Quantitative Proteomic Analysis of Staphylococcus aureus Treated With Punicalagin, a Natural Antibiotic From Pomegranate That Disrupts Iron Homeostasis and Induces SOS

Staphylococcus aureus SOS response: Activation, impact, and drug targets

Staphylococcus aureus is a common cause of diverse infections, ranging from superficial to invasive, affecting both humans and animals. The widespread use of antibiotics in clinical treatments has led to the emergence of antibiotic-resistant strains and small colony variants. This surge presents a significant challenge in eliminating infections and undermines the efficacy of available treatments. The bacterial Save Our Souls (SOS) response, triggered by genotoxic stressors, encompasses host immune defenses and antibiotics, playing a crucial role in bacterial survival, invasiveness, virulence, and drug resistance. Accumulating evidence underscores the pivotal role of the SOS response system in the pathogenicity of S. aureus. Inhibiting this system offers a promising approach for effective bactericidal treatments and curbing the evolution of antimicrobial resistance. Here, we provide a comprehensive review of the activation, impact, and key proteins associated with the SOS response in S. aureus. Additionally, perspectives on therapeutic strategies targeting the SOS response for S. aureus, both individually and in combination with traditional antibiotics are proposed.

Staphylococcus aureus/Staphylococcus epidermidis from skin microbiota are balanced by Pomegranate peel extract: An eco-sustainable approach

The imbalance in skin microbiota is characterized by an increased number of pathogens in respect to commensal microorganisms. Starting from a skin microbiota collection, the aim of this work was to evaluate the possible role of Pomegranate (Punica granatum L.) Peel Extract (PPE) in restoring the skin microbiota balance acting on Staphylococcus spp. PPE was extracted following green methodology by using n-butane and the Dimethyl Ether (DME) solvents and analyzed for phytochemical composition and antimicrobial activity. The PPE antimicrobial action was evaluated against Gram +, Gram - bacteria and yeast reference strains and the most effective extract was tested against the main skin microbiota isolated strains. PPE extracted with DME showed the best antimicrobial action with MICs ranging from 1 to 128 mg/mL; the main active compounds were Catechin, Quercetin, Vanillic acid and Gallic acid. The PPE in DME anti-adhesive effect was examined against S. epidermidis and S. aureus mono and dual-species biofilm formation by biomass quantification and CFU/mL determination. The extract toxicity was evaluated by using Galleria mellonella larvae in vivo model. The extract displayed a significant anti-adhesive activity with a remarkable species-specific action at 4 and 8 mg/mL against S. epidermidis and S. aureus mono and dual-species biofilms. PPE in DME could represent an eco-sustainable non-toxic strategy to affect the Staphylococcal skin colonization in a species-specific way. The innovation of this work is represented by the reuse of food waste to balance skin microbiota.

Bioactive Compounds from Fruits as Preservatives

The use of additives with preservative effects is a common practice in the food industry. Although their use is regulated, natural alternatives have gained more attention among researchers and professionals in the food industry in order to supply processed foods with a clean label. Fruits are essential components in a healthy diet and have also been associated with improved health status and a lower risk of developing diseases. This review aims to provide an overview of the main bioactive compounds (polyphenols, betalain, and terpenes) naturally found in fruits, their antioxidant and antimicrobial activity in vitro, and their preservative effect in different foods. Many extracts obtained from the skin (apple, grape, jabuticaba, orange, and pomegranate, for instance), pulp (such as red pitaya), and seeds (guarana, grape, and jabuticaba) of fruits are of great value due to the presence of multiple compounds (punicalagin, catechin, gallic acid, limonene, β-pinene, or γ-terpinene, for instance). In terms of antioxidant activity, some fruits that stand out are date, jabuticaba, grape, and olive, which interact with different radicals and show different mechanisms of action in vitro. Antimicrobial activity is observed for natural extracts and essential oils (especially from citrus fruits) that limit the growth of many microorganisms (Bacillus subtilis, Escherichia coli, Penicillium digitatum, and Pseodomonas aeruginosa, for instance). Studies in foods have revealed that the use of extracts or essential oils as free or encapsulated forms or incorporated into films and coatings can inhibit microbial growth, slow oxidative reactions, reduce the accumulation of degradative products, and also preserve sensory attributes, especially with films and coatings. Future studies could focus on the advances of extracts and essential oils to align their use with the development of healthier foods (especially for meat products) and explore the inhibition of spoilage microorganisms in dairy products, for instance.

