Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane

Accurate Quantification of Metals in Individual Synechocystis sp. PCC 6803 Cells by Single-Cell ICP-MS: Dual-Calibration and Sample Stabilization Strategies

Single-cell inductively coupled plasma mass spectrometry (SC-ICP-MS) is an emerging technique to investigate metal heterogeneity in individual cells. However, due to the absence of consistent calibration and suitable stabilization strategy for cells, accurate quantification of cellular heterogeneity and the content of metals remains a challenge. Herein, an accurate quantification method for the content and heterogeneous distribution of metals among individual microalgae cells was developed based on SC-ICP-MS using dual-calibration strategies and robust pretreatment methods. Gold nanoparticles (AuNPs) were used as calibration for measuring metal contents in single cells, but it would lead to a 13.6-63.1% underestimation of cell numbers due to inaccurate detection of cells' transport efficiency. To avoid this inaccuracy, we proposed an additional calibration strategy to measure cellular transport efficiency and cell numbers using endogenous Mg, enabling a more accurate assessment of cell heterogeneity. Then, an effective pretreatment method was optimized through fixation of cells with glutaraldehyde for 1 h to maintain the cellular stability and obtain accurate results, with satisfactory recoveries for cell number (98.4%) and Mg contents (91.7%), even after long-time storage. After optimization, the proposed method showed high sensitivity and repeatability in both cellular metal contents (Mg, Hg, Cd, and Co) and cell number, with detection limits (LODs) to be 0.14-0.53 fg/cell and 5.5 × 103 cells/mL, respectively. Finally, the proposed method was successfully used for detecting various metals and their heterogeneity in Synechocystis sp. PCC 6803 cells provided an accurate and robust tool for investigating the uptake and heterogeneous distribution of metals in microalgae.

In silico insights into the membrane disruption induced by the protonation of ionizable lipids

CONTEXT

Lipid nanoparticles (LNPs) are a novel type of drug delivery carrier, which play a protective role in nucleic acid drug delivery. LNPs are composed of various organic materials and these compositions assume corresponding tasks. Among these components, ionizable lipids undergo localized accumulation of lipids after exposure to the acidic pH environment of endosomes due to electrostatic interactions between lipid nanoparticles and phospholipids in endosomal membranes, which contributes to membrane fusion-disruption, endosomal escape, and cargo release. However, these extrapolations lack intuitive evidence at the molecular level, so we perform computational simulations to provide a microscopic view of molecular and cellular biological events. In this work, we performed molecular dynamics (MD) simulations to study the microscopic mechanism of membrane disruption induced by the protonation of ionizable lipids. Models containing different concentrations of ionizable lipids were obtained by simulating the uptake process of ionizable lipids by the endosomal membrane. The simulated results showed that the protonated ionizable lipids accumulated on one side of the endosomal membrane. Through the analysis of intermolecular interactions, it was found that the accumulation was due to the strong association of the head groups of the protonated ionizable lipids with the membrane lipids. Whereas the unprotonated ionizable lipids were dispersed on both sides of the bilayer, which served to stabilize the nanoparticles. The accumulation of ionizable lipids caused a sustained effect on lipid order parameters and the thickness of the simulated bilayer, which may be responsible for endosomal membrane rupture.

METHODS

In this study, we employed MD simulations and used the GROMOS 54A7 united-atom force field to investigate the passive diffusion process of ionizable lipids. MD simulations were performed using the GROMACS 2019 software, focusing on the changes in the energy and molecular distribution of the system during the uptake process of ionizable lipids. Characteristics such as SDC, thickness, and energy of the system configuration at the end of the process are also analyzed. These configurations of the simulations were visualized using VMD. The GridMAT-MD package was adopted to analyze the thickness of the membrane. The other characters such as density distribution profiles and energies were analyzed using the tools within the GROMACS package.

Global change effects on biogeochemical mercury cycling

Past and present anthropogenic mercury (Hg) release to ecosystems causes neurotoxicity and cardiovascular disease in humans with an estimated economic cost of $117 billion USD annually. Humans are primarily exposed to Hg via the consumption of contaminated freshwater and marine fish. The UNEP Minamata Convention on Hg aims to curb Hg release to the environment and is accompanied by global Hg monitoring efforts to track its success. The biogeochemical Hg cycle is a complex cascade of release, dispersal, transformation and bio-uptake processes that link Hg sources to Hg exposure. Global change interacts with the Hg cycle by impacting the physical, biogeochemical and ecological factors that control these processes. In this review we examine how global change such as biome shifts, deforestation, permafrost thaw or ocean stratification will alter Hg cycling and exposure. Based on past declines in Hg release and environmental levels, we expect that future policy impacts should be distinguishable from global change effects at the regional and global scales.

Kinetic characteristics of and critical stages for mercury accumulation in rice (Oryza sativa L.)

