accuracies, independently of the algorithms, and at all levels of MOA. Particularly, an ensemble of subspace discriminants predicted the known pathway (98.6%), antibiotic classes (100%), and individual antibiotics (97.8%) with exceptional accuracy, and similar results were obtained for simulated novel MOA. Even at very low concentrations (1 μg/mL) and growth inhibition (15%), over 70% pathway and class accuracy was achieved, suggesting FTIR spectroscopy can probe the grey chemical matter. Prediction of inhibitory effect was also examined, for which a squared exponential Gaussian process regression yielded a root mean square error of 0.33 and a R² of 0.92, indicating that metabolic alterations leading to growth inhibition are intrinsically reflected on FTIR spectra beyond cell density. KEY POINTS: • Antibiotic MOA and potency estimated with high-throughput FTIR spectroscopy • Sub-inhibitory MOA identification suggests ability to explore grey chemical matter • Data analysis optimization improved MOA identification at antibiotic level by 38.

Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome

Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.

The Role of Proteomics in Bacterial Response to Antibiotics

For many years, we have tried to use antibiotics to eliminate the persistence of pathogenic bacteria. However, these infectious agents can recover from antibiotic challenges through various mechanisms, including drug resistance and antibiotic tolerance, and continue to pose a global threat to human health. To design more efficient treatments against bacterial infections, detailed knowledge about the bacterial response to the commonly used antibiotics is required. Proteomics is a well-suited and powerful tool to study molecular response to antimicrobial compounds. Bacterial response profiling from system-level investigations could increase our understanding of bacterial adaptation, the mechanisms behind antibiotic resistance and tolerance development. In this review, we aim to provide an overview of bacterial response to the most common antibiotics with a focus on the identification of dynamic proteome responses, and through published studies, to elucidate the formation mechanism of resistant and tolerant bacterial phenotypes.

Design, synthesis and evaluation of phenylthiazole and phenylthiophene pyrimidindiamine derivatives targeting the bacterial membrane

As the continuous rise in the incidence of antibiotic resistance, it is urgent to develop novel chemical scaffolds with antibacterial activities to control the spread of resistance to conventional antibiotics. In this study, a series of phenylthiazole and phenylthiophene pyrimidindiamine derivatives were designed and synthesized by modifying the hit compound (N²-isobutyl-N⁴-((4-methyl-2-phenylthiazol-5-yl)methyl) pyrimidine-2,4-diamine) and their antibacterial activities were evaluated both in vitro and in vivo. Among the tested compounds, compound 14g (N⁴-((5-(3-bromophenyl)thiophen-2-yl)methyl)-N²-isobutylpyrimidine-2,4-diamine) displayed the best antibacterial activities, which was not only capable of inhibiting E. coli and S. aureus growth at concentrations as low as 2 and 3 μg/mL in vitro, but also efficacious in a mice model of bacteremia in vivo. Unlike conventional antibiotics, compound 14g was elucidated to mainly destroy the bacterial cell membrane, with the dissipation of membrane potential and leakage of contents, ultimately leading to cell death. The destruction of cell structure is challenging to induce bacterial resistance, which suggested that compound 14g may be a kind of promising alternatives to antibiotics against bacteria.

More Than a Pore: A Current Perspective on the In Vivo Mode of Action of the Lipopeptide Antibiotic Daptomycin

Daptomycin is a cyclic lipopeptide antibiotic, which was discovered in 1987 and entered the market in 2003. To date, it serves as last resort antibiotic to treat complicated skin infections, bacteremia, and right-sided endocarditis caused by Gram-positive pathogens, most prominently methicillin-resistant Staphylococcus aureus. Daptomycin was the last representative of a novel antibiotic class that was introduced to the clinic. It is also one of the few membrane-active compounds that can be applied systemically. While membrane-active antibiotics have long been limited to topical applications and were generally excluded from systemic drug development, they promise slower resistance development than many classical drugs that target single proteins. The success of daptomycin together with the emergence of more and more multi-resistant superbugs attracted renewed interest in this compound class. Studying daptomycin as a pioneering systemic membrane-active compound might help to pave the way for future membrane-targeting antibiotics. However, more than 30 years after its discovery, the exact mechanism of action of daptomycin is still debated. In particular, there is a prominent discrepancy between in vivo and in vitro studies. In this review, we discuss the current knowledge on the mechanism of daptomycin against Gram-positive bacteria and try to offer explanations for these conflicting observations.

