Microbial membrane lipid adaptations to high hydrostatic pressure in the marine environment

Fatty acid desaturases in non-photosynthetic bacteria: classification, regulation, and roles in plasma membrane function and cellular homeostasis

Fatty acid desaturases are key enzymes that catalyze the desaturation of acyl lipid chains by regioselectively introducing double bonds into saturated or pre-existing alkene fatty acids to produce unsaturated fatty acids. While extensive studies have focused on desaturases in higher organisms, research on these enzymes in non-photosynthetic bacteria remains limited, largely due to insufficient structural and functional data. This review aims to summarize the current knowledge on the structural features and catalytic mechanisms of desaturases in non-photosynthetic bacteria, shedding light on the sophisticated regulatory strategies underlying unsaturated fatty acid biosynthesis. In addition, factors influencing desaturase activity are presented and analyzed. This comprehensive review provides insights into bacterial homeostatic adaptation to environmental changes and highlights potential applications in nutraceutical development and therapeutic target identification.

High-pressure continuous culturing: life at the extreme

Microorganisms adapted to high hydrostatic pressures at depth in the oceans and within the subsurface of Earth's crust represent a phylogenetically diverse community thriving under extreme pressure, temperature, and nutrient availability conditions. To better understand the microbial function, physiological responses, and metabolic strategies at in-situ conditions requires high-pressure (HP) continuous culturing techniques that, although commonly used in bioengineering and biotechnology applications, remain relatively rare in the study of the Earth's microbiomes. Here, we focus on recent developments in the design of HP chemostats, with particular emphasis on adaptations for delivery and sampling of dissolved gases. We present protocols for sterilization, inoculation, agitation, and sampling strategies that minimize cell lysis, applicable to a wide range of chemostat designs.

Measurement of phospholipid lateral diffusion at high pressure by in situ magic-angle spinning NMR spectroscopy

The development of experimental methodologies that enable investigations of biochemistry at high pressure promises to yield significant advances in our understanding of life on Earth and its origins. Here, we introduce a method for studying lipid membranes at thermodynamic conditions relevant for life at deep sea hydrothermal vents. Using in situ high pressure magic-angle spinning solid state nuclear magnetic resonance spectroscopy (NMR), we measure changes in the fluidity of model microbial membranes at pressures up to 28 MPa. We find that the fluid-phase lateral diffusion of phospholipids at high pressure is significantly affected by the stoichiometric ratio of lipids in the membrane. Our results were facilitated by an accessible pressurization strategy that we have developed to enable routine preparation of solid state NMR rotors to pressures of 30 MPa or greater.

Degenerated vision, altered lipid metabolism, and expanded chemoreceptor repertoires enable Lindaspio polybranchiata to thrive in deep-sea cold seeps

BACKGROUND

Lindaspio polybranchiata, a member of the Spionidae family, has been reported at the Lingshui Cold Seep, where it formed a dense population around this nascent methane vent. We sequenced and assembled the genome of L. polybranchiata and performed comparative genomic analyses to investigate the genetic basis of adaptation to the deep sea. Supporting this, transcriptomic and fatty acid data further corroborate our findings.

RESULTS

We report the first genome of a deep-sea spionid, L. polybranchiata. Over long-term adaptive evolution, genes associated with vision and biological rhythmicity were lost, which may indirectly benefit oligotrophy by eliminating energetically costly processes. Compared to its shallow-sea relatives, L. polybranchiata has a significantly higher proportion of polyunsaturated fatty acids (PUFAs) and expanded gene families involved in the biosynthesis of unsaturated fatty acids and chromatin stabilization, possibly in response to high hydrostatic pressure. Additionally, L. polybranchiata has broad digestive scope, allowing it to fully utilize the limited food resources in the deep sea to sustain a large population. As a pioneer species, L. polybranchiata has an expanded repertoire of genes encoding potential chemoreceptor proteins, including ionotropic receptors (IRs) and gustatory receptor-like receptors (GRLs). These proteins, characterized by their conserved 3D structures, may enhance the organism's ability to detect chemical cues in chemosynthetic ecosystems, facilitating rapid settlement in suitable environments.

