How Do Cyclopropane Fatty Acids Protect the Cell Membrane of Escherichia coli in Cold Shock?

A Minimalist Model Lipid System Mimicking the Biophysical Properties of Escherichia coli's Inner Membrane

Biological membranes are essential for the development and survival of organisms. They can be highly complex, usually comprising a variety of lipids, proteins, and other biomolecules organized around a lipid bilayer structure. This complexity makes studying specific features of biological membranes difficult, with many research studies relying on simplified models, such as artificial vesicles or supported lipid bilayers. Here, we search for a minimal, lipid-only model system of the Escherichia coli inner membrane. We aim to retain the main lipidomic components in their native ratio while mimicking the membrane's thermal and mechanical properties. Based on previous studies, we identify 18 potential model systems reflecting key aspects of the known lipidomic composition and progressively narrow down our selection based on the systems' phase transition temperature and mechanical properties. We identify three ternary model systems able to form stable bilayers that can be made of the commercially available synthetic lipids 16:0-18:1 phosphatidylethanolamine (POPE), 16:0-18:1 phosphatidylglycerol (POPG), and 16:0-18:1 cardiolipin (CL). We anticipate our results to be of interest for future studies making use of E. coli models, for example, investigating membrane proteins' function or macromolecule-membrane interactions.

Current status of cyclopropane fatty acids on bacterial cell membranes characteristics and physiological functions

Wide-ranging sophisticated physiological activities of cell membranes are associated with changes in fatty acid structure and composition. The cfa gene is a core regulator of cell membrane fatty acid cyclopropanation reaction. Its encoded cyclopropane fatty acid synthase (CFA synthase) catalyzes the binding of unsaturated fatty acid (UFA) to methylene groups, which undergoes cyclopropanation modification to produce cyclopropane fatty acids (CFAs). Compelling evidence suggests a large role for the cfa gene and CFAs in bacterial adaptive responses. This review provides an overview of the relationship of CFAs with bacterial cell membrane properties and physiological functions, including the roles of cell membrane fluidity, stability, and permeability to protons, bacterial growth, acid resistance, and especially in bacterial antibiotic resistance and pathogenicity. The dysregulation and inhibition of the cfa gene may serve as potential therapeutic targets against bacterial drug resistance and pathogenicity. Therefore, elucidating the biological function of CFAs during the stationary growth phase therefore provides invaluable insights into the bacterial pathogenesis and the development of novel antimicrobial agents.

Examining the Biophysical Properties of the Inner Membrane of Gram-Negative ESKAPE Pathogens

The World Health Organization has identified multidrug-resistant bacteria as a serious global health threat. Gram-negative bacteria are particularly prone to antibiotic resistance, and their high rate of antibiotic resistance has been suggested to be related to the complex structure of their cell membrane. The outer membrane of Gram-negative bacteria contains lipopolysaccharides that protect the bacteria against threats such as antibiotics, while the inner membrane houses 20-30% of the bacterial cellular proteins. Given the cell membrane's critical role in bacterial survival, antibiotics targeting the cell membrane have been proposed to combat bacterial infections. However, a deeper understanding of the biophysical properties of the bacterial cell membrane is crucial to developing effective and specific antibiotics. In this study, Martini coarse-grain molecular dynamics simulations were used to investigate the interplay between membrane composition and biophysical properties of the inner membrane across four pathogenic bacterial species: Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, and Escherichia coli. The simulations indicate the impact of species-specific membrane composition on the overall membrane properties. Specifically, the cardiolipin concentration in the inner membrane is a key factor influencing the membrane features. Model membranes with varying concentrations of bacterial lipids (phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin) further support the significant role of cardiolipin in determining the membrane biophysical properties. The bacterial inner membrane models developed in this work pave the way for future simulations of bacterial membrane proteins and for simulations investigating novel strategies aimed at disrupting the bacterial membrane to treat antibiotic-resistant infections.

