Lipid Compositions in Escherichia coli and Bacillus subtilis During Growth as Determined by MALDI-TOF and TOF/TOF Mass Spectrometry

Improvement of lipid production from glucose/xylose mixed-sugar by the oleaginous yeast Lipomyces starkeyi through ultra-violet mutagenesis

The oleaginous yeast Lipomyces starkeyi is a promising triacylglycerol (TAG) producer for biodiesel fuel. However, it is necessary to further improve TAG productivity in L. starkeyi from a mixed sugar of glucose and xylose. This study aimed to construct an L. starkeyi mutant with increased TAG productivity from glucose/xylose mixed-sugar and to elucidate the causes underlying increased lipid productivity. Ultra-violet (UV) mutagenesis combined with enrichment culture with ethanol and H2O2 and selection of low-density cells was applied to L. starkeyi to obtain the L. starkeyi mutant strain UMP47, which exhibited higher TAG production from glucose/xylose. Transcriptome analysis revealed high expression of genes involved in transporter activity and carbohydrate metabolism, whereas genes involved in DNA replication exhibited lower expression in the mutant strain UMP47 than in the wild-type strain. Altogether, the lipid productivity of L. starkeyi was successfully improved by UV mutagenesis. Transcriptome analysis suggested the importance of previously unidentified genes in TAG production. This study provides information on potential target genes for improving TAG production through the genetic modification of oleaginous yeast.

Viral Genome Delivery Across Bacterial Cell Surfaces

In 1952, Hershey and Chase used bacteriophage T2 genome delivery inside Escherichia coli to demonstrate that DNA, not protein, is the genetic material. Over 70 years later, our understanding of bacteriophage structure has grown dramatically, mainly thanks to the cryogenic electron microscopy revolution. In stark contrast, phage genome delivery in prokaryotes remains poorly understood, mainly due to the inherent challenge of studying such a transient and complex process. Here, we review the current literature on viral genome delivery across bacterial cell surfaces. We focus on icosahedral bacterial viruses that we arbitrarily sort into three groups based on the presence and size of a tail apparatus. We inventory the building blocks implicated in genome delivery and critically analyze putative mechanisms of genome ejection. Bacteriophage genome delivery into bacteria is a topic of growing interest, given the renaissance of phage therapy in Western medicine as a therapeutic alternative to face the antibiotic resistance crisis.

Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations

Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.

The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes

It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.

The Mla system and its role in maintaining outer membrane barrier function in Stenotrophomonas maltophilia

Stenotrophomonas maltophilia are ubiquitous Gram-negative bacteria found in both natural and clinical environments. It is a remarkably adaptable species capable of thriving in various environments, thanks to the plasticity of its genome and a diverse array of genes that encode a wide range of functions. Among these functions, one notable trait is its remarkable ability to resist various antimicrobial agents, primarily through mechanisms that regulate the diffusion across cell membranes. We have investigated the Mla ABC transport system of S. maltophilia, which in other Gram-negative bacteria is known to transport phospholipids across the periplasm and is involved in maintaining outer membrane homeostasis. First, we structurally and functionally characterized the periplasmic substrate-binding protein MlaC, which determines the specificity of this system. The predicted structure of the S. maltophilia MlaC protein revealed a hydrophobic cavity of sufficient size to accommodate the phospholipids commonly found in this species. Moreover, recombinant MlaC produced heterologously demonstrated the ability to bind phospholipids. Gene knockout experiments in S. maltophilia K279a revealed that the Mla system is involved in baseline resistance to antimicrobial and antibiofilm agents, especially those with divalent-cation chelating activity. Co-culture experiments with Pseudomonas aeruginosa also showed a significant contribution of this system to the cooperation between both species in the formation of polymicrobial biofilms. As suggested for other Gram-negative pathogenic microorganisms, this system emerges as an appealing target for potential combined antimicrobial therapies.

Study of sample preparation influence on bacterial lipids profile in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Lipids are one of the cell components therefore it is important to be able to accurately assess them. One of the analytical techniques used to study lipid profiles is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS). The present study attempted to select optimal conditions for sample preparation and MALDI MS analysis of bacterial lipidome in both positive and negative ion modes using different extraction protocols-Folch, Matyash, and Bligh & Dyer, solvents used to apply samples, and matrices such as 9-aminoacridine (9-AA), α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (DHB), 2-mercaptobenzothiazole (MBT), and 2,4,6-trihydroxyacetophenone (THAP). The obtained results allowed concluding that DHB or CHCA matrices are suitable for lipid analysis in the positive mode, and in the negative mode THAP or 9-AA. The most appropriate protocol for extracting lipids from bacterial cells was the Bligh & Dyer method in both ionization modes. The use of the solvent TA30, which was a mixture of acetonitrile and 0.1% trifluoroacetic acid in water, provided on the spectra a significant number of signals from lipids in all groups analyzed, such as fatty acyls, glycerolipids, and glycerophospholipids.

Facilitating flip-flop: Structural tuning of molecule-membrane interactions in living bacteria

The first barrier that a small molecule must overcome before trespassing into a living cell is the lipid bilayer surrounding the intracellular content. It is imperative, therefore, to understand how the structure of a small molecule influences its fate in this region. Through the use of second harmonic generation, we show how the differing degrees of ionic headgroups, conjugated system, and branched hydrocarbon tail disparities of a series of four styryl dye molecules influence the propensity to "flip-flop" or to be further organized in the outer leaflet by the membrane. We show here that initial adsorption experiments match previous studies on model systems; however, more complex dynamics are observed over time. Aside from probe molecule structure, these dynamics also vary between cell species and can deviate from trends reported based on model membranes. Specifically, we show here that the membrane composition is an important factor to consider for headgroup-mediated small-molecule dynamics. Overall, the findings presented here on how structural variability of small molecules impacts their initial adsorption and eventual destinations within membranes in the context of living cells could have practical applications in antibiotic and drug adjuvant design.

