Stress response of Escherichia coli to essential oil components - insights on low-molecular-weight proteins from MALDI-TOF

Essential and virulence-related protein interactions of pathogens revealed through deep learning

Identification of bacterial protein-protein interactions and predicting the structures of the complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here, we developed a deep learning-based pipeline that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.

Chemical and Biological Characterization of Melaleuca alternifolia Essential Oil

The essential oil of Melaleuca alternifolia, commonly known as tea tree oil, has many beneficial properties due to its bioactive compounds. The aim of this research was to characterize the tea tree essential oil (TTEO) from Slovakia and its biological properties, which are specific to the chemical composition of essential oil. Gas chromatography/mass spectroscopy revealed that terpinen-4-ol was dominant with a content of 40.3%. γ-Terpinene, 1,8-cineole, and p-cymene were identified in contents of 11.7%, 7.0%, and 6.2%, respectively. Antioxidant activity was determined at 41.6% radical inhibition, which was equivalent to 447 μg Trolox to 1 mL sample. Antimicrobial activity was observed by the disk diffusion method against Gram-positive (G⁺), Gram-negative (G^-) bacteria and against yeasts, where the best antimicrobial activity was against Enterococcus faecalis and Candida albicans with an inhibition zone of 10.67 mm. The minimum inhibitory concentration showed better susceptibility by G⁺ and G^- planktonic cells, while yeast species and biofilm-forming bacteria strains were more resistant. Antibiofilm activity was observed against Pseudomonas fluorescens and Salmonella enterica by MALDI-TOF, where degradation of the protein spectra after the addition of essential oil was obtained. Good biological properties of tea tree essential oil allow its use in the food industry or in medicine as an antioxidant and antimicrobial agent.

Thymus serpyllum Essential Oil and Its Biological Activity as a Modern Food Preserver

The aim of this study was to analyze the chemical composition and biological and antibiofilm activity of the essential oil (EO) of Thymus serpyllum with the use of a MALDI-TOF MS Biotyper. The main compounds of the EO were thymol, 18.8%; carvacrol, 17.4%; o-cymene, 15.4%; and geraniol, 10.7%. It was found that free-radical scavenging activity was high. The highest antimicrobial activity was observed against Pseudomonas aeruginosa, Salmonella enteritidis, and biofilm-forming bacteria. The changes in the biofilm structure after T. serpyllum EO application confirmed the inhibitory action and the most pronounced effect was observed on Bacillus subtilis biofilm. The antifungal activity of the vapor phase was the most effective against Penicillium crustosum. T. serpyllum should be a suitable alternative to synthetic antioxidants as well as antimicrobials. The EO of T. serpyllum can be used in the vapor phase in the storage of root vegetables as well as a growth inhibitor of Penicillium on bread.

An Overview of the Potential Therapeutic Applications of Essential Oils

The emergence of antimicrobial resistance (AMR) has urged researchers to explore therapeutic alternatives, one of which includes the use of natural plant products such as essential oils (EO). In fact, EO obtained from clove, oregano, thymus, cinnamon bark, rosemary, eucalyptus, and lavender have been shown to present significant inhibitory effects on bacteria, fungi, and viruses; many studies have been done to measure EO efficacy against microorganisms. The strategy of combinatory effects via conventional and non-conventional methods revealed that the combined effects of EO-EO or EO-antibiotic exhibit enhanced efficacy. This paper aims to review the antimicrobial effects of EO, modes of EO action (membrane disruption, efflux inhibition, increase membrane permeability, and decrease in intracellular ATP), and their compounds' potential as effective agents against bacteria, fungi, and viruses. It is hoped that the integration of EO applications in this work can be used to consider EO for future clinical applications.

Proteomic Analysisof Food Allergens by MALDI TOF/TOF Mass Spectrometry

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is largely recognized as an important tool in the analysis of many biomolecules such as proteins and peptides. The MS analysis of digested peptides to identify a protein or some of its modifications is a key step in proteomics. MALDI-MS is well suited for the peptide mass fingerprinting (PMF) technique, as well as selected fragmentation of various precursors using collisional-induced dissociation (CID) or post-source decay (PSD).In the last few years, MALDI-MS has played a significant role in food chemistry, especially in the detection of food adulterations, characterization of food allergens, and investigation of protein structural modifications induced by various industrial processes that could be an issue in terms of food quality and safety.Here, we present simple extraction protocols of allergenic proteins in food commodities such as milk, egg, hazelnut , and lupin seeds. Classic bottom-up approaches based on Sodium Dodecyl Sulphate (SDS) gel electrophoresis separation followed by in-gel digestion or direct in-solution digestion of whole samples are described. MALDI-MS and MS /MS analyses are discussed along with a comparison of data obtained by using the most widespread matrices for proteomic studies, namely, α-cyano-4-hydroxy-cinnamic acid (CHCA) and α-cyano-4-chloro-cinnamic acid (CClCA). The choice of the most suitable MALDI matrix is fundamental for high-throughput screening of putative food allergens.