Effect of Light Regime on Candidatus Puniceispirillum marinum IMCC1322 in Nutrient-Replete Conditions

Previous studies showed no improvement in bacterial biomass for Candidatus Puniceispirillum marinum IMCC1322 under light regimes. Nevertheless, in nutrient-replete cultures with higher inoculating cell densities, strain IMCC1322 exhibited proteorhodopsin photoheterotrophy. Increasing both inoculum size and the amino acid pool can eliminate quorum sensing and starvation responses in strain IMCC1322. Light regimes affected IMCC1322 cultures in stationary/death phases, where cellular ATP levels ranged from 0.0331 to 1.74 mM, with ATP/cell ranging from 13.9 to 367 zeptomoles. In nutrient-depleted conditions, strain IMCC1322 may suffer from excessive protons generated by proteorhodopsin under light conditions. IMCC1322 may tolerate excessive periplasmic protons through ATP-dependent proton pumping and protonation of augmented amino acids. Meanwhile, acid stress could also be mitigated by refining membrane permeability through unsaturation and cyclopropanation of phospholipids. Oceanic bacteria such as IMCC1322 and SAR11 preferred anaplerotic TCA cycles over glycolysis and rely on the Entner-Doudoroff (ED) pathway for growth. Although ATP generation is less efficient in the ED pathway, it offers advantages during rapid growth owing to its strong thermodynamic driving force. The metabolism of IMCC1322 favors gluconeogenesis over glycolysis, aligning with the metabolism of SAR11 reported in previous studies. However, the additional light-driven, PR-dependent ATP synthesis in IMCC1322 is expected to be insufficient to support protein turnover after the log phase, as well as in nutrient-limited conditions. Stable isotope measurements showed no significant differences in the inorganic carbon assimilation between constant light and constant dark cultures in late log phase.

How do Photoswitchable Lipids Influence the Intercalation of Anticancer Drug in Lipid Membrane? Investigation using Molecular Dynamics Simulation

Photoswitchable lipids, particularly azobenzene-derivatized phosphatidylcholine (azoPC) lipids, offer a unique mechanism for reversible modification of membrane properties upon exposure to ultraviolet (UV) radiation. Through all-atom molecular dynamics simulations, we explore how UV irradiation-induced trans-to-cis photoisomerization (TCPI) of AzoPC lipid influences the structure and dynamics of a lipid membrane, composed of dipalmitoylphosphatidylcholine (DPPC) and cholesterol with similar composition to that of the DOXIL®. Structural and dynamical analyses of two states of the membrane, 'dark' state (containing cis-azoPC lipid) and 'bright' state (containing 85 % cis-azoPC and 15 % trans-azoPC lipids) reveal that the TCPI reduces membrane packing density and increases diffusivity of lipids. We have demonstrated an enhanced intercalation of doxorubicin (DOX), an anticancer drug, in the 'bright' state of the membrane compared to that in the 'dark' state. This study - elucidating the complex interplay between lipid composition, photoswitching, and lipid-drug interactions - contributes to the design of lipid-based systems for targeted drug delivery and biomedical applications.

Extreme makeover: the incredible cell membrane adaptations of extremophiles to harsh environments

The existence of life beyond Earth has long captivated humanity, and the study of extremophiles-organisms surviving and thriving in extreme environments-provides crucial insights into this possibility. Extremophiles overcome severe challenges such as enzyme inactivity, protein denaturation, and damage of the cell membrane by adopting several strategies. This feature article focuses on the molecular strategies extremophiles use to maintain the cell membrane's structure and fluidity under external stress. Key strategies include homeoviscous adaptation (HVA), involving the regulation of lipid composition, and osmolyte-mediated adaptation (OMA), where small organic molecules protect the lipid membrane under stress. Proteins also have direct and indirect roles in protecting the lipid membrane. Examining the survival strategies of extremophiles provides scientists with crucial insights into how life can adapt and persist in harsh conditions, shedding light on the origins of life. This article examines HVA and OMA and their mechanisms in maintaining membrane stability, emphasizing our contributions to this field. It also provides a brief overview of the roles of proteins and concludes with recommendations for future research directions.