CONCLUSIONS

Our results shed light on the adaptation of Lindaspio to the darkness, high hydrostatic pressure, and food deprivation in the deep sea, providing insights into the molecular basis for L. polybranchiata becoming a pioneer species.

Atomistic Simulations and Analysis of Peripheral Membrane Proteins with Model Lipid Bilayers

All-atom molecular dynamics (AAMD) is a computational technique that predicts the movement of particles based on the intermolecular forces acting on the system. It enables the study of biological systems at atomic detail, complements observations from experiments, and can help the selection of experimental targets. Here, we describe the applications of MD simulations to study the interaction between peripheral membrane proteins and lipid bilayers. Specifically, we provide step-by-step instructions to set up MD simulations to study the binding and interaction of ALPS, the amphipathic helix of the lipid transport protein Osh4, and Thanatin, an antimicrobial peptide with model membranes. We describe examples of systems built with fully atomistic lipid tails and those truncated with the highly-mobile-membrane-mimetic method to enhance conformational sampling. We also comment on the importance of lipid diversity, molecular resolution, and best practices for constructing, running, and analyzing protein-lipid simulation systems. In this second edition, we include a brief discussion on alternative approaches and software to construct protein-membrane coordinate systems, as well as analysis tools and practices that have become relevant to examining protein-lipid interactions since the first edition of this chapter.

Exploring robustness of hybrid membranes under high hydrostatic pressure and temperature

Bacterial membranes are typically composed of ester-bonded fatty acid (FA), while archaeal membranes consist of ether-bonded isoprenoids, differentiation referred to as the 'lipid divide'. Some exceptions to this rule are bacteria harboring ether-bonded membrane lipids. Previous research engineered the bacterium Escherichia coli to synthesize archaeal isoprenoid-based ether-bonded lipids together with the bacterial FA ester-linked lipids, showing that heterochiral membranes are stable and more robust to temperature, cold shock, and solvents. However, the impact of ether-bonded lipids, either bacterial or archaeal, on membrane robustness, remains unclear. Here, we investigated the robustness, as survival after shock, of E. coli synthesizing either archaeal or bacterial ether-bonded membrane lipids, under high temperature and/or high hydrostatic pressure (HHP). Our findings reveal E. coli with bacterial ether-bonded lipids is more robust under HHP and high temperature. On the contrary, the presence of archaeal ether-bonded membrane lipids in E. coli does not affect the robustness under HHP nor high temperature under the tested conditions. We observed morphological changes induced by the shock treatments including reduced length under high temperature or HHP, and the presence of elongated cells after a shock of HHP and high temperature combined, suggesting the combined treatments impaired cell division. Our results contribute to a deeper understanding of membrane adaptation to extreme environmental conditions and highlight the significance of HHP as a key parameter to investigate the differentiation of membranes during the lipid divide.

Thermodynamic compensation to temperature extremes in B. subtilis vs T. maritima lysine riboswitches

