Live-cell high resolution magic angle spinning magnetic resonance spectroscopy for in vivo analysis of Pseudomonas aeruginosa metabolomics

NMR spectroscopy for metabolomics in the living system: recent progress and future challenges

Metabolism is a fundamental process that underlies human health and diseases. Nuclear magnetic resonance (NMR) techniques offer a powerful approach to identify metabolic processes and track the flux of metabolites at the molecular level in living systems. An in vitro study through in-cell NMR tracks metabolites in real time and investigates protein structures and dynamics in a state close to their most natural environment. This technique characterizes metabolites and proteins involved in metabolic pathways in prokaryotic and eukaryotic cells. In vivo magnetic resonance spectroscopy (MRS) enables whole-organism metabolic monitoring by visualizing the spatial distribution of metabolites and targeted proteins. One limitation of these NMR techniques is the sensitivity, for which a possible improved approach is through isotopic enrichment or hyperpolarization methods, including dynamic nuclear polarization (DNP) and parahydrogen-induced polarization (PHIP). DNP involves the transfer of high polarization from electronic spins of radicals to surrounding nuclear spins for signal enhancements, allowing the detection of low-abundance metabolites and real-time monitoring of metabolic activities. PHIP enables the transfer of nuclear spin polarization from parahydrogen to other nuclei for signal enhancements, particularly in proton NMR, and has been applied in studies of enzymatic reactions and cell signaling. This review provides an overview of in-cell NMR, in vivo MRS, and hyperpolarization techniques, highlighting their applications in metabolic studies and discussing challenges and future perspectives.

Screening and Metabolomic Analysis of Lactic Acid Bacteria-Antagonizing Pseudomonas aeruginosa

Pseudomonas aeruginosa is a conditional Gram-negative pathogen that produces extracellular virulence factors that can lead to bloodstream invasion, severely harm tissues, and disseminate bacteria, ultimately leading to various diseases. In this study, lactic acid bacteria (LAB) with strong antagonistic ability against P. aeruginosa were screened, and the regulatory mechanism of LAB against P. aeruginosa was evaluated. The results showed that the three selected LAB strains had strong inhibition ability on the growth, biofilm formation, and pyocyanin expression of P. aeruginosa and a promoting effect on the expression of autoinducer-2. Among them, Lactipantibacillus plantarum (Lp. plantarum) LPyang is capable of affecting the metabolic processes of P. aeruginosa by influencing metabolic substances, such as LysoPC, oxidized glutathione, betaine, etc. These results indicate that LPyang reduces the infectivity of P. aeruginosa through inhibition of its growth, biofilm formation, pyocyanin expression, and regulation of its metabolome. This study provides new insights into the antagonistic activity of Lp. plantarum LPyang against P. aeruginosa.

Metabolomics in Cell Biology

Metabolomics has long been used in a biomedical context. The most typical samples are body fluids in which small molecules can be detected and quantified using technologies such as Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). Many studies, in particular in the wider field of cancer research, are based on cellular models. Different cancer cells can have vastly different ways of regulating metabolism and responses to drug treatments depend on specific metabolic mechanisms which are often cell type specific. This has led to a series of publications using metabolomics to study metabolic mechanisms. Cell-based metabolomics has specific requirements and allows for interesting approaches where metabolism is followed in real-time. Here applications of metabolomics in cell biology have been reviewed, providing insight into specific technologies used and showing exemplary case studies with an emphasis towards applications which help to understand drug mechanisms.

Metabolomic studies of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a common, Gram-negative environmental organism. It can be a significant pathogenic factor of severe infections in humans, especially in cystic fibrosis patients. Due to its natural resistance to antibiotics and the ability to form biofilms, infection with this pathogen can cause severe therapeutic problems. In recent years, metabolomic studies of P. aeruginosa have been performed. Therefore, in this review, we discussed recent achievements in the use of metabolomics methods in bacterial identification, differentiation, the interconnection between genome and metabolome, the influence of external factors on the bacterial metabolome and identification of new metabolites produced by P. aeruginosa. All of these studies may provide valuable information about metabolic pathways leading to an understanding of the adaptations of bacterial strains to a host environment, which can lead to new drug development and/or elaboration of new treatment and diagnostics strategies for Pseudomonas.

Simultaneous metabolic mapping of different anatomies by 1H HR-MAS chemical shift imaging

Localized information on a specimen is considered indispensable for deciphering biological activity. Magnetic resonance spectroscopy is a notable method because of its versatility; however, one limitation is the spectral quality on a static sample. This study explores an amalgamated method with two magnetic resonance experiments: high-resolution magic-angle spinning (HR-MAS) for high-quality spectral acquisition from a spinning sample and chemical shift imaging (CSI) for spatial localization. The advantage of HR-MAS CSI is its amenity for simultaneously profiling the metabolome-with good spectral data-at different spatial regions in a single experiment. Herein, ¹H HR-MAS CSI (including a T₂-contrast CSI) was described and performed on various food tissues and an intact organism. Different data analyses such as multivariate and quantification were explored to identify the metabolic variants in different anatomical regions and in one case, to assist in a spatial allocation. The limitation and drawback of the experiment are also discussed. Graphical abstract.