Potential of siRNA-Bearing Subtilosomes in the Treatment of Diethylnitrosamine-Induced Hepatocellular Carcinoma

Therapeutics, based on small interfering RNA (siRNA), have demonstrated tremendous potential for treating cancer. However, issues such as non-specific targeting, premature degradation, and the intrinsic toxicity of the siRNA, have to be solved before they are ready for use in translational medicines. To address these challenges, nanotechnology-based tools might help to shield siRNA and ensure its specific delivery to the target site. Besides playing a crucial role in prostaglandin synthesis, the cyclo-oxygenase-2 (COX-2) enzyme has been reported to mediate carcinogenesis in various types of cancer, including hepatocellular carcinoma (HCC). We encapsulated COX-2-specific siRNA in Bacillus subtilis membrane lipid-based liposomes (subtilosomes) and evaluated their potential in the treatment of diethylnitrosamine (DEN)-induced hepatocellular carcinoma. Our findings suggested that the subtilosome-based formulation was stable, releasing COX-2 siRNA in a sustained manner, and has the potential to abruptly release encapsulated material at acidic pH. The fusogenic property of subtilosomes was revealed by FRET, fluorescence dequenching, content-mixing assay, etc. The subtilosome-based siRNA formulation was successful in inhibiting TNF-α expression in the experimental animals. The apoptosis study indicated that the subtilosomized siRNA inhibits DEN-induced carcinogenesis more effectively than free siRNA. The as-developed formulation also suppressed COX-2 expression, which in turn up-regulated the expression of wild-type p53 and Bax on one hand and down-regulated Bcl-2 expression on the other. The survival data established the increased efficacy of subtilosome-encapsulated COX-2 siRNA against hepatocellular carcinoma.

Transient Complexity of E. coli Lipidome Is Explained by Fatty Acyl Synthesis and Cyclopropanation

In the case of many bacteria, such as Escherichia coli, the composition of lipid molecules, termed the lipidome, temporally adapts to different environmental conditions and thus modifies membrane properties to permit growth and survival. Details of the relationship between the environment and lipidome composition are lacking, particularly for growing cultures under either favourable or under stress conditions. Here, we highlight compositional lipidome changes by describing the dynamics of molecular species throughout culture-growth phases. We show a steady cyclopropanation of fatty acyl chains, which acts as a driver for lipid diversity. There is a bias for the cyclopropanation of shorter fatty acyl chains (FA 16:1) over longer ones (FA 18:1), which likely reflects a thermodynamic phenomenon. Additionally, we observe a nearly two-fold increase in saturated fatty acyl chains in response to the presence of ampicillin and chloramphenicol, with consequences for membrane fluidity and elasticity, and ultimately bacterial stress tolerance. Our study provides the detailed quantitative lipidome composition of three E. coli strains across culture-growth phases and at the level of the fatty acyl chains and provides a general reference for phospholipid composition changes in response to perturbations. Thus, lipidome diversity is largely transient and the consequence of lipid synthesis and cyclopropanation.

The catalytic and structural basis of archaeal glycerophospholipid biosynthesis

Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.

Characterization of Two Wheat-Derived Glycoside Hydrolase Family-10 Xylanases Resistant to Xylanase Inhibitors

Xylanase inhibitors inhibit the activities of microbial xylanases and seriously compromise the efficacy of microbial xylanases added to modify cereals. Cereal endogenous xylanases are unaffected by these xylanase inhibitors, but little information is available regarding their effects in improving cereal quality, a neglected potential application. As a strategy for circumventing the negative effects of xylanase inhibitors, the objective of this study was to use genetic engineering to obtain sufficient amounts of active endo-1,4-β-D-xylanase from wheat to analyze the characteristics of its structure. The endo-1,4-β-D-xylanase from wheat was heterologously expressed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), western blotting, MALDI-TOF/TOF (MS) analyses, and enzyme activity determination confirmed 2 active endo-1,4-β-D-xylanases (EXY3 and EXY4) were successfully obtained. The molecular weights (MW) and isoelectric point (pI) of EXY3 were 36.108 kDa and 5.491, while those of the EXY4 protein were 41.933 kDa and 5.726. They both contained the same catalytic domain of GH10 xylanases from G266 to V276 and have the same catalytic site, Glu273. They shared the same putative N-glycosylation sites (N62-T63-S64 and N280–V281–S282) and 3 putative O-glycosylation sites (Ser8, Ser9, and Thr21), but EXY4 had an additional O-glycosylation site (Thr358). EXY3 was smaller than EXY4 by 51 amino acids because of a nonsense mutation and premature termination. They both had the 8-fold beta/alpha-barrel (TIM-barrel) fold. The specific activities of EXY3 and EXY4 were 152.0891 and 67.2928 U/mg, respectively. This work demonstrates a promising way to obtain wheat xylanases by genetic engineering; the properties of the enzymes indicate their potential application in cereal-based industries.

Low membrane fluidity triggers lipid phase separation and protein segregation in living bacteria

All living organisms adapt their membrane lipid composition in response to changes in their environment or diet. These conserved membrane-adaptive processes have been studied extensively. However, key concepts of membrane biology linked to regulation of lipid composition including homeoviscous adaptation maintaining stable levels of membrane fluidity, and gel-fluid phase separation resulting in domain formation, heavily rely upon in vitro studies with model membranes or lipid extracts. Using the bacterial model organisms Escherichia coli and Bacillus subtilis, we now show that inadequate in vivo membrane fluidity interferes with essential complex cellular processes including cytokinesis, envelope expansion, chromosome replication/segregation and maintenance of membrane potential. Furthermore, we demonstrate that very low membrane fluidity is indeed capable of triggering large-scale lipid phase separation and protein segregation in intact, protein-crowded membranes of living cells; a process that coincides with the minimal level of fluidity capable of supporting growth. Importantly, the in vivo lipid phase separation is not associated with a breakdown of the membrane diffusion barrier function, thus explaining why the phase separation process induced by low fluidity is biologically reversible.

Bacterial growth monitored by two-dimensional tandem mass spectrometry

The growth of the bacterium E. coli was monitored by targeting the phospholipid constituents through desorption electrospray ionization and characterizing individual sets of isomers by recording the full 2D MS/MS data domain in a single scan of a modified quadrupole ion trap mass spectrometer. The experiments tested the applicability of the new instrumental capabilities which include sample interrogation at the molecular level for multiple components at speeds of <10 seconds/sample. The major lipids observed were phosphatidylethanolamines and phosphatidylglycerols and the growth experiment showed fatty acid chain modification from alkene to cyclopropyl groups over time. Notably, these novel MS scans were also performed using desorption electrospray ionization (DESI) to quickly sample complex mixtures without pre-separation. This demonstration experiment has implications for the value of ambient ionization mass spectrometry for monitoring biological systems on physiologically relevant timescales.

Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes

Molecular dynamics (MD) simulations of biological membranes have achieved such levels of sophistication that are commonly used to predict unresolved structures and various properties of lipids and to substantiate experimental data. While achieving sufficient sampling of lipid dynamics remains a major challenge, a commonly used method to improve lipid sampling, e.g., in terms of specific interactions with membrane-associated proteins, is to randomize the initial arrangement of lipid constituents in multiple replicas of simulations, without changing the overall lipid composition of the membrane of interest. Here, we introduce a method that can rapidly generate multiple replicas of lipid bilayers with different spatial and conformational configurations for any given lipid composition. The underlying algorithm, which allows one to shuffle lipids at any desired level, relies on the application of an external potential, here referred to as the "carving potential", that removes clashes/entanglements before lipid positions are exchanged (shuffled), thereby minimizing the energy penalty due to abrupt lipid repositioning. The method is implemented as "Membrane Mixer Plugin (MMP) 1.0" in VMD, with a convenient graphical user interface that guides the user in setting various options and parameters. The plugin is fully automated and generates new membrane replicas more rapidly and conveniently than other analogous tools. The plugin and its capabilities introduced here can be extended to include additional features in future versions.

Multi-Omic Analysis to Characterize Metabolic Adaptation of the E. coli Lipidome in Response to Environmental Stress

As an adaptive survival response to exogenous stress, bacteria undergo dynamic remodelling of their lipid metabolism pathways to alter the composition of their cellular membranes. Here, using Escherichia coli as a well characterised model system, we report the development and application of a ‘multi-omics’ strategy for comprehensive quantitative analysis of the temporal changes in the lipidome and proteome profiles that occur under exponential growth phase versus stationary growth phase conditions i.e., nutrient depletion stress. Lipidome analysis performed using ‘shotgun’ direct infusion-based ultra-high resolution accurate mass spectrometry revealed a quantitative decrease in total lipid content under stationary growth phase conditions, along with a significant increase in the mol% composition of total cardiolipin, and an increase in ‘odd-numbered’ acyl-chain length containing glycerophospholipids. The inclusion of field asymmetry ion mobility spectrometry was shown to enable the enrichment and improved depth of coverage of low-abundance cardiolipins, while ultraviolet photodissociation-tandem mass spectrometry facilitated more complete lipid structural characterisation compared with conventional collision-induced dissociation, including unambiguous assignment of the odd-numbered acyl-chains as containing cyclopropyl modifications. Proteome analysis using data-dependent acquisition nano-liquid chromatography mass spectrometry and tandem mass spectrometry analysis identified 83% of the predicted E. coli lipid metabolism enzymes, which enabled the temporal dependence associated with the expression of key enzymes responsible for the observed adaptive lipid metabolism to be determined, including those involved in phospholipid metabolism (e.g., ClsB and Cfa), fatty acid synthesis (e.g., FabH) and degradation (e.g., FadA/B,D,E,I,J and M), and proteins involved in the oxidative stress response resulting from the generation of reactive oxygen species during β-oxidation or lipid degradation.

All-Atom Modeling of Complex Cellular Membranes

Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.

Use of MALDI-TOF mass spectrometry for virus identification: a review

The possibilities of virus identification, including SARS-CoV-2, by MALDI-TOF mass spectrometry are discussed in this review.

Leaflet Asymmetry Modeling in the Lipid Composition of Escherichia coli Cytoplasmic Membranes

Lipid composition asymmetry between leaflets is important to cell function and plays a key role in the "positive inside" rule in transmembrane proteins. In this work, Escherichia coli inner plasma membrane models reflecting this asymmetry have been investigated at the early-log and stationary stages during the bacterial lifecycle using all-atom molecular dynamics simulations. The CHARMM36 lipid force field is used, and selected membrane properties are tested for variations between two leaflets and whole membranes. Our models include bacterial lipids with a cyclopropane moiety on the sn-2 acyl chain in the stationary membrane model. The PE/PG ratio for two leaflets reflects the "positive inside" rule of membrane proteins, set to 6.8 and 2.8 for the inner and outer leaflets of the two models, respectively. We are the first to model leaflet asymmetry in the lipid composition of E. coli cytoplasmic membranes and observe the effect on membrane properties in leaflets and whole membranes. Specifically, our results show that for the stationary phase bilayer, the surface area per lipid (SA/lipid) is larger, the thickness (2D_C and D_B) is smaller, the tilt angle is larger, the tilt modulus is smaller, and the deuterium order parameters (S_CD) of sn-1 and sn-2 tails are lower, compared to the early-log stage. Moreover, the stationary stage bilayer has a positive spontaneous curvature, while the early-log stage has a near flat spontaneous curvature. For leaflet asymmetry, the inner leaflet has a larger SA/lipid, a smaller thickness, a smaller elastic tilt modulus (a larger tilt angle), and lower S_CD, compared to the outer leaflet in both stages. Moreover, an asymmetric membrane involves a lipid tilt and a lateral extension, varying from a reference state of a pre-equilibrium membrane. This work encourages a more profound exploration of leaflet asymmetry in various other membrane models and how this might affect the structure and function of membrane-associated peptides and proteins.

A supramolecular host for phosphatidylglycerol (PG) lipids with antibacterial activity

Lipids fulfill a variety of important physiological functions, such as energy storage, providing a hydrophobic barrier, and signal transduction. Despite this plethora of biological roles, lipids are rarely considered a potential target for medical applications. Here, we report a set of neutral small molecules that contain boronic acid and urea functionalities to selectively recognize the bacterial lipid phosphatidylglycerol (PG). The affinity and selectivity was determined using ¹H NMR titrations and a liposome-based Alizarin Red S assay. Minimum inhibitory concentrations (MIC) were determined to assess antibacterial activity. The most potent compounds display an association constant with PG in liposomes of at least 5 × 10³ M^-1, function as antibacterial agents against Gram-positive bacteria (MIC = 12.5-25 μM), and show little hemolytic activity. Mode of action studies suggest that the boronic acids bind to the headgroup of the PG lipids, which leads to a change in membrane fluidity and ultimately causes membrane depolarization and cell death.