By studying the dynamic characteristics of and key growth stages for mercury (Hg) enrichment in rice, the Hg migration and translocation processes in this species can be better understood. In this study, a pot experiment was conducted, wherein two rice cultivars, Tianyouhuazhan (TYHZ, indica) and Zhendao 18 (ZD18, japonica), were selected and planted for analysing the Hg accumulation kinetic characteristics in rice plants. The plants were sampled at each growth stage, and the biomass and total Hg (THg) and methylmercury (MeHg) concentrations of each tissue were measured. The relative Hg contribution rates (CRs) in whole rice plants and rice grains were calculated, and the growth stage with the highest relative contribution was identified as the key growth stage for Hg accumulation. The results indicated that in rice, the MeHg translocation capability was stronger than the THg translocation capability. Significant differences in the kinetic characteristics of Hg accumulation were found between the two rice cultivars, and the TYHZ rice grains had a stronger Hg accumulation ability than the ZD18 rice grains. The key growth stages for THg accumulation in whole rice plants of both cultivars were the tillering and booting stages, while that for MeHg accumulation was the tillering stage. The key period for Hg accumulation in rice grains was the grain filling stage for both cultivars. The insights from this study could provide scientific guidance for the safe production of rice in Hg-contaminated soil.

Inorganic versus organic fertilizers: How do they lead to methylmercury accumulation in rice grains

Both inorganic and organic fertilizers are widely used to increase rice yield. However, these fertilizers are also found to aggravate mercury methylation and methylmercury (MeHg) accumulation in paddy fields. The aim of this study was to reveal the mechanisms of inorganic and organic fertilizers on MeHg accumulation in rice grains, which are not yet well understood. Potting cultures were conducted in which different fertilizers were applied to a paddy soil. The results showed that both inorganic and organic fertilizers increased MeHg concentrations rather than biological accumulation factors (BAFs) of MeHg in mature rice grains. Inorganic fertilizers, especially nitrogen fertilizer, enhanced the bioavailability of mercury and the relative amount Hg-methylating microbes and therefore intensified mercury methylation in paddy soil and MeHg accumulation in rice grains. Unlike inorganic fertilizers, organic matter (OM) in organic fertilizers was the main reason for the increase of MeHg concentrations in rice grains, and it also could immobilize Hg in soil when it was deeply degraded. The enhancement of MeHg concentrations in rice grains induced by inorganic fertilizers (5.18-41.69%) was significantly (p < 0.05) lower than that induced by organic fertilizers (80.49-106.86%). Inorganic fertilizers led to a larger increase (50.39-99.28%) in thousand-kernel weight than MeHg concentrations (5.18-41.69%), resulting in a dilution of MeHg concentrations in mature rice grains. Given the improvement of soil properties by organic fertilizer, increasing the proportion of inorganic fertilizer application may be a better option to alleviate MeHg accumulation in rice grains and guarantee the rice yield in the agricultural production.

Theoretical insights into the uptake of sulfonamides onto phospholipid bilayers: Mechanisms, interaction and toxicity evaluation

Sulfonamides (SAs) are now recognized as the main emerging environmental pollutants in aquatic environments. Although the bioaccumulation capacities of SAs have been confirmed, the pathway for the penetration of the SAs into lipid bilayer has been not fully understood. In this study, the bioaccumulation mechanism of four typical SAs onto the dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer and their effects on the properties of DPPC bilayer were employed and evaluated respectively by using molecular dynamics simulations. Results show that from the viewpoint of thermodynamics, it is favorable for these SAs partitioning to DPPC bilayer. The accommodation of four SAs onto the lipid membrane needs to undergo several processes, which include the contact stage, transformation stage, and absorption stage. Besides, the sulfamethoxazole (SMX) and sulfamethazine (SMZ) show a strong preference for the DPPC phase rather than the interface region while the sulfadiazine (SDZ) and sulfametoxydiazine (SMD) have similar tendencies in the interface region and DPPC phase. Furthermore, the cytotoxicity of SAs is reflected in their ability to affect the electrostatic potential of the membrane and to reduce the thickness of phospholipid bilayers. This molecular-level study provided an insightful understanding of the toxicity and bioaccumulation of SAs.

Diffusion of H2 S from anaerobic thiolated ligand biodegradation rapidly generated bioavailable mercury

Methylmercury (MeHg) is a potent neurotoxin that biomagnifies through food webs and which production depends on anaerobic microbial uptake of inorganic mercury (Hg) species. One outstanding knowledge gap in understanding Hg methylation is the nature of bioavailable Hg species. It has become increasingly obvious that Hg bioavailability is spatially diverse and temporally dynamic but current models are built on single thiolated ligand systems, mostly omitting ligand exchanges and interactions, or the inclusion of dissolved gaseous phases. In this study, we used a whole-cell anaerobic biosensor to determine the role of a mixture of thiolated ligands on Hg bioavailability. Serendipitously, we discovered how the diffusion of trace amounts of exogenous biogenic H₂ S, originating from anaerobic microbial ligand degradation, can alter Hg speciation - away from H₂ S production site - to form bioavailable species. Regardless of its origins, H₂ S stands as a mobile mediator of microbial Hg metabolism, connecting spatially separated microbial communities. At a larger scale, global planetary changes are expected to accelerate the production and mobilization of H₂ S and Hg, possibly leading to increased production of the potent neurotoxin; this work provides mechanistic insights into the importance of co-managing biogeochemical cycle disruptions. This article is protected by copyright. All rights reserved.