The Detriment of Salicylic Acid to the Pseudomonas savastanoi pv. phaseolicola Proteome

Salicylic acid (SA), a natural product, is the major hormonal regulator of the plant immune system. SA also has antibacterial activity that is not completely elucidated. To gain a better understanding of this, Pseudomonas savastanoi pv. phaseolicola, a bacterial pathogen of beans, was exposed to sub-inhibitory amounts of SA and was then examined using quantitative mass spectrometry. Among the 2,185 proteins quantified, there were pronounced increases in p-hydroxybenzoic acid efflux pumps and multidrug efflux pumps. By contrast there were significant decreases in porin proteins, high-osmolarity response proteins, and protein components of the type VI secretion system. In addition, there were alterations in enzymes likely affecting the production of alginate, which is needed for infection. Furthermore, there was a decrease in an enzyme needed to detoxify methylglyoxal. Assays confirmed a reduction in alginate production and an increase in cellular methylglyoxal concentrations after SA treatment. Culture assays demonstrated that SA altered bacterial growth curves more so than other hydroxylated benzoic acid isomers. These data reveal that SA is antibiotic and that P. savastanoi pv. phaseolicola significantly alters its proteome in response to SA in vitro. Similar alterations to the bacterial proteome occur in beans during an immune reaction when SA increases at the site of infection. Thus, in beans, SA likely deters bacterial infection by adversely altering the bacterial proteome. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Salicylic Acid and Phytoalexin Induction by a Bacterium that Causes Halo Blight in Beans

Pseudomonas savastanoi pv. phaseolicola is a bacterium that causes halo blight in beans. Different varieties of beans have hypersensitive resistance to specific races of P. savastanoi pv. phaseolicola. During hypersensitive resistance, also known as effector-triggered immunity (ETI), beans produce hormones that signal molecular processes to produce phytoalexins that are presumed to be antibiotic to bacteria. To shed light on hormone and phytoalexin production during immunity, we inoculated beans with virulent and avirulent races of P. savastanoi pv. phaseolicola. We then used mass spectrometry to measure the accumulation of salicylic acid (SA), the primary hormone that controls immunity in plants, and other hormones including jasmonate, methyljasmonate, indole-3-acetic acid, abscisic acid, cytokinin, gibberellic acid, and 1-aminocyclopropane-1-carboxylic acid. SA, but no other examined hormone, consistently increased at sites of infection to greater levels in resistant beans compared with susceptible beans at 4 days after inoculation. We then monitored 10 candidate bean phytoalexins. Daidzein, genistein, kievitone, phaseollin, phaseollidin, coumestrol, and resveratrol substantially increased alongside SA in resistant beans but not in susceptible beans. In vitro culture assays revealed that SA, daidzein, genistein, coumestrol, and resveratrol inhibited P. savastanoi pv. phaseolicola race 5 culture growth. These results demonstrate that these phytoalexins may be regulated by SA and work with SA during ETI to restrict bacterial replication. This is the first report of antibiotic activity for daidzein, genistein, and resveratrol to P. savastanoi pv. phaseolicola. These results improve our understanding of the mechanistic output of ETI toward this bacterial pathogen of beans.

Leveraging big data bioinformatics approaches to extract knowledge from Staphylococcus aureus public omics data

Staphylococcus aureus is a notorious pathogen posing challenges in the medical industry due to drug resistance and biofilm formation. The horizon of knowledge on S. aureus pathogenesis has expanded with the advancement of data-driven bioinformatics techniques. Mining information from sequenced genomes and their expression data is an economic approach that alleviates wastage of resources and redundancy in experiments. The current review covers how big data bioinformatics has been used in the analysis of S. aureus from publicly available -omics data to uncover mechanisms of infection and inhibition. Particularly, advances in the past two decades in biomarker discovery, host responses, phenotype identification, consolidation of information, and drug development are discussed highlighting the challenges and shortcomings. Overall, the review summarizes the diverse aspects of scrupulous re-analysis of S. aureus proteomic and transcriptomic expression datasets retrieved from public repositories in terms of the efforts taken, benefits offered, and follow-up actions. The detailed review thus serves as a reference and aid for (i) Computational biologists by briefing the approaches utilized for bacterial omics re-analysis concerning S. aureus and (ii) Experimental biologists by elucidating the potential of bioinformatics in biological research to generate reliable postulates in a prompt and economical manner.