T. maritima and B. subtilis are bacteria that inhabit significantly different thermal environments, ∼80 vs. ∼40°C, yet employ similar lysine riboswitches to aid in the transcriptional regulation of the genes involved in the synthesis and transport of amino acids. Despite notable differences in G-C basepair frequency and primary sequence, the aptamer moieties of each riboswitch have striking similarities in tertiary structure, with several conserved motifs and long-range interactions. To explore genetic adaptation in extreme thermal environments, we compare the kinetic and thermodynamic behaviors in T. maritima and B. subtilis lysine riboswitches via single-molecule fluorescence resonance energy transfer analysis. Kinetic studies reveal that riboswitch folding rates increase with lysine concentration while the unfolding rates are independent of lysine. This indicates that both riboswitches bind lysine through an induced-fit ("bind-then-fold") mechanism, with lysine binding necessarily preceding conformational changes. Temperature-dependent van't Hoff studies reveal qualitative similarities in the thermodynamic landscapes for both riboswitches in which progression from the open, lysine-unbound state to both transition states (‡) and closed, lysine-bound conformations is enthalpically favored yet entropically penalized, with comparisons of enthalpic and entropic contributions extrapolated to a common [K+] = 100 mM in quantitative agreement. Finally, temperature-dependent Eyring analysis reveals the TMA and BSU riboswitches to have remarkably similar folding/unfolding rate constants when extrapolated to their respective (40 and 80°C) environmental temperatures. Such behavior suggests a shared strategy for ligand binding and aptamer conformational change in the two riboswitches, based on thermodynamic adaptations in number of G-C basepairs and/or modifications in tertiary structure that stabilize the ligand-unbound conformation to achieve biocompetence under both hyperthermophilic and mesothermophilic conditions.

Computational analysis of the simultaneous application of ultrasound and electric fields in a lipid bilayer

The combined application of electric fields and ultrasonic waves has shown promise in controlling cell membrane permeability, potentially resulting in synergistic effects that can be explored in the biotechnology industry. However, further clarification on how these processes interact is still needed. The objective of the present study was to investigate the atomic-scale effects of these processes on a DPPC lipid bilayer using molecular dynamics simulations. For higher electric fields, capable of independently forming pores, the application of an ultrasonic wave in the absence of cavitation yielded no additional effects on pore formation. However, for lower electric fields, the reduction in bilayer thickness induced by the shock wave catalyzed the electroporation process, effectively shortening the mean path that water molecules must traverse to form pores. When cavitation was considered, synergistic effects were evident only if the wave alone was able to generate pores through the formation of a water nanojet. In these cases, sonoporation acted as a mean to focus the electroporation effects on the initial pore formed by the nanojet. This study contributes to a better understanding of the synergy between electric fields and ultrasonic waves and to an optimal selection of processing parameters in practical applications of these processes.

Bucking the trend: understanding lipopolysaccharide structure and outer membrane dynamics in cold-adapted Pseudomonas isolated from Enigma Lake, Antarctica

Cold environments are predominant over the Earth and are inhabited by bacteria able to cope with a series of simultaneous environmental pressures. Gram-negative species of the Pseudomonas genus are the predominant ones isolated from cold habitats, making them an excellent model for studying the mechanisms of bacterial adaptation to the most extreme habitats on our planet. Here we focused on the lipopolysaccharide (LPS) structure and the outer membrane dynamics of Pseudomonas sp. EW#7, a strain isolated from Enigma Lake in Antarctica where, among other extreme characteristics, water temperature can reach 0.4 °C. We show that near-zero growth temperature mostly affects the LPS lipid A component. An uncommon tendency of decreasing lipid A secondary hydroxylation while increasing its phosphorylation degree was observed. This resulted in a faster lateral diffusion of lipid chains in the membrane and therefore in an enhancement of its fluctuations that guarantee membrane integrity and flexibility.

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.

N-terminus GTPase domain of the cytoskeleton protein FtsZ plays a critical role in its adaptation to high hydrostatic pressure