Analysis of silver-associated proteins in pathogen via combination of native SDS-PAGE, fluorescent staining, and inductively coupled plasma mass spectrometry

Characterization of silver-associated proteins is important to elucidate underlined mechanisms of silver-containing materials against microbes. Gel electrophoresis based methods are the most popular and basic strategy for the analysis of biomolecules, i.e., proteins and nucleic acids. It solely provides molecular weights of analytes. Extending the method from molecular weight to elemental composition is highly desired when investigating metal-containing molecules. Herein, a gel electrophoresis based method combining native sodium dodecyl sulfate-polyacrylamide gel electrophoresis (native SDS-PAGE), fluorescent staining, and inductively coupled plasma mass spectrometry (ICP-MS) strategy was developed for separation and detection of silver-associated proteins. Two home-made silver-labeled proteins, carbonic anhydrase and ovalbumin, were used for validation of the strategy performance. Silver-associated proteins in Pseudomonas aeruginosa and Staphylococcus aureus treated with silver nanoparticles were further characterized by this method. Some well-known and new proteins were identified to associate to silver in both P. aeruginosa and S. aureus, demonstrating the feasibility of the developed strategy. In conclusion, the current study provides a convenient method for readily identification of silver-associated proteins in biological samples.

Little Antimicrobial Peptides with Big Therapeutic Roles

Antimicrobial Peptides (AMPs) are short amphipathic biological molecules generally with less than 100 amino acids. AMPs not only present high bioactivities against bacteria, fungi or protists-induced infections, but also play important roles in anticancer activity, immune response and inflammation regulation. AMPs are classified as ribosomally synthesized, non-ribosomally synthesized and post-translationally modified, non-ribosomally synthesized ones and several synthetic or semisynthetic peptides according to their synthesis with or without the involvement of ribosomes. The molecular characterization and bioactivity action mechanisms are summarized for several ribosomally synthesized AMPs and main non-ribosomally synthesized members (cyclopeptides, lipopeptides, glycopeptides, lipoglycopeptides). We also analyze challenges and new strategies to overcome drug resistance and application limitations for AMP discovery. In conclusion, the growing novel small molecular AMPs have huge therapeutic potentials of antibacterial, antiviral, anticancer and immunoregulatory bioactivities through new techniquesdriven drug discovery strategy including bioinformatics prediction, de novo rational design and biosynthesis.

Protein expression profiles in methicillin-resistant Staphylococcus aureus (MRSA) under effects of subminimal inhibitory concentrations of imipenem

Imipenem is a beta-lactam antibiotic mainly active against gram-negative bacterial pathogens and also could cause cell wall impairment in methicillin-resistant Staphylococcus aureus(MRSA). However, related antibacterial mechanisms of imipenem on MRSA and mixed infections of MRSA and gram-negative bacteria are relatively poorly revealed. This study was to identify proteins in the MRSA response to subminimal inhibitory concentrations (sub-MICs) of imipenem treatment. Our results showed that 240 and 58 different expression proteins (DEPs) in sub-MICs imipenem-treated S3 (a standard MRSA strain) and S23 (a clinical MRSA strain) strains were identified through the isobaric tag for relative and absolute quantitation method when compared with untreated S3 and S23 strains, respectively, which was further confirmed by multiple reactions monitoring. Our result also demonstrated that expressions of multiple DEPs involved in cellular proliferation, metabolism and virulence were significantly changed in S3 and S23 strains, which was proved by gene ontology annotations and qPCR analysis. Further, transmission electron microscopy and scanning electron microscopy analysis showed cell wall deficiency, cell lysis and abnormal nuclear mitosis on S23 strain. Our study provides important information for understanding the antibacterial mechanisms of imipenem on MRSA and for better usage of imipenem on patients co-infected with MRSA and other multidrug-resistant gram-negative bacteria.