Membrane composition and organization of Bacillus subtilis 168 and its genome-reduced derivative miniBacillus PG10

A form of lateral membrane compartmentalization in bacteria is represented by functional membrane microdomains (FMMs). FMMs are important for various cellular processes and offer application possibilities in microbial biotechnology. We designed a lipidomics method to directly measure relative abundances of lipids in detergent‐resistant and detergent‐sensitive membrane fractions of the model bacterium Bacillus subtilis 168 and the biotechnologically attractive miniBacillus PG10 strain. Our study supports previous work suggesting that cardiolipin and prenol lipids are enriched in FMMs of B. subtilis. Additionally, structural analysis of acyl chains of major phospholipids indicated that FMMs display increased order and thickness compared with the surrounding bilayer. Despite the 36% genome reduction, membrane and FMM integrity are largely preserved in miniBacillus PG10, as supported by analysis of membrane fluidity, flotillin distribution and gene expression data. The novel insights in FMM architecture reported here will contribute to further explore the biological significance of FMMs and the means by which FMMs can be exploited as heterologous production platforms. Moreover, our lipidomics method enables comparative FMM lipid profiling between different bacteria.

A new approach to identifying pathogens, with particular regard to viruses, based on capillary electrophoresis and other analytical techniques

Fast determination, identification and characterization of pathogens is a significant challenge in many fields, from industry to medicine. Standard approaches (e.g., culture media and biochemical tests) are known to be very time-consuming and labor-intensive. Conversely, screening techniques demand a quick and low-cost grouping of microbial isolates, and current analysis call for broad reports of pathogens, involving the application of molecular, microscopy, and electromigration techniques, DNA fingerprinting and also MALDI-TOF methods. The present COVID-19 pandemic is a crisis that affects rich and poor countries alike. Detection of SARS-CoV-2 in patient samples is a critical tool for monitoring disease spread, guiding therapeutic decisions and devising social distancing protocols. The goal of this review is to present an innovative methodology based on preparative separation of pathogens by electromigration techniques in combination with simultaneous analysis of the proteome, lipidome, and genome using laser desorption/ionization analysis.

The phospholipid membrane compositions of bacterial cells, cancer cell lines and biological samples from cancer patients

While cancer now impacts the health and well-being of more of the human population than ever before, the exponential rise in antimicrobial resistant (AMR) bacterial infections means AMR is predicted to become one of the greatest future threats to human health. It is therefore vital that novel therapeutic strategies are developed that can be used in the treatment of both cancer and AMR infections. Whether the target of a therapeutic agent be inside the cell or in the cell membrane, it must either interact with or cross this phospholipid barrier to elicit the desired cellular effect. Here we summarise findings from published research into the phospholipid membrane composition of bacterial and cancer cell lines and biological samples from cancer patients. These data not only highlight key differences in the membrane composition of these biological samples, but also the methods used to elucidate and report the results of this analogous research between the microbial and cancer fields.

Problems with identifying and distinguishing salivary streptococci: a multi-instrumental approach

Aim: The purpose of this study was to create an alternative protocol for the DNA-based identification of salivary microbiota focused on the distinguishing of Streptococcus species. Materials & methods: Salivary bacteria were identified using 16S rDNA sequencing and proteins and lipids profiling using MALDI-TOF/MS as well as FTIR analysis. Results: Most of the isolates belonged to streptococci - mostly the salivarious group indistinguishable by the molecular technique. In turn, MALDI analysis allowed for their fast and reliable classification. Although FTIR spectroscopy demonstrated the correct species classification, the spectra interpretation was time consuming and complicated. Conclusion: MALDI-TOF/MS demonstrated the biggest effectiveness in the identification and discrimination between the salivary streptococci, which could be easily incorporated in the workflow of routine microbiological laboratories.

Rapid Detection of Viral Envelope Lipids Using Lithium Adducts and AP-MALDI High-Resolution Mass Spectrometry

There is an unmet need to develop analytical strategies that not only characterize the lipid composition of the viral envelope but also do so on a time scale that would allow for high-throughput analysis. With that in mind, we report the use of atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) high-resolution mass spectrometry (HRMS) combined with lithium adduct consolidation to profile total lipid extracts rapidly and confidently from enveloped viruses. The use of AP-MALDI reduced the dependency of using a dedicated MALDI mass spectrometer and allowed for interfacing the MALDI source to a mass spectrometer with the desired features, which included high mass resolving power (>100000) and tandem mass spectrometry. AP-MALDI combined with an optimized MALDI matrix system, featuring 2',4',6'-trihydroxyacetophenone spiked with lithium salt, resulted in a robust and high-throughput lipid detection platform, specifically geared to sphingolipid detection. Application of the developed workflow included the structural characterization of prominent sphingolipids and detection of over 130 lipid structures from Influenza A virions. Overall, we demonstrate a high-throughput workflow for the detection and structural characterization of total lipid extracts from enveloped viruses using AP-MALDI HRMS and lithium adduct consolidation.

Promiscuous phospholipid biosynthesis enzymes in the plant pathogen Pseudomonas syringae

Bacterial membranes are primarily composed of phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and cardiolipin (CL). In the canonical PE biosynthesis pathway, phosphatidylserine (PS) is decarboxylated by the Psd enzyme. CL formation typically depends on CL synthases (Cls) using two PG molecules as substrates. Only few bacteria produce phosphatidylcholine (PC), the hallmark of eukaryotic membranes. Most of these bacteria use phospholipid N-methyltransferases to successively methylate PE to PC and/or a PC synthase (Pcs) to catalyze the condensation of choline and CDP-diacylglycerol (CDP-DAG) to PC. In this study, we show that membranes of Pseudomonas species able to interact with eukaryotes contain PE, PG, CL and PC. More specifically, we report on PC formation and a poorly characterized CL biosynthetic pathway in the plant pathogen P. syringae pv. tomato. It encodes a Pcs enzyme responsible for choline-dependent PC biosynthesis. CL formation is catalyzed by a promiscuous phospholipase D (PLD)-type enzyme (PSPTO_0095) that we characterized in vivo and in vitro. Like typical bacterial CL biosynthesis enzymes, it uses PE and PG for CL production. This enzyme is also able to convert PE and glycerol to PG, which is then combined with another PE molecule to synthesize CL. In addition, the enzyme is capable of converting ethanolamine or methylated derivatives into the corresponding phospholipids such as PE both in P. syringae and in E. coli. It can also hydrolyze CDP-DAG to yield phosphatidic acid (PA). Our study adds an example of a promiscuous Cls enzyme able to synthesize a suite of products according to the available substrates.