Synthesis and Matrix Properties of α-Cyano-5-phenyl-2,4-pentadienic Acid (CPPA) for Intact Proteins Analysis by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

The effectiveness of a synthesized matrix, α-cyano-5-phenyl-2,4-pentadienic acid (CPPA), for protein analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in complex samples such as foodstuff and bacterial extracts, is demonstrated. Ultraviolet (UV) absorption along with laser desorption/ionization mass spectrometry (LDI-MS) experiments were systematically conducted in positive ion mode under standard Nd:YLF laser excitation with the aim of characterizing the matrix in terms of wavelength absorption and proton affinity. Besides, the results for standard proteins revealed that CPPA significantly enhanced the protein signals, reduced the spot-to-spot variability and increased the spot homogeneity. The CPPA matrix was successful employed to investigate intact microorganisms, milk and seed extracts for protein profiling. Compared to conventional matrices such as sinapinic acid (SA), α-cyano-4-hydroxycinnamic acid (CHCA) and 4-chloro-α-cyanocinnamic acid (CClCA), CPPA exhibited better signal-to-noise (S/N) ratios and a uniform response for most examined proteins occurring in milk, hazelnut and in intact bacterial cells of E. coli. These findings not only provide a reactive proton transfer MALDI matrix with excellent reproducibility and sensitivity, but also contribute to extending the battery of useful matrices for intact protein analysis.

Shift of Volatile Organic Compounds (VOCs) in Gluten-Free Hemp-Enriched Sourdough Bread: A Metabolomic Approach

Hemp seed flour represents a potential ingredient for protein enrichment of gluten-free bakery products, the nutritional value of which could be further increased by fermentation with sourdough or with beneficial lactic acid bacteria strains. In this study, a metabolomic approach was used to evaluate the effect of hemp seed flour addition and sourdough fermentation on the production of flavoring and health-related volatile organic compounds (VOCs) in a gluten-free bread. Multivariate analysis of VOCs provided an in-depth description of the effects of hemp seed flour addition and sourdough fermentation on flavoring and bioactive compounds. In particular, an increased concentration of antimicrobial compounds, a larger spectrum of bioactive VOCs and a typical flavoring profile was evidenced in comparison to standard products. Furthermore, an increase of fermentation metabolites was observed in comparison to a standard dough, relating to abundances of 2-butanone-3-hydroxy, acetic acid, ethanol, and 1,4-butanediol. This study provides new insights on the evolution of flavoring and bioactive hemp seed flour constituents during sourdough fermentation, evidencing their retention in baked goods, and describes a new approach that could guide the formulation of innovative, fermented food with enhanced nutritional value.

Prebiotic potential of hemp blended drinks fermented by probiotics

Plant-based drinks as substitute for milk consumption are raising striking interest in the food industry. Soy and rice drinks are the most studied and successful milk substitutes. An untapped source is hemp seed, which is a powerhouse of nutrients bearing bioactive compounds, but the production of derived drink is limited. The present work is about introducing new formulations of commercial hemp seed-derived drink to be fermented with probiotics (Lactobacillus fermentum, Lb. plantarum and Bifidobacterium bifidum). In this work for the first time the prebiotic activity of different hemp seed drinks was assessed by cultural and quantitative PCR methods. In addition, to better describe the prebiotic potential, VOCs alkenes and volatile organic acids were characterized by a metabolomic approach via GC-MS SPME. Obtained results showed that the hemp seed drinks had strong prebiotic activity, ability to support probiotics growth and to increase the content of some bioactive compounds. These outputs are in part due to the presence of different terpenes that inhibit the growth of enteropathogens and to high levels of acetate, propionate and butyrate produced during fermentation that support the growth of probiotics. Although the health potential of hemp seed is well known, derived drinks are hitherto scarcely transformed and distributed, thus this work could provide some basics to produce prebiotic and probiotic fermented hemp seed drinks.

Data on low-molecular weight proteins of Escherichia coli treated by essential oils components, tetracycline, chlorine and peroxide by MALDI-TOF MS

In this dataset we provide MALDI-TOF MS spectra of Escherichia coli. The data presented in this article are related to the article entitled “Stress response of Escherichia coli to essential oil components – insights on low-molecular-weight proteins from MALDI-TOF” (Božik et al., 2018) [1]. Essential oils and their components are known for their antibacterial effect. Many studies evaluated the effect of essential oil components (EOCs) on the cell wall, bacterial membranes, and energetic metabolism. But data about low molecular weight proteins (<20 kDa) are limited. Provided data are focused on bacterial response to EOCs; tetracycline, peroxide and chlorine was used as control as common antibiotic and disinfectant agents used against bacteria. These data describe the effect of tested substances to bacterial protein synthesis.