Effects of a small, volatile bacterial molecule on Pseudomonas aeruginosa bacteria using whole cell high-resolution magic angle spinning nuclear magnetic resonance spectroscopy and genomics

In the present study, high-resolution magic-angle spinning (HRMAS) nuclear magnetic resonance (NMR) spectroscopy was applied to live Pseudomonas aeruginosa (PA) bacterial cells to determine the metabolome of this opportunistic Gram-negative human pathogen, and in particular, its response to the volatile aromatic low molecular weight signaling molecule, 2-aminoacetophenone (2-AA). Multi-dimensional HRMAS NMR is a promising method which may be used to determine the in vivo metabolome of live intact bacterial cells; 2-AA is produced by PA and triggers the emergence of phenotypes that promote chronic infection phenotypes in in vitro and in vivo (animal) models. In the present study, we applied one-dimensional and two-dimensional proton (¹H) HRMAS NMR to PA cells which were grown with or without 2-AA in order to examine the associations between metabolites and cellular processes in response to 2-AA. We also compared whole-genome transcriptome profiles of PA cells grown with or without 2-AA and found that 2-AA promoted profound metabolic changes in the PA cells. By comparing the whole-genome transcriptome profiles and metabolomic analysis, we demonstrated that 2-AA profoundly reprogramed the gene expression and metabolic profiles of the cells. Our in vivo¹H HRMAS NMR spectroscopy may prove to be a helpful tool in the validation of gene functions, the study of pathogenic mechanisms, the classification of microbial strains into functional/clinical groups and the testing of anti-bacterial agents.

Metabolite localization in living drosophila using High Resolution Magic Angle Spinning NMR

We have developed new methods enabling in vivo localization and identification of metabolites through their ¹H NMR signatures, in a drosophila. Metabolic profiles in localized regions were obtained using HR-MAS Slice Localized Spectroscopy and Chemical Shift Imaging at high magnetic fields. These methods enabled measurement of metabolite contents in anatomic regions of the fly, demonstrated by a decrease in β-alanine signals in the thorax of flies showing muscle degeneration.

NMR use to quantify phlorotannins: the case of Cystoseira tamariscifolia, a phloroglucinol-producing brown macroalga in Brittany (France)

Among the most renowned natural products from brown algae, phlorotannins are phloroglucinol polymers that have been extensively studied, both for their biotechnological potential and their interest in chemical ecology. The accurate quantification of these compounds is a key point to understand their role as mediators of chemical defense. In recent years, the Folin-Ciocalteu assay has remained a classic protocol for phlorotannin quantification, even though it frequently leads to over-estimations. Furthermore, the quantification of the whole pool of phlorotannins may not be relevant in ecological surveys. In this study, we propose a rapid (1)H qNMR method for the quantification of phlorotannins. We identified phloroglucinol as the main phenolic compound produced by the brown macroalga Cystoseira tamariscifolia. This monomer was detected in vivo using (1)H HR-MAS spectroscopy. We quantified this molecule through (1)H qNMR experiments using TSP as internal standard. The results are discussed by comparison with a standard Folin-Ciocalteu assay performed on purified extracts. The accuracy and simplicity of qNMR makes this method a good candidate as a standard phlorotannin assay.

Analysis of metabolic characteristics in a rat model of chronic pancreatitis using high-resolution magic-angle spinning nuclear magnetic resonance spectroscopy

Pathological and metabolic alterations co-exist and co-develop in the progression of chronic pancreatitis (CP). The aim of the present study was to investigate the metabolic characteristics and disease severity of a rat model of CP in order to determine associations in the observed pathology and the metabolites of CP using high-resolution magic-angle spinning nuclear magnetic resonance spectroscopy (HR-MAS NMR). Wistar rats (n=36) were randomly assigned into 6 groups (n=6 per group). CP was established by administering dibutyltin dichloride solution into the tail vein. After 0, 7, 14, 21, 28 and 35 days, the pancreatic tissues were collected for pathological scoring or for HR-MAS NMR. Correlation analyses between the major pathological scores and the integral areas of the major metabolites were determined. The most representative metabolites, aspartate, betaine and fatty acids, were identified as possessing the greatest discriminatory significance. The Spearman’s rank correlation coefficients between the pathology and metabolites of the pancreatic tissues were as follows: Betaine and fibrosis, 0.454 (P=0.044); betaine and inflammatory cell infiltration, 0.716 (P=0.0001); aspartate and fibrosis, −0.768 (P=0.0001); aspartate and inflammatory cell infiltration, −0.394 (P=0.085); fatty acid and fibrosis, −0.764 (P=0.0001); and fatty acid and inflammatory cell infiltration, −0.619 (P=0.004). The metabolite betaine positively correlated with fibrosis and inflammatory cell infiltration in CP. In addition, aspartate negatively correlated with fibrosis, but exhibited no significant correlation with inflammatory cell infiltration. Furthermore, the presence of fatty acids negatively correlated with fibrosis and inflammatory cell infiltration in CP. HR-MAS NMR may be used to analyze metabolic characteristics in a rat model of different degrees of chronic pancreatitis.

(1)H high resolution magic-angle coil spinning (HR-MACS) μNMR metabolic profiling of whole Saccharomyces cervisiae cells: a demonstrative study

The low sensitivity and thus need for large sample volume is one of the major drawbacks of Nuclear Magnetic Resonance (NMR) spectroscopy. This is especially problematic for performing rich metabolic profiling of scarce samples such as whole cells or living organisms. This study evaluates a ¹H HR-MAS approach for metabolic profiling of small volumes (250 nl) of whole cells. We have applied an emerging micro-NMR technology, high-resolution magic-angle coil spinning (HR-MACS), to study whole Saccharomyces cervisiae cells. We find that high-resolution high-sensitivity spectra can be obtained with only 19 million cells and, as a demonstration of the metabolic profiling potential, we perform two independent metabolomics studies identifying the significant metabolites associated with osmotic stress and aging.