The Study on Molecular Profile Changes of Pathogens via Zinc Nanocomposites Immobilization Approach

The most critical group of all includes multidrug resistant bacteria that pose a particular threat in hospitals, as they can cause severe and often deadly infections. Modern medicine still faces the difficult task of developing new agents for the effective control of bacterial-based diseases. The targeted administration of nanoparticles can enhance the efficiency of conventional pharmaceutical agents. However, the interpretation of interfaces' interactions between nanoparticles and biological systems still remains a challenge for researchers. In fact, the current research presents a strategy for using ZnO NPs immobilization with ampicillin and tetracycline. Firstly, the study provides the mechanism of the ampicillin and tetracycline binding on the surface of ZnO NPs. Secondly, it examines the effect of non-immobilized ZnO NPs, immobilized with ampicillin (ZnONPs/AMP) and tetracycline (ZnONPs/TET), on the cells' metabolism and morphology, based on the protein and lipid profiles. A sorption kinetics study showed that the antibiotics binding on the surface of ZnONPs depend on their structure. The efficiency of the process was definitely higher in the case of ampicillin. In addition, flow cytometry results showed that immobilized nanoparticles present a different mechanism of action. Moreover, according to the MALDI approach, the antibacterial activity mechanism of the investigated ZnO complexes is mainly based on the destruction of cell membrane integrity by lipids and proteins, which is necessary for proper cell function. Additionally, it was noticed that some of the identified changes indicate the activation of defense mechanisms by cells, leading to a decrease in the permeability of a cell's external barriers or the synthesis of repair proteins.

Control of n-Butanol Induced Lipidome Adaptations in E. coli

The versatile compound n-butanol is one of the most promising biofuels for use in existing internal combustion engines, contributing to a smooth transition towards a clean energy society. Furthermore, n-butanol is a valuable resource to produce more complex molecules such as bioplastics. Microbial production of n-butanol from waste materials is hampered by the biotoxicity of n-butanol as it interferes with the proper functioning of lipid membranes. In this study we perform a large-scale investigation of the complete lipid-related enzyme machinery and its response to exposure to a sublethal concentration of n-butanol. We profiled, in triplicate, the growth characteristics and phospholipidomes of 116 different genetic constructs of E. coli, both in the presence and absence of 0.5% n-butanol (v/v). This led to the identification of 230 lipid species and subsequently to the reconstruction of the network of metabolites, enzymes and lipid properties driving the homeostasis of the E. coli lipidome. We were able to identify key lipids and biochemical pathways leading to altered n-butanol tolerance. The data led to new conceptual insights into the bacterial lipid metabolism which are discussed.

The Pseudomonas aeruginosa substrate-binding protein Ttg2D functions as a general glycerophospholipid transporter across the periplasm

In Pseudomonas aeruginosa, Ttg2D is the soluble periplasmic phospholipid-binding component of an ABC transport system thought to be involved in maintaining the asymmetry of the outer membrane. Here we use the crystallographic structure of Ttg2D at 2.5 Å resolution to reveal that this protein can accommodate four acyl chains. Analysis of the available structures of Ttg2D orthologs shows that they conform a new substrate-binding-protein structural cluster. Native and denaturing mass spectrometry experiments confirm that Ttg2D, produced both heterologously and homologously and isolated from the periplasm, can carry two diacyl glycerophospholipids as well as one cardiolipin. Binding is notably promiscuous, allowing the transport of various molecular species. In vitro binding assays coupled to native mass spectrometry show that binding of cardiolipin is spontaneous. Gene knockout experiments in P. aeruginosa multidrug-resistant strains reveal that the Ttg2 system is involved in low-level intrinsic resistance against certain antibiotics that use a lipid-mediated pathway to permeate through membranes.

Yero et al. elucidate the function of Ttg2D, a Pseudomonas aeruginosa periplasmic protein, in maintaining phospholipid asymmetry between the outer and inner membrane. Gram negative bacteria have inner and outer membranes that differ in phospholipd composition. Using X-ray crystallography and mass spectrometry, the authors show that Ttg2D can carry two diacyl glycerophospholipids or a cardiolipin. The authors also identify a role for Ttg2D in resistance against antibiotics that use a lipid-mediated pathway into the cell.

An investigation of the impact of triclosan adaptation on Proteus mirabilis clinical isolates from an Egyptian university hospital

Antibiotic resistance is a main threat to the public health. It is established that the overuse and misuse of antibiotics are highly contributing to antibiotic resistance. However, the impact of nonantibiotic antimicrobial agents like biocides on antibiotic resistance is currently investigated and studied. Triclosan (TCS) is a broad-spectrum antibacterial agent widely used as antiseptic and disinfectant. In this study, we aimed to evaluate the effect of exposure of Proteus mirabilis clinical isolates to sublethal concentrations of TCS on their antibiotic susceptibility, membrane characteristics, efflux activity, morphology, and lipid profile. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of TCS were determined for 31 P. mirabilis clinical isolates. The tested isolates were adapted to increasing sublethal concentrations of TCS. The MICs of 16 antibiotics were determined before and after adaptation. Membrane characteristics, efflux activity, ultrastructure, and lipid profile of the tested isolates were examined before and after adaptation. Most adapted P. mirabilis isolates showed increased antibiotic resistance, lower membrane integrity, lower outer and inner membrane permeability, and higher membrane depolarization. Nonsignificant change in membrane potential and lipid profile was found in adapted cells. Various morphological changes and enhanced efflux activity was noticed after adaptation. The findings of the current study suggest that the extensive usage of TCS at sublethal concentrations could contribute to the emergence of antibiotic resistance in P. mirabilis clinical isolates. TCS could induce changes in the bacterial membrane properties and increase the efflux activity and in turn decrease its susceptibility to antibiotics which would represent a public health risk.

Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.

LetB Structure Reveals a Tunnel for Lipid Transport across the Bacterial Envelope

Gram-negative bacteria are surrounded by an outer membrane composed of phospholipids and lipopolysaccharide, which acts as a barrier and contributes to antibiotic resistance. The systems that mediate phospholipid trafficking across the periplasm, such as MCE (Mammalian Cell Entry) transporters, have not been well characterized. Our ~3.5 Å cryo-EM structure of the E. coli MCE protein LetB reveals an ~0.6 megadalton complex that consists of seven stacked rings, with a central hydrophobic tunnel sufficiently long to span the periplasm. Lipids bind inside the tunnel, suggesting that it functions as a pathway for lipid transport. Cryo-EM structures in the open and closed states reveal a dynamic tunnel lining, with implications for gating or substrate translocation. Our results support a model in which LetB establishes a physical link between the two membranes and creates a hydrophobic pathway for the translocation of lipids across the periplasm.