Studies in model microorganisms showed that cell division is highly vulnerable to high hydrostatic pressure (HHP). Disassembly of FtsZ filaments induced by HHP results in the failure of cell division and formation of filamentous cells in E. coli. The specific characteristics of FtsZ that allow for functional cell division in the deep-sea environments, especially in obligate piezophiles that grow exclusively under HHP condition, remain enigmatic. In this study, by using a self-developed HHP in-situ fixation apparatus, we investigated the effect of HHP on FtsZ by examining the subcellular localization of GFP-tagged FtsZ in vivo and the stability of FtsZ filament in vitro. We compared the pressure tolerance of FtsZ proteins from pressure-sensitive strain Shewanella oneidensis MR-1 (FtsZSo) and obligately piezophilic strain Shewanella benthica DB21MT-2 (FtsZSb). Our findings showed that, unlike FtsZSo, HHP hardly affected the Z-ring formation of FtsZSb, and filaments composed of FtsZSb were more stable after incubation under 50 MPa. By constructing chimeric and single amino acid mutated FtsZ proteins, we identified five residues in the N-terminal GTPase domain of FtsZSb whose mutation would impair the Z-ring formation under HHP conditions. Overall, these results demonstrate that FtsZ from the obligately piezophilic strain exhibits superior pressure tolerance than its homologue from shallow water species, both in vivo and in vitro. Differences in pressure tolerance of FtsZ are largely attributed to the N-terminal GTPase domain. This represents the first in-depth study of the adaptation of microbial cytoskeleton protein FtsZ to high hydrostatic pressure, which may provide insights into understanding the complex bioprocess of cell division under extreme environments.

The effect of hydrostatic pressure on lipid membrane lateral structure

High pressure is both an environmental challenge to which deep sea biology has to adapt, and a highly sensitive thermodynamic tool that can be used to trigger structural changes in biological molecules and assemblies. Lipid membranes are amongst the most pressure sensitive biological assemblies and pressure can have a large influence on their structure and properties. In this chapter, we will explore the use of high pressure small angle X-ray diffraction and high pressure microscopy to measure and quantify changes in the lateral structure of lipid membranes under both equilibrium high pressure conditions and in response to pressure jumps.

Increasing outer membrane complexity: the case of the lipopolysaccharide lipid A from marine Cellulophaga pacifica

Gram-negative bacteria living in marine waters have evolved peculiar adaptation strategies to deal with the numerous stress conditions that characterize aquatic environments. Among the multiple mechanisms for efficient adaptation, these bacteria typically exhibit chemical modifications in the structure of the lipopolysaccharide (LPS), which is a fundamental component of their outer membrane. In particular, the glycolipid anchor to the membrane of marine bacteria LPSs, i.e. the lipid A, frequently shows unusual chemical structures, which are reflected in equally singular immunological properties with potential applications as immune adjuvants or anti-sepsis drugs. In this work, we determined the chemical structure of the lipid A from Cellulophaga pacifica KMM 3664T isolated from the Sea of Japan. This bacterium showed to produce a heterogeneous mixture of lipid A molecules that mainly display five acyl chains and carry a single phosphate and a D-mannose disaccharide on the glucosamine backbone. Furthermore, we proved that C. pacifica KMM 3664T LPS acts as a weaker activator of Toll-like receptor 4 (TLR4) compared to the prototypical enterobacterial Salmonella typhimurium LPS. Our results are relevant to the future development of novel vaccine adjuvants and immunomodulators inspired by marine LPS chemistry.

Biological functions at high pressure: transcriptome response of Shewanella oneidensis MR-1 to hydrostatic pressure relevant to Titan and other icy ocean worlds