Multifunctional Pharmaceutical Effects of the Antibiotic Daptomycin

Daptomycin (DAP), a cyclic lipopeptide produced by Streptomyces roseosporus, is a novel antibiotic to clinically treat various Gram-positive pathogenic bacteria-induced infections. Although DAP has a strong broad-spectrum bactericidal effect, recently rare bacterial antibiotic resistance against DAP gradually arises. The review is to summarize the normal indications of DAP, its off-label usage against several clinical pathogen infections, the unique antibacterial mechanisms of DAP, and the combination of antibiotic therapies for highly DAP-resistant pathogens. More noticeably, rising evidences demonstrate that DAP has new potential activity of anticancer and immunomodulatory effects. So far the multifunctional pharmaceutical effects of DAP deserve to be further explored for future clinical applications.

Fengycins, Cyclic Lipopeptides from Marine Bacillus subtilis Strains, Kill the Plant-Pathogenic Fungus Magnaporthe grisea by Inducing Reactive Oxygen Species Production and Chromatin Condensation

Rice (Oryza sativa L.) is the most important crop and a primary food source for more than half of the world's population. Notably, scientists in China have developed several types of rice that can be grown in seawater, avoiding the use of precious freshwater resources and potentially creating enough food for 200 million people. The plant-affecting fungus Magnaporthe grisea is the causal agent of rice blast disease, and biological rather than chemical control of this threatening disease is highly desirable. In this work, we discovered fengycin BS155, a cyclic lipopeptide material produced by the marine bacterium Bacillus subtilis BS155, which showed strong activity against M. grisea. Our results elucidate the mechanism of fengycin BS155-mediated M. grisea growth inhibition and highlight the potential of B. subtilis BS155 as a biocontrol agent against M. grisea in rice cultivation under both fresh- and saltwater conditions.

Rice blast caused by the phytopathogen Magnaporthe grisea poses a serious threat to global food security and is difficult to control. Bacillus species have been extensively explored for the biological control of many fungal diseases. In the present study, the marine bacterium Bacillus subtilis BS155 showed a strong antifungal activity against M. grisea. The active metabolites were isolated and identified as cyclic lipopeptides (CLPs) of the fengycin family, named fengycin BS155, by the combination of high-performance liquid chromatography (HPLC) and electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (ESI-MS/MS). Analyses using scanning and transmission electron microscopy revealed that fengycin BS155 caused morphological changes in the plasma membrane and cell wall of M. grisea hyphae. Using comparative proteomic and biochemical assays, fengycin BS155 was demonstrated to reduce the mitochondrial membrane potential (MMP), induce bursts of reactive oxygen species (ROS), and downregulate the expression level of ROS-scavenging enzymes. Simultaneously, fengycin BS155 caused chromatin condensation in fungal hyphal cells, which led to the upregulation of DNA repair-related protein expression and the cleavage of poly(ADP-ribose) polymerase (PARP). Altogether, our results indicate that fengycin BS155 acts by inducing membrane damage and dysfunction of organelles, disrupting MMP, oxidative stress, and chromatin condensation, resulting in M. grisea hyphal cell death. Therefore, fengycin BS155 and its parent bacterium are very promising candidates for the biological control of M. grisea and the associated rice blast and should be further investigated as such.

IMPORTANCE Rice (Oryza sativa L.) is the most important crop and a primary food source for more than half of the world's population. Notably, scientists in China have developed several types of rice that can be grown in seawater, avoiding the use of precious freshwater resources and potentially creating enough food for 200 million people. The plant-affecting fungus Magnaporthe grisea is the causal agent of rice blast disease, and biological rather than chemical control of this threatening disease is highly desirable. In this work, we discovered fengycin BS155, a cyclic lipopeptide material produced by the marine bacterium Bacillus subtilis BS155, which showed strong activity against M. grisea. Our results elucidate the mechanism of fengycin BS155-mediated M. grisea growth inhibition and highlight the potential of B. subtilis BS155 as a biocontrol agent against M. grisea in rice cultivation under both fresh- and saltwater conditions.