Matrix-assisted ionization Fourier transform mass spectrometry for the analysis of lipids

RATIONALE

Assessing the utility of vacuum matrix-assisted ionization (MAI) for the direct and rapid analysis of lipids in complex samples with emphasis on bacterial taxonomy.

METHODS

Matrix-assisted ionization Fourier transform mass spectrometry (MAI-FTMS) was used to characterize polar and non-polar lipids in mixtures.

RESULTS

For non-polar lipid triacylglycerols (TAGs), MAI-FTMS produced lipid-specific ions for eight different edible oils and allowed these oils to be identified based on their MAI-FTMS profiles. For polar lipids from bacteria, MAI-FTMS of crude lipid extracts allowed taxonomic identification of eight blind-coded samples based on taxonomy-specific phospholipid profiles. MAI produced results comparable and complementary to benchmark MALDI and ESI methods currently used for characterization of polar and non-polar lipids in the same mixtures.

CONCLUSIONS

The newly developed MAI technique is a rapid, simple and complementary method for the characterization of polar and non-polar lipids in complex mixtures.

The impact of antibacterial peptides on bacterial lipid membranes depends on stage of growth

Impact of maculatin 1.1 on supported lipid bilayers (SLBs) derived from early growth phase (EGP) or stationary growth phase (SGP) E. coli lipid extracts, monitored by atomic force microscopy which images bilayer morphology in real time.

Towards the Prediction of Antimicrobial Efficacy for Hydrogen Bonded, Self-Associating Amphiphiles

Herein we report 50 structurally related supramolecular self-associating amphiphilic (SSA) salts and related compounds. These SSAs are shown to act as antimicrobial agents, active against model Gram-positive (methicillin-resistant Staphylococcus aureus) and/or Gram-negative (Escherichia coli) bacteria of clinical interest. Through a combination of solution-state, gas-phase, solid-state and in silico measurements, we determine 14 different physicochemical parameters for each of these 50 structurally related compounds. These parameter sets are then used to identify molecular structure-physicochemical property-antimicrobial activity relationships for our model Gram-negative and Gram-positive bacteria, while simultaneously providing insight towards the elucidation of SSA mode of antimicrobial action.

Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions

The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. Since receptor-phage interactions are crucial to successful infections, they are major determinants of phage host range and, by extension, of the broader effects that phages have on bacterial communities. Many receptor molecules, particularly membrane proteins, are difficult to isolate because their stability is supported by their native membrane environments. Styrene maleic acid lipid particles (SMALPs), a recent advance in membrane protein studies, are the result of membrane solubilizations by styrene maleic acid (SMA) copolymer chains. SMALPs thereby allow for isolation of membrane proteins while maintaining their native environment. Here, we explore SMALPs as a tool to isolate and study phage-receptor interactions. We show that SMALPs produced from taxonomically distant bacterial membranes allow for receptor-specific decrease of viable phage counts of several model phages that span the three largest phage families. After characterizing the effects of incubation time and SMALP concentration on the activity of three distinct phages, we present evidence that the interaction between two model phages and SMALPs is specific to bacterial species and the phage receptor molecule. These interactions additionally lead to DNA ejection by nearly all particles at high phage titers. We conclude that SMALPs are a potentially highly useful tool for phage-host interaction studies.IMPORTANCE Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study, we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions and furthermore show that they lead to genome ejection by the phage. The results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions.

Cationic π-Conjugated Polyelectrolyte Shows Antimicrobial Activity by Causing Lipid Loss and Lowering Elastic Modulus of Bacteria

Cationic, π-conjugated oligo-/polyelectrolytes (CCOEs/CCPEs) have shown great potential as antimicrobial materials to fight against antibiotic resistance. In this work, we treated wild-type and ampicillin-resistant (amp-resistant) Escherichia coli (E. coli) with a promising cationic, π-conjugated polyelectrolyte (P1) with a phenylene-based backbone and investigated the resulting morphological, mechanical, and compositional changes of the outer membrane of bacteria in great detail. The cationic quaternary amine groups of P1 led to electrostatic interactions with negatively charged moieties within the outer membrane of bacteria. Using atomic force microscopy (AFM), high-resolution transmission electron microscopy (TEM), we showed that due to this treatment, the bacterial outer membrane became rougher, decreased in stiffness/elastic modulus (AFM nanoindentation), formed blebs, and released vesicles near the cells. These evidences, in addition to increased staining of the P1-treated cell membrane by lipophilic dye Nile Red (confocal laser scanning microscopy (CLSM)), suggested loosening/disruption of packing of the outer cell envelope and release and exposure of lipid-based components. Lipidomics and fatty acid analysis confirmed a significant loss of phosphate-based outer membrane lipids and fatty acids, some of which are critically needed to maintain cell wall integrity and mechanical strength. Lipidomics and UV-vis analysis also confirmed that the extracellular vesicles released upon treatment (AFM) are composed of lipids and cationic P1. Such surface alterations (vesicle/bleb formation) and release of lipids/fatty acids upon treatment were effective enough to inhibit further growth of E. coli cells without completely disintegrating the cells and have been known as a defense mechanism of the cells against cationic antimicrobial agents.

Lipid Composition Affects the Efficiency in the Functional Reconstitution of the Cytochrome c Oxidase

The transmembrane protein cytochrome c oxidase (CcO) is the terminal oxidase in the respiratory chain of many aerobic organisms and catalyzes the reduction of dioxygen to water. This process maintains an electrochemical proton gradient across the membrane hosting the oxidase. CcO is a well-established model enzyme in bioenergetics to study the proton-coupled electron transfer reactions and protonation dynamics involved in these processes. Its catalytic mechanism is subject to ongoing intense research. Previous research, however, was mainly focused on the turnover of oxygen and electrons in CcO, while studies reporting proton turnover rates of CcO, that is the rate of proton uptake by the enzyme, are scarce. Here, we reconstitute CcO from R. sphaeroides into liposomes containing a pH sensitive dye and probe changes of the pH value inside single proteoliposomes using fluorescence microscopy. CcO proton turnover rates are quantified at the single-enzyme level. In addition, we recorded the distribution of the number of functionally reconstituted CcOs across the proteoliposome population. Studies are performed using proteoliposomes made of native lipid sources, such as a crude extract of soybean lipids and the polar lipid extract of E. coli, as well as purified lipid fractions, such as phosphatidylcholine extracted from soybean lipids. It is shown that these lipid compositions have only minor effects on the CcO proton turnover rate, but can have a strong impact on the reconstitution efficiency of functionally active CcOs. In particular, our experiments indicate that efficient functional reconstitution of CcO is strongly promoted by the addition of anionic lipids like phosphatidylglycerol and cardiolipin.