Antifungal and Anti-inflammatory Effect of Punicalagin on Murine Aspergillus fumigatus Keratitis

PURPOSE

This study aimed to investigate the anti-inflammatory effect and antifungal effect of punicalagin in murine fungal keratitis.

METHODS

We used in vitro and in vivo protocols to assess the anti-inflammatory effect and antifungal effect of punicalagin. In vitro, time kill and mycelial stain were done. In vivo, murine fungal keratitis was established and treated with PBS or PUN. Clinical scores were taken on days 1, 3, and 5 post infection. The mRNA and protein levels of inflammatory factors were detected by RT-PCR and Western blot, and the number and location of macrophages were analyzed by flow cytometry and immunofluorescence. Also, fungal plate counting was used to assess the antifungal effect. The DCFH-DA fluorescence probe detected the ROS level.

RESULTS

In vitro, PUN showed activity against A.fumigatus. (A.F.), with MIC90 values of 250 μg/ml, and significantly reduced A.F. biofilm formation (p < .001). In vivo, the mouse fungal keratitis model after punicalagin treatment exhibited less disease, lower clinical scores (p < .05), lower reduced macrophage infiltrate (p < .001), and fungal load (p < .001) than those treated with PBS. Treatment with punicalagin also reduced the mRNA expression and protein level of pro-inflammatory factors. At the cellular level, PUN significantly reduced the mRNA expression of inflammatory factors and ROS production caused by the stimulation of mycelia in RAW264.7 (p < .001).

CONCLUSIONS

The results show that punicalagin is beneficial in the treatment of murine fungal keratitis. The mechanism of its anti-inflammatory effect was synthetical, including antifungal activity, an inhibitory effect of proinflammatory factor and macrophages, and anti-oxidation.

Ongoing and potential novel trends of pomegranate fruit peel; a comprehensive review of its health benefits and future perspectives as nutraceutical

Pomegranate is an ancient shrub, globally distributed nowadays. It has been used in the middle east as a medicinal food and traditional medicine for thousands of years. Pomegranate peel (PP) constitutes about 50% of the total fruit, however, it has been previously regarded as a waste. Recent research points to PP as a rich source of phenolics (e.g., ellagitannins, flavonoids, and anthocyanins), polysaccharides, in addition to its biotransformed metabolites viz. urolithins making it a valuable waste with promising pharmacological actions. Compared to the pulp and the juice, PP exhibited stronger antioxidant and antimicrobial activities. Besides, it inhibited inflammation in several conditions, including colitis, arthritis, hepatitis, contact dermatitis, and lung inflammation. Moreover, it displayed anti-osteoporosis, anti-hyperglycemic, antidiabetic, antihypertensive, vasculoprotective, hepatoprotective, neuroprotective, and immunomodulatory effects. Additionally, it was effective as a prebiotic and in obesity control, besides it promoted wound healing. Furthermore, PP demonstrated anticancer effects against different cancer types, for example, colon, liver, thyroid, uterine, breast, bladder, prostate, leukemia, and osteosarcoma. Despite PP safety, it may interfere with the metabolism of other drugs because it inhibits cytochromes (CYP) changing their bioavailability, effectiveness, and toxicity. PP biowaste valorization not only avoids against its environmental and economic burden but can also provide a promising platform to produce novel or improved nutraceuticals. This study provides a comprehensive overview of PP biological activities with the reported action mechanisms related to its phytochemicals and further biotransformed metabolites inside the body. Future research prospects to unravel the merits of such waste and optimize its use are discussed. PRACTICAL APPLICATION: Pomegranate is widely distributed throughout the world. Although its peel was previously considered a waste, recent research regards it as a rich source of bioactive compounds with promising biological activities. Its recycling not only overcomes the bio-waste problems, but also provides a source of valuable compounds with several health benefits. In recent years, PP has been demonstrated to exhibit excellent pharmacological bioactivities, for example, antioxidant, anti-inflammatory, antimicrobial, antiosteoporosis, antihyperlipidemic, and anticancer activities. Its health-promoting power is mostly attributed to the phenolic and polysaccharide content, in addition to its amazing biotransformed metabolites. The underlying action mechanisms of such pharmacological activities are discussed and related to its chemical content. This review presents the latest research progress on the role of PP in the prevention and treatment of various chronic diseases, and its protective health effects for future research to be used in nutraceuticals.