High hydrostatic pressure (HHP) is a key driver of life's evolution and diversification on Earth. Icy moons such as Titan, Europa, and Enceladus harbor potentially habitable high-pressure environments within their subsurface oceans. Titan, in particular, is modeled to have subsurface ocean pressures ≥ 150 MPa, which are above the highest pressures known to support life on Earth in natural ecosystems. Piezophiles are organisms that grow optimally at pressures higher than atmospheric (0.1 MPa) pressure and have specialized adaptations to the physical constraints of high-pressure environments - up to ~110 MPa at Challenger Deep, the highest pressure deep-sea habitat explored. While non-piezophilic microorganisms have been shown to survive short exposures at Titan relevant pressures, the mechanisms of their survival under such conditions remain largely unelucidated. To better understand these mechanisms, we have conducted a study of gene expression for Shewanella oneidensis MR-1 using a high-pressure experimental culturing system. MR-1 was subjected to short-term (15 min) and long-term (2 h) HHP of 158 MPa, a value consistent with pressures expected near the top of Titan's subsurface ocean. We show that MR-1 is metabolically active in situ at HHP and is capable of viable growth following 2 h exposure to 158 MPa, with minimal pressure training beforehand. We further find that MR-1 regulates 264 genes in response to short-term HHP, the majority of which are upregulated. Adaptations include upregulation of the genes argA, argB, argC, and argF involved in arginine biosynthesis and regulation of genes involved in membrane reconfiguration. MR-1 also utilizes stress response adaptations common to other environmental extremes such as genes encoding for the cold-shock protein CspG and antioxidant defense related genes. This study suggests Titan's ocean pressures may not limit life, as microorganisms could employ adaptations akin to those demonstrated by terrestrial organisms.

Changes in environmental and engineered conditions alter the plasma membrane lipidome of fractured shale bacteria

IMPORTANCE

Microorganisms inadvertently introduced into the shale reservoir during fracturing face multiple stressors including brine-level salinities and starvation. However, some anaerobic halotolerant bacteria adapt and persist for long periods of time. They produce hydrogen sulfide, which sours the reservoir and corrodes engineering infrastructure. In addition, they form biofilms on rock matrices, which decrease shale permeability and clog fracture networks. These reduce well productivity and increase extraction costs. Under stress, microbes remodel their plasma membrane to optimize its roles in protection and mediating cellular processes such as signaling, transport, and energy metabolism. Hence, by observing changes in the membrane lipidome of model shale bacteria, Halanaerobium congolense WG10, and mixed consortia enriched from produced fluids under varying subsurface conditions and growth modes, we provide insight that advances our knowledge of the fractured shale biosystem. We also offer data-driven recommendations for improving biocontrol efficacy and the efficiency of energy recovery from unconventional formations.

A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation

BACKGROUND

Chiridota heheva is a cosmopolitan holothurian well adapted to diverse deep-sea ecosystems, especially chemosynthetic environments. Besides high hydrostatic pressure and limited light, high concentrations of metal ions also represent harsh conditions in hydrothermal environments. Few holothurian species can live in such extreme conditions. Therefore, it is valuable to elucidate the adaptive genetic mechanisms of C. heheva in hydrothermal environments.

FINDINGS

Herein, we report a high-quality reference genome assembly of C. heheva from the Kairei vent, which is the first chromosome-level genome of Apodida. The chromosome-level genome size was 1.43 Gb, with a scaffold N50 of 53.24 Mb and BUSCO completeness score of 94.5%. Contig sequences were clustered, ordered, and assembled into 19 natural chromosomes. Comparative genome analysis found that the expanded gene families and positively selected genes of C. heheva were involved in the DNA damage repair process. The expanded gene families and the unique genes contributed to maintaining iron homeostasis in an iron-enriched environment. The positively selected gene RFC2 with 10 positively selected sites played an essential role in DNA repair under extreme environments.

CONCLUSIONS

This first chromosome-level genome assembly of C. heheva reveals the hydrothermal adaptation of holothurians. As the first chromosome-level genome of order Apodida, this genome will provide the resource for investigating the evolution of class Holothuroidea.

The membrane regulator squalane increases membrane rigidity under high hydrostatic pressure in archaeal membrane mimics

Apolar lipids within the membranes of archaea are thought to play a role in membrane regulation. In this work we explore the effect of the apolar lipid squalane on the dynamics of a model archaeal-like membrane, under pressure, using neutron spin echo spectroscopy. To the best of our knowledge, this is the first report on membrane dynamics at high pressure using NSE spectroscopy. Increasing pressure leads to an increase in membrane rigidity, in agreement with other techniques. The presence of squalane in the membrane results in a stiffer membrane supporting its role as a membrane regulator.