Nanoscale battery cathode materials induce DNA damage in bacteria

The increasing use of nanoscale lithium nickel manganese cobalt oxide (Li x Ni y Mn z Co1-y-z O2, NMC) as a cathode material in lithium-ion batteries poses risk to the environment. Learning toxicity mechanisms on molecular levels is critical to promote proactive risk assessment of these complex nanomaterials and inform their sustainable development. We focused on DNA damage as a toxicity mechanism and profiled in depth chemical and biological changes linked to DNA damage in two environmentally relevant bacteria upon nano-NMC exposure. DNA damage occurred in both bacteria, characterized by double-strand breakage and increased levels of many putative chemical modifications on bacterial DNA bases related to direct oxidative stress and lipid peroxidation, measured by cutting-edge DNA adductomic techniques. Chemical probes indicated elevated intracellular reactive oxygen species and transition metal ions, in agreement with DNA adductomics and gene expression analysis. By integrating multi-dimensional datasets from chemical and biological measurements, we present rich mechanistic insights on nano-NMC-induced DNA damage in bacteria, providing targets for biomarkers in the risk assessment of reactive materials that may be extrapolated to other nano-bio interactions.

Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria

β-Barrel outer membrane proteins (OMPs) represent the major proteinaceous component of the outer membrane (OM) of Gram-negative bacteria. These proteins perform key roles in cell structure and morphology, nutrient acquisition, colonization and invasion, and protection against external toxic threats such as antibiotics. To become functional, OMPs must fold and insert into a crowded and asymmetric OM that lacks much freely accessible lipid. This feat is accomplished in the absence of an external energy source and is thought to be driven by the high thermodynamic stability of folded OMPs in the OM. With such a stable fold, the challenge that bacteria face in assembling OMPs into the OM is how to overcome the initial energy barrier of membrane insertion. In this review, we highlight the roles of the lipid environment and the OM in modulating the OMP-folding landscape and discuss the factors that guide folding in vitro and in vivo We particularly focus on the composition, architecture, and physical properties of the OM and how an understanding of the folding properties of OMPs in vitro can help explain the challenges they encounter during folding in vivo Current models of OMP biogenesis in the cellular environment are still in flux, but the stakes for improving the accuracy of these models are high. OMP folding is an essential process in all Gram-negative bacteria, and considering the looming crisis of widespread microbial drug resistance it is an attractive target. To bring down this vital OMP-supported barrier to antibiotics, we must first understand how bacterial cells build it.

Controllable hydrogen bonded self-association for the formation of multifunctional antimicrobial materials

SSAs are a class of supramolecular self-associating amphiphilic salt, the anionic component of which contains a covalently bound hydrogen bond donor-acceptor motif. This results in a monomeric unit which can adopt multiple hydrogen bonding modes simultaneously. Previous investigations have shown examples of SSAs to act as antimicrobial agents against clinically relevant methicillin-resistant Staphylococcus aureus (MRSA). Herein, we report an intrinsically fluorescent SSA which can self-associate producing dimers, spherical aggregates and hydrogels dependent on solvent environment, while retaining antimicrobial activity against both model Gram-positive (MRSA) and Gram-negative (Escherichia coli) bacteria. Finally, we demonstrate the SSA supramolecular hydrogel to tolerate the inclusion of the antibiotic ampicillin, leading to the enhanced inhibition of growth with both model bacteria, and derive initial molecular structure-physicochemical property-antimicrobial activity relationships.

The Influence of Different Forms of Silver on Selected Pathogenic Bacteria

The application of silver nanoparticles as an antibacterial agent is becoming more common. Unfortunately, their effect on microorganisms is still not fully understood. Therefore, this paper attempts to investigate the influence of silver ions, biologically synthesized silver nanoparticles and nanoparticles functionalized with antibiotics on molecular bacteria profiles. The initial stage of research was aimed at the mechanism determination involved in antibiotics sorption onto nanoparticles' surface. For this purpose, the kinetics study was performed. Next, the functionalized formulations were characterized by Fourier transform infrared spectroscopy (FT-IR), dynamic light scattering (DLS) and a zeta potential study. The results reveal that functionalization is a complex process, but does not significantly affect the stability of biocolloids. Furthermore, the antimicrobial assays, in most cases, have shown no increases in antibacterial activity after nanoparticle functionalization, which suggests that the functionalization process does not always generate the improved antimicrobial effect. Finally, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique was employed to characterize the changes in the molecular profile of bacteria treated with various antibacterial agents. The recorded spectra proved many differences in bacterial lipids and proteins profiles compared to untreated cells. In addition, the statistical analysis of recorded spectra revealed the strain-dependent nature of stress factors on the molecular profile of microorganisms.

Application of Thin-Layer Chromatography-Flame Ionization Detection (TLC-FID) to Total Lipid Quantitation in Mycolic-Acid Synthesizing Rhodococcus and Williamsia Species

In addition to cell membrane phospholipids, Actinobacteria in the order Corynebacteriales possess a waxy cell envelope containing mycolic acids (MA). In optimized culture condition, some species can also accumulate high concentrations of intracellular triacylglycerols (TAG), which are a potential source of biodiesel. Bacterial lipid classes and composition alter in response to environmental stresses, including nutrient availability, thus understanding carbon flow into different lipid classes is important when optimizing TAG synthesis. Quantitative and qualitative analysis of lipid classes normally requires combinations of different extraction, derivatization, chromatographic and detection methods. In this study, a single-step thin-layer chromatography-flame ionization detection (TLC-FID) technique was applied to quantify lipid classes in six sub-Antarctic Corynebacteriales strains identified as Rhodococcus and Williamsia species. A hexane:diethyl-ether:acetic acid solvent system separated the total cellular lipids extracted from cells lysed by bead beating, which released more bound and unbound MA than sonication. Typical profiles included a major broad non-polar lipid peak, TAG and phospholipids, although trehalose dimycolates, when present, co-eluted with phospholipids. Ultra-performance liquid chromatography-tandem mass-spectrometry and nuclear magnetic resonance spectroscopy detected MA signatures in the non-polar lipid peak and indicated that these lipids were likely bound, at least in part, to sugars from cell wall arabinogalactan. Waxy esters were not detected. The single-solvent TLC-FID procedure provides a useful platform for the quantitation and preliminary screening of cellular lipid classes when testing the impacts of growth conditions on TAG synthesis.