PCA, PC-CVA, and Random Forest of GCIB-SIMS Data for the Elucidation of Bacterial Envelope Differences in Antibiotic Resistance Research

Antibiotic resistance can rapidly spread through bacterial populations via bacterial conjugation. The bacterial membrane has an important role in facilitating conjugation, thus investigating the effects on the bacterial membrane caused by conjugative plasmids, antibiotic resistance, and genes involved in conjugation is of interest. Analysis of bacterial membranes was conducted using gas cluster ion beam-secondary ion mass spectrometry (GCIB-SIMS). The complexity of the data means that data analysis is important for the identification of changes in the membrane composition. Preprocessing of data and several analytical methods for identification of changes in bacterial membranes have been investigated. GCIB-SIMS data from Escherichia coli samples were subjected to principal components analysis (PCA), principal components-canonical variate analysis (PC-CVA), and Random Forests (RF) data analysis with the aim of extracting the maximum biological information. The influence of increasing replicate data was assessed, and the effect of diminishing biological variation was studied. Optimized m/z region-specific scaling provided improved clustering, with an increase in biologically significant peaks contributing to the loadings. PC-CVA improved clustering, provided clearer loadings, and benefited from larger data sets collected over several months. RF required larger sample numbers and while showing overlap with the PC-CVA, produced additional peaks of interest. The combination of PC-CVA and RF allowed very subtle differences between bacterial strains and growth conditions to be elucidated for the first time. Specifically, comparative analysis of an E. coli strain with and without the F-plasmid revealed changes in cyclopropanation of fatty acids, where the addition of the F-plasmid led to a reduction in cyclopropanation.

Investigating the Influence of Photoswitchable Lipids on the Structure and Dynamics of Lipid Membranes: Fundamentals and Potential Applications

In this work, we delve into the impact of photoisomerization of photoswitchable lipids (PSLs) on the membrane structure and dynamics at a molecular level. Through all-atom molecular dynamics simulations, we explore how UV irradiation-induced trans-to-cis isomerization of these lipids, particularly the azobenzene-derivatized phosphatidylcholine (AzoPC) lipid, influences the structure and dynamics of a simplified lipid membrane, mimicking those of E. coli bacteria across different temperatures. Our findings align with previous experimental observations regarding membrane properties and offer insights into localized effects and microscopic heterogeneity. Additionally, we estimate the relaxation time scale of the lipid membrane following AzoPC photoisomerization. Moreover, we demonstrate the feasibility of photoactivated drug release, exemplified by the controlled liberation of doxorubicin, an anticancer agent, through the membrane, suggesting the potential of PSLs in engineering photoactivated liposomes, coined as photoazosomes, for precise targeted drug delivery applications.