SILAC-based quantitative MS approach for real-time recording protein-mediated cell-cell interactions

In tumor microenvironment, interactions among multiple cell types are critical for cancer progression. To understand the molecular mechanisms of these complex interplays, the secreted protein analysis between malignant cancer cells and the surrounding nonmalignant stroma is a good viewpoint to investigate cell-cell interactions. Here, we developed two stable isotope labeling of amino acids in cell culture (SILAC)-based mass spectrometry (MS)/MS approaches termed spike-in SILAC and triple-SILAC to quantify changes of protein secretion level in a cell co-cultured system. Within the co-culture system of CT26 and Ana-1 cells, the spike-in SILAC and triple-SILAC MS approaches are sensitive to quantitatively measure protein secretion changes. Three representative quantified proteins (Galectin-1, Cathepsin L1 and Thrombospondin-1) by two SILAC-based MS methods were further validated by Western blotting, and the coming result matched well with SILACs’. We further applied these two SILACs to human cell lines, NCM460 and HT29 co-culture system, for evaluating the feasibility, which confirmed the spike-in and triple SILAC were capable of monitoring the changed secreted proteins of human cell lines. Considering these two strategies in time consuming, sample complexity and proteome coverage, the triple-SILAC way shows more efficiency and economy for real-time recording secreted protein levels in tumor microenvironment.

Antimicrobial and anti-biofilm activity of hexadentated macrocyclic complex of copper (II) derived from thiosemicarbazide against Staphylococcus aureus

Multidrug-resistant pathogens causing nosocomial and community acquired infections delineate a significant threat to public health. It had urged to identify new antimicrobials and thus, generated interest in studying macrocyclic metal complex, which has been studied in the past for their antimicrobial activity. Hence, in the present study, we have evaluated the antimicrobial activity of the hexadentated macrocyclic complex of copper (II) (Cu Complex) derived from thiosemicarbazide against Gram-positive and Gram-negative bacteria. We observed increased susceptibility against standard isolates of Staphylococcus aureus with a minimum inhibitory concentration (MIC) range of 6.25 to 12.5 μg/mL. Similar activity was also observed towards methicillin resistant and sensitive clinical isolates of S. aureus from human (n = 20) and animal (n = 20) infections. The compound has rapid bactericidal activity, and we did not observe any resistant mutant of S. aureus. The compound also exhibited antibiofilm activity and was able to disrupt pre-formed biofilms. Cu complex showed increased susceptibility towards intracellular S. aureus and was able to reduce more than 95% of the bacterial load at 10 μg/mL. Overall, our results suggest that Cu complex with its potent anti-microbial and anti-biofilm activity can be used to treat MRSA infections and evaluated further clinically.

Data of the interacting protein networks and nucleotide metabolism pathways related to NDK and NT5

The data presented in this article are related to the research article entitled "Antibacterial mechanism of daptomycin antibiotic against Staphylococcus aureus based on a quantitative bacterial proteome analysis" (Ma et al., 2016) [1]. Nucleoside diphosphate kinase (NDK) and 5'-nucleotidase (NT5) are two proteins related to bacterial growth. Here, a bioinformatics analysis was presented to explore NDK and NT5-invovled in the interacting protein network and purine metabolism.

Proteomics progresses in microbial physiology and clinical antimicrobial therapy

Clinical microbial identification plays an important role in optimizing the management of infectious diseases and provides diagnostic and therapeutic support for clinical management. Microbial proteomic research is aimed at identifying proteins associated with microbial activity, which has facilitated the discovery of microbial physiology changes and host–pathogen interactions during bacterial infection and antimicrobial therapy. Here, we summarize proteomic-driven progresses of host–microbial pathogen interactions at multiple levels, mass spectrometry-based microbial proteome identification for clinical diagnosis, and antimicrobial therapy. Proteomic technique progresses pave new ways towards effective prevention and drug discovery for microbial-induced infectious diseases.