Bacterial identification by lipid profiling using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry

Background

In recent years, mass spectrometry (MS) has been applied to clinical microbial biotyping, exploiting the speed of matrix-assisted laser desorption/ionization (MALDI) in recording microbe-specific MS profiles. More recently, liquid atmospheric pressure (AP) MALDI has been shown to produce extremely stable ion flux from homogenous samples and ‘electrospray ionization (ESI)-like’ multiply charged ions for larger biomolecules, whilst maintaining the benefits of traditional MALDI including high tolerance to contaminants, low analyte consumption and rapid analysis. These and other advantages of liquid AP-MALDI MS have been explored in this study to investigate its potential in microbial biotyping.

Methods

Genetically diverse bacterial strains were analyzed using liquid AP-MALDI MS, including clinically relevant species such as Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Bacterial cultures were subjected to a simple and fast extraction protocol using ethanol and formic acid. Extracts were spotted with a liquid support matrix (LSM) and analyzed using a Synapt G2-Si mass spectrometer with an in-house built AP-MALDI source.

Results

Each species produces a unique lipid profile in the m/z range of 400–1100, allowing species discrimination. Traditional (solid) MALDI MS produced spectra containing a high abundance of matrix-related clusters and an absence of lipid peaks. The MS profiles of the bacterial species tested form distinct clusters using principle component analysis (PCA) with a classification accuracy of 98.63% using a PCA-based prediction model.

Conclusions

Liquid AP-MALDI MS profiles can be sufficient to distinguish clinically relevant bacterial pathogens and other bacteria, based on their unique lipid profiles. The analysis of the lipid MS profiles is typically excluded from commercial instruments approved for clinical diagnostics.

Phospholipid Content of Pseudomonas aeruginosa PAO1 Is Modulated by the Growth Phase Rather Than the Immobilization State

Biofilms have significance in medical, industrial, and environmental settings, and can cause important damage. As biofilms are tolerant to various stresses, including antibiotics, it is necessary to better understand their formation. For this reason, we characterized the phospholipidome of Pseudomonas aeruginosa, an opportunistic pathogen involved in numerous infections, during the first steps of the biofilm development. By a liquid chromatography-tandem mass spectrometry time-course analysis over a 24-h period, we compared the phospholipid (PL) composition of immobilized (attached) and planktonic (unattached) P. aeruginosa PAO1 cells. Our results showed that the PL content of P. aeruginosa PAO1 was mainly modulated by the incubation time, thus related to bacterial growth but also, more modestly, by the immobilization state. We observed that relative amounts of PL varied over time with two main profiles and that these profiles are correlated to its fatty acid composition, including the degree of unsaturation. A statistical analysis revealed that the PL contents of both attached and unattached PAO1 cells were significantly different mainly after 3 and 6 h of incubation and that the amounts of two PL presented a statistical difference between attached and unattached cells all along the 24-h period: PtdEtn 16:0_18:1 and PtdEtn 18:1_18:1.

Decoding the Fatty Acid Profile of Bacillus licheniformis I89 and Its Adaptation to Different Growth Conditions to Investigate Possible Biotechnological Applications

Bacillus licheniformis I89 is a Gram-positive bacterium, a producer of the lantibiotic lichenicidin. No information is available on its fatty acid (FA) composition. Bacillus species are rich in branched FA (BrFA), claimed to be beneficial to human health and to treat diseases. Herein, the FA profile of B. licheniformis I89 was evaluated under different growth conditions: at two growth temperatures (37 and 50 °C) and at different growth phases (lag, exponential, and stationary), using gas chromatography-mass spectrometry. The FA profile revealed predominant BrFA of the iso-series and anteiso-series (i-15:0, ai-15:0, i-16:0, i-17:0, and ai-17:0) and low amounts of saturated FA (14:0, 16:0, and 18:0). Comparing the FA profiles at different temperatures, in the lag phase, at 50 °C, there was a decrease of ai-17:0 and a decrease of i-15:0 in the exponential phase, in comparison with 37 °C. In all growth phases, there was a decrease of ai-15:0 and an increase of i-17:0. From the lag to the stationary phase, at 50 °C, there was a decrease of ai-17:0 and i-16:0, whereas i-15:0 increased, while at 37 °C, there was an increase of i-15:0 and i-16:0, and a decrease in ai-15:0 and ai-17:0. B. licheniformis I89 can adapt its FA profile, at moderate temperatures, by changing the iso-FA and anteiso-FA composition and the iso/anteiso ratio. This nonpathogenic bacterium species can be used as a source of BrFA with putative beneficial health effects for gut protection and with reported antitumor properties, foreseeing its use for producing compounds with biotechnological applications.

Indole Pulse Signalling Regulates the Cytoplasmic pH of E. coli in a Memory-Like Manner

Bacterial cells are critically dependent upon pH regulation. Here we demonstrate that indole plays a critical role in the regulation of the cytoplasmic pH of Escherichia coli. Indole is an aromatic molecule with diverse signalling roles. Two modes of indole signalling have been described: persistent and pulse signalling. The latter is illustrated by the brief but intense elevation of intracellular indole during stationary phase entry. We show that under conditions permitting indole production, cells maintain their cytoplasmic pH at 7.2. In contrast, under conditions where no indole is produced, the cytoplasmic pH is near 7.8. We demonstrate that pH regulation results from pulse, rather than persistent, indole signalling. Furthermore, we illustrate that the relevant property of indole in this context is its ability to conduct protons across the cytoplasmic membrane. Additionally, we show that the effect of the indole pulse that occurs normally during stationary phase entry in rich medium remains as a "memory" to maintain the cytoplasmic pH until entry into the next stationary phase. The indole-mediated reduction in cytoplasmic pH may explain why indole provides E. coli with a degree of protection against stresses, including some bactericidal antibiotics.