Multi-targeted metallo-ciprofloxacin derivatives rationally designed and developed to overcome antimicrobial resistance

Antimicrobial resistance is a major global threat to human health due to the rise, spread and persistence of multi-drug-resistant bacteria or 'superbugs'. There is an urgent need to develop novel chemotherapeutics to overcome this overarching challenge. The authors derivatized a clinically used fluoroquinolone antibiotic ciprofloxacin (Cip), and complexed it to a copper phenanthrene framework. This resulted in the development of two novel metallo-antibiotics of general formula [Cu(N,N)(CipHA)]NO₃ where N,N represents a phenanthrene ligand and CipHA represents a hydroxamic acid of Cip derivative. Comprehensive studies, including a detailed proteomic study in which Staphylococcus aureus cells were exposed to the complexes, were undertaken to gain an insight into their mode of action. These new complexes possess potent antibacterial activity against S. aureus and methicillin-resistant S. aureus. In addition, they were found to be well tolerated in vivo in Galleria mellonella larvae, which has both functional and structural similarities to the innate immune system of mammals. These findings suggest that proteins involved in virulence, pathogenesis, and the synthesis of nucleotides and DNA repair mechanisms are most affected. In addition, both complexes affected similar cell pathways when compared with clinically used Cip, including cationic antimicrobial peptide resistance. The Cu-DPPZ-CipHA (DPPZ = dipyrido[3,2-a:2',3'-c]phenazine) analogue also induces cell leakage, which leads to an altered proteome indicative of reduced virulence and increased stress.

Bacterial Immobilization and Toxicity Induced by a Bean Plant Immune System

Pseudomonas savastanoi pv. phaseolicola causes halo blight disease in the common bean Phaseolus vulgaris. The bacterium invades the leaf apoplast and uses a type III secretion system to inject effector proteins into a bean cell to interfere with the bean immune system. Beans counter with resistance proteins that can detect effectors and coordinate effector-triggered immunity responses transduced by salicylic acid, the primary defense hormone. Effector-triggered immunity halts bacterial spread, but its direct effect on the bacterium is not known. In this study, mass spectrometry of bacterial infections from immune and susceptible beans revealed that immune beans inhibited the accumulation of bacterial proteins required for virulence, secretion, motility, chemotaxis, quorum sensing, and alginate production. Sets of genes encoding these proteins appeared to function in operons, which implies that immunity altered the coregulated genes in the bacterium. Immunity also reduced amounts of bacterial methylglyoxal detoxification enzymes and their transcripts. Treatment of bacteria with salicylic acid, the plant hormone produced during immunity, reduced bacterial growth, decreased gene expression for methylglyoxal detoxification enzymes, and increased bacterial methylglyoxal concentrations in vitro. Increased methylglyoxal concentrations reduced bacterial reproduction. These findings support the hypothesis that plant immunity involves the chemical induction of adverse changes to the bacterial proteome to reduce pathogenicity and to cause bacterial self-toxicity.

Antibiotic resistance genes attenuation in anaerobic microorganisms during iron uptake from zero valent iron: An iron-dependent form of homeostasis and roles as regulators

Zero valent iron (ZVI) has been previously documented to attenuate the propagation of antibiotic resistance genes (ARGs) in microbes, while how ZVI affects the evolution of ARGs remains unclear. Herein, we investigated the influences of ZVI on ARGs dissemination in anaerobic bioreactor treating oxytetracycline (tet) containing wastewater, by deciphering the roles of iron homeostasis and regulatory effects. A net reduction of tet gene targets ranging from 0.75 to 1.88 and 0.67 to 2.08 log unit in intracellular and extracellular DNA was achieved at the optimal dosage of 5 g/L ZVI, whereas 20 g/L ZVI made no effects on ARGs reduction. The reduced ARGs abundance by ZVI was directly related to the inhibited horizontal transfer of ARGs and decreased proliferation of resistant strains (mainly Paludibacter and WCHB1-32). The potential mechanisms included the increased antioxidant capacity, the depressed efflux pump system and the weakened energy driving force by Fur regulon in microbes (especially for Cloacibacterium and Dechloromonas). The negligible influence of 20 g/L ZVI on ARGs reduction was ascribed to the iron-catalyzed oxidative damage and reduced physiological activity. This study firstly illustrated the potential relationships among activation of iron uptake regulator leading to protection against oxidative stress, alternation of physiological metabolisms and reduction of ARGs dissemination. This work extents our understanding about the priority of ZVI in mitigating ARGs proliferation and sheds light on its potential application in wastewater treatment plants.