Fatty acids of Helicobacter pylori lipoproteins CagT and Lpp20

Bacterial lipoproteins are post-translationally modified by the addition of acyl chains that anchor the protein to bacterial membranes. This modification includes two ester-linked and one amide-linked acyl chain on lipoproteins from Gram-negative bacteria. Helicobacter pylori lipoproteins have important functions in pathogenesis (including delivering the CagA oncoprotein to mammalian cells) and are recognized by host innate and adaptive immune systems. The number and variety of acyl chains on lipoproteins impact the innate immune response through Toll-like receptor 2. The acyl chains added to lipoproteins are derived from membrane phospholipids. H. pylori membrane phospholipids have previously been shown to consist primarily of C14:0 and C19:0 cyclopropane-containing acyl chains. However, the acyl composition of H. pylori lipoproteins has not been determined. In this study, we characterized the acyl composition of two representative H. pylori lipoproteins, Lpp20 and CagT. Fatty acid methyl esters were prepared from both purified lipoproteins and analyzed by gas chromatography-mass spectrometry. For comparison, we also analyzed H. pylori phospholipids. Consistent with previous studies, we observed that the H. pylori phospholipids contain primarily C14:0 and C19:0 cyclopropane-containing fatty acids. In contrast, both the ester-linked and amide-linked fatty acids found in H. pylori lipoproteins were observed to be almost exclusively C16:0 and C18:0. A discrepancy between the acyl composition of membrane phospholipids and lipoproteins as reported here for H. pylori has been previously reported in other bacteria including Borrelia and Brucella. We discuss possible mechanisms.IMPORTANCEColonization of the stomach by Helicobacter pylori is an important risk factor in the development of gastric cancer, the third leading cause of cancer-related death worldwide. H. pylori persists in the stomach despite an immune response against the bacteria. Recognition of lipoproteins by TLR2 contributes to the innate immune response to H. pylori. However, the role of H. pylori lipoproteins in bacterial persistence is poorly understood. As the host response to lipoproteins depends on the acyl chain content, defining the acyl composition of H. pylori lipoproteins is an important step in characterizing how lipoproteins contribute to persistence.

Molecular Modeling and Simulation of the Mycobacterial Cell Envelope: From Individual Components to Cell Envelope Assemblies

Unlike typical Gram-positive bacteria, the cell envelope of mycobacteria is unique and composed of a mycobacterial outer membrane, also known as the mycomembrane, a peptidoglycan layer, and a mycobacterial inner membrane, which is analogous to that of Gram-negative bacteria. Despite its importance, however, our understanding of this complex cell envelope is rudimentary at best. Thus, molecular modeling and simulation of such an envelope can benefit the scientific community by proposing new hypotheses about the biophysical properties of its different layers. In this Perspective, we present recent advances in molecular modeling and simulation of the mycobacterial cell envelope from individual components to cell envelope assemblies. We also show how modeling other types of cell envelopes, such as that of Escherichia coli, may help modeling part of the mycobacterial envelopes. We hope that the studies presented here are just the beginning of the road and more and more new modeling and simulation studies help us to understand crucial questions related to mycobacteria such as antibiotic resistance or bacterial survival in the host.

Anomalous lateral diffusion of lipids during the fluid/gel phase transition of a lipid membrane

A lipid membrane undergoes a phase transition from fluid to gel phase upon changing external thermodynamic conditions, such as decreasing temperature and increasing pressure. Extremophilic organisms face the challenge of preventing this deleterious phase transition. The main focus of their adaptive strategy is to facilitate effective temperature sensing through sensor proteins, relying on the drastic changes in packing density and membrane fluidity during the phase transition. Although the changes in packing density parameters due to the fluid/gel phase transition are studied in detail, the impact on membrane fluidity is less explored in the literature. Understanding the lateral diffusive dynamics of lipids in response to temperature, particularly during the fluid/gel phase transition, is albeit crucial. Here we have simulated the phase transition of a single component lipid membrane composed of dipalmitoylphosphatidylcholine (DPPC) lipids using a coarse-grained (CG) model and studied the changes of the structural and dynamical properties. It is observed that near the phase transition point, both fluid and gel phase domains coexist together. The dynamics remains highly non-Gaussian for a long time even when the mean square displacement reaches the Fickian regime at a much earlier time. This Fickian yet non-Gaussian diffusion (FnGD) is a characteristic of a highly heterogeneous system, previously observed for the lateral diffusion of lipids in raft mimetic membranes having liquid-ordered and liquid-disordered phases co-existing together. We have analyzed the molecular trajectories and calculated the jump-diffusion of the lipids, stemming from sudden jump translations, using a translational jump-diffusion (TJD) approach. An overwhelming contribution of the jump-diffusion of the lipids is observed suggesting anomalous diffusion of lipids during fluid/gel phase transition of the membrane. These results are important in unravelling the intricate nature of lipid diffusion during the phase transition of the membrane and open up a new possibility of investigating the most significant change of membrane properties during phase transition, which can be effectively sensed by proteins.