Pomegranate Peel Extracts as Safe Natural Treatments to Control Plant Diseases and Increase the Shelf-Life and Safety of Fresh Fruits and Vegetables

Although the Green Revolution was a milestone in agriculture, it was accompanied by intensive use of synthetic pesticides, which has raised serious concerns due to their impact on human and environmental health. This is increasingly stimulating the search for safer and more eco-friendly alternative means to control plant diseases and prevent food spoilage. Among the proposed alternatives, pomegranate peel extracts (PPEs) are very promising because of their high efficacy. In the present review, we discuss the complex mechanisms of action that include direct antimicrobial activity and induction of resistance in treated plant tissues and highlight the importance of PPE composition in determining their activity. The broad spectrum of activity, wide range of application and high efficiency of PPEs against bacterial, fungal and viral plant pathogens suggest a potential market not only restricted to organic production but also integrated farming systems. Considering that PPEs are non-chemical by-products of the pomegranate industry, they are perceived as safe by the public and may be integrated in circular economy strategies. This will likely encourage agro-pharmaceutical industries to develop commercial formulations and speed up the costly process of registration.

Quantitative proteomics approach to investigate the antibacterial response of Helicobacter pylori to daphnetin, a traditional Chinese medicine monomer

Helicobacter pylori is a Gram-negative bacterium related to the development of peptic ulcers and stomach cancer. An increasing number of infected individuals are found to harbor antibiotic-resistant H. pylori, which results in treatment failure. Daphnetin, a traditional Chinese medicine, has a broad spectrum of antibacterial activity without the development of bacterial resistance. However, the antibacterial mechanisms of daphnetin have not been elucidated entirely. To better understand the mechanisms of daphnetin's effect on H. pylori, a label-free quantitative proteomics approach based on an EASY-nLC 1200 system coupled with an Orbitrap Fusion Lumos mass spectrometer was established to investigate the key protein differences between daphnetin- and non-daphnetin-treated H. pylori. Using the criteria of greater than 1.5-fold changes and adjusted p value <0.05, proteins related to metabolism, membrane structure, nucleic acid and protein synthesis, ion binding, H. pylori colonization and infection, stress reaction, flagellar assembly and so on were found to be changed under daphnetin pressure. And the changes of selected proteins in expression level were confirmed by targeted proteomics. These new data provide us a more comprehensive horizon of the proteome changes in H. pylori that occur in response to daphnetin.

Systematic stress adaptation of Bacillus subtilis to tetracycline exposure

To alleviate the harmful effects of antibiotics on the environment and human health, the stress response and molecular network of Bacillus under tetracycline stress were investigated using a proteomics approach. During the exposure process, Bacillus subtilis exhibited a strong adaptation mechanism. Cell membrane and intracellular reactive oxygen species (ROS) level returned to normal after 5 h. A total of 312 upregulated and 65 downregulated proteins were identified, mainly involved in metabolism and the synthesis of ribosomes, DNA, and RNA. After tetracycline exposure, the core metabolism network was accelerated to supply precursors for the synthesis of DNA, RNA, proteins, peptidoglycans, and saturated fatty acids that were involved in ribosome protection, and strengthened the cell wall and cell membrane. The signal transduction pathways involved were analyzed in association with the stress response of B. subtilis at 15 min of exposure to tetracycline. The primary damage to the ribosome by tetracycline activated a series of response proteins. Antitoxin and heat-shock proteins were activated for the global regulation of transcription and metabolism. Trigger factor Tig was upregulated to ensure proper initiation of transcription and aerobic respiration. Temperature-sensor protein VicR from the two-component system was used by the cell to regulate the composition of the cell wall and cell membrane. The over-consumption of metabolites, such as phosphoribosyl diphosphate (PRPP), purine nucleoside triphosphate (GTP), and acetyl-CoA forced the cells to assimilate more sugar for glycolysis. To this end, methyl-accepting chemotaxis proteins (MCPs) and sugar transportation protein PtsG were upregulated, simultaneously. Ultimately, peroxidase was activated to eliminate the redundant ROS, to minimize cell damage. These findings presented a system-level understanding of adaption processes of bacteria to antibiotic stress.

The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator

The complexity of plant microbial communities provides a rich model for investigating biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rot Enterobacteriaceae (SRE) represents an emerging group of plant-pathogens causing soft rot/blackleg diseases resulting in economic losses worldwide in a variety of crops. A preliminary screening using next-generation sequencing of 16S rRNA comparatively analyzing healthy and diseased potato tubers, identified several taxa from Proteobacteria to Firmicutes as potential potato endophytes/plant pathogens. Subsequent to this, a range of molecular and computational techniques were used to determine the contribution of antimicrobial factors such as bacteriocins, carbapenem and type VI secretion system (T6SS), found in an aggressive SRE (Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692) against these endophytes/plant pathogens. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targeted Firmicutes, only the Pcb1692 pyocin seems to play a role in growth inhibition. Furthermore, production of carbapenem by Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of fur, slyA and expI regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Finally, the results demonstrated that although T6SS confers no relevant advantage during in vitro competition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observed in planta.

IMPORTANCE

Soft rot Enterobacteriaceae (SRE) represents important phytopathogens causing soft rot/blackleg diseases in a variety of crops leading to huge economic losses worldwide. These pathogens have been isolated alongside other bacteria from different environments such as potato tubers, stems, roots and from the soil. In these environments, SREs coexist with other bacteria where they have to compete for scarce nutrients and other resources. In this report, we show that Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692, which represents one of the SREs, inhibits growth of several different bacteria by producing different antimicrobial compounds. These antimicrobial compounds can be secreted inside or outside the plant host, allowing Pcb1692 to effectively colonize different types of ecological niches. By analyzing the genome sequences of several SREs, we show that other SREs likely deploy similar antimicrobials to target other bacteria.

Preparation and in Vitro Evaluation of New Composite Mesh Functionalized with Cationic Antimicrobial Peptide

Infection caused by bacteria in hernia repair site is a severe complication, and patients have to undergo a second surgery to remove the infected prosthesis. In this study, we developed a composite biological safe mesh with antibacterial activity. The composite mesh is composed of large pore polypropylene (PP) mesh, poly-caprolactone (PCL) and antimicrobial peptide (PEP-1), which we synthesized in our lab. Fourier transformed infrared (FTIR) spectroscopy was utilized to analyze the functional groups. The surface morphology, in vitro release characters, mechanical properties, antibacterial activities, and in vitro cytotoxicity of modified mesh were evaluated. Results showed that PEP-1 was loaded in fibers successfully and could diffuse from nanofibers to inhibit bacteria (E. coli) growth. However, the modified mesh did not show inhibition to S. aureus. The mechanical properties of fabricated mesh showed no difference with two commercial surgical meshes. What is more, modified mesh was proved to be nontoxic to human dermal fibroblasts, indicating that this method to fabricate meshes with antibacterial activity is feasible and provides a new strategy for the development of surgical meshes.

Improved SILAC method for double labeling of bacterial proteome

Stable isotope labeling with amino acids in cell culture (SILAC) is a robust proteomics method with advantages such as reproducibility and easy handling. This method is popular for the analysis of mammalian cells. However, amino acid conversion in bacteria decreases the labeling efficiency and quantification accuracy, limiting the application of SILAC in bacterial proteomics to auxotrophic bacteria or to single labeling with lysine. In this study, we found that adding high concentrations of isotope-labeled (heavy) and natural (light) amino acids into SILAC minimal medium can efficiently inhibit the complicated amino acid conversions. This simple and straightforward strategy facilitated complete incorporation of amino acids into the bacterial proteome with good accuracy. High labeling efficiency can be achieved in different bacteria by slightly modifying the supplementation of amino acids in culture media, promoting the widespread application of SILAC technique in bacterial proteomics. SIGNIFICANCE: Amino acid conversion in bacteria decreases labeling efficiency, limiting the application of Stable isotope labeling with amino acids in cell culture (SILAC) in bacterial proteomics to auxotrophic bacteria or single labeling with lysine. In this study, we found that high concentrations of isotope-labeled (heavy) and natural (light) amino acids facilitate full incorporation of amino acids into the bacterial proteome with good reproducibility. This improved double labeling SILAC technique using medium supplemented with high concentrations of amino acids is suitable for quantitative proteomics research on both gram-positive and -negative bacteria, facilitating the broad application of quantitative proteomics in bacterial studies.