Use smaller size of straw to alleviate mercury methylation and accumulation induced by straw incorporation in paddy field

Straw sizes were found to affect the methylmercury (MeHg) accumulation in rice grains induced by straw incorporation. The mechanism behind, however, still remains unclear. Here, we incorporated rice straw in different sizes (powder, 2 cm and 5 cm) into a Hg-contaminated paddy soil. Our results showed that straw sizes regulated the release of different fractions of organic matter (OM) in straw residues and further Hg methylation in paddy soil. The easily degradable OM (EDOM) was a key driving factor that facilitated net Hg methylation, though it only occupied a small fraction (1.12-3.12%) of the soil OM. Powdered straw reduced the duration of net Hg methylation by 74.39% compared to 5 cm straw, resulting in a strong and rapid net Hg methylation in paddy soil before the rice flowering. After the release of EDOM, the humified OM dominated in paddy soil and bound to MeHg, leading to less MeHg being transported to rice grains during the grain filling. Powdered straw decreased MeHg accumulation by 25.32% in the mature rice grains compared with 5 cm straw. Our study suggests that straw powdering before incorporation provides a feasible pathway for reducing MeHg accumulation in rice grains induced by straw incorporation.

Understanding mercury methylation in the changing environment: Recent advances in assessing microbial methylators and mercury bioavailability

Methylmercury (MeHg) is a neurotoxin, mainly derived from microbial mercury methylation in natural aquatic environments, and poses threats to human health. Polar regions and paddy soils are potential hotspots of mercury methylation and represent environmental settings that are susceptible to natural and anthropogenic perturbations. The effects of changing environmental conditions on the methylating microorganisms and mercury speciation due to global climate change and farming practices aimed for sustainable agriculture were discussed for polar regions and paddy soils, respectively. To better understand and predict microbial mercury methylation in the changing environment, we synthesized current understanding of how to effectively identify active mercury methylators and assess the bioavailability of different mercury species for methylation. The application of biomarkers based on the hgcAB genes have demonstrated the occurrence of potential mercury methylators, such as sulfate-reducing bacteria, iron-reducing bacteria, methanogen and syntrophs, in a diverse variety of microbial habitats. Advanced techniques, such as enriched stable isotope tracers, whole-cell biosensor and diffusive gradient thin film (DGT) have shown great promises in quantitatively assessing mercury availability to microbial methylators. Improved understanding of the complex structure of microbial communities consisting mercury methylators and non-methylators, chemical speciation of inorganic mercury under geochemically relevant conditions, and the pathway of cellular mercury uptake will undoubtedly facilitate accurate assessment and prediction of in situ microbial mercury methylation.

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins

The mer operon in bacteria encodes a set of proteins and enzymes that impart resistance to environmental mercury toxicity by importing Hg2+ and reducing it to volatile Hg(0). Because the reduction occurs in the cytoplasm, mercuric ions must first be transported across the cytoplasmic membrane by one of a few known transporters. MerF is the smallest of these, containing only two transmembrane helices and two pairs of vicinal cysteines that coordinate mercuric ions. In this work, we use molecular dynamics simulations to characterize the dynamics of MerF in its apo and Hg2+ -bound states. We find that the apo state positions one of the cysteine pairs closer to the periplasmic side of the membrane, while in the bound state the same pair approaches the cytoplasmic side. This finding is consistent with the functional requirement of accepting Hg2+ from the periplasmic space, sequestering it on acceptance, and transferring it to the cytoplasm. Conformational changes in the TM helices facilitate the functional interaction of the two cysteine pairs. Free-energy calculations provide a barrier of 16 kcal/mol for the association of the periplasmic Hg2+ -bound protein MerP with MerF and 7 kcal/mol for the subsequent association of MerF's two cysteine pairs. Despite the significant conformational changes required to move the binding site across the membrane, coarse-grained simulations of multiple copies of MerF support the expectation that it functions as a monomer. Our results demonstrate how conformational changes and binding thermodynamics could lead to such a small membrane protein acting as an ion transporter. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.

Mercury Uptake by Desulfovibrio desulfuricans ND132: Passive or Active?

Recent studies have identified HgcAB proteins as being responsible for mercury [Hg(II)] methylation by certain anaerobic microorganisms. However, it remains controversial whether microbes take up Hg(II) passively or actively. Here, we examine the dynamics of concurrent Hg(II) adsorption, uptake, and methylation by both viable and inactivated cells (heat-killed or starved) or spheroplasts of the sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 in laboratory incubations. We show that, without addition of thiols, >60% of the added Hg(II) (25 nM) was taken up passively in 48 h by live and inactivated cells and also by cells treated with the proton gradient uncoupler, carbonylcyanide-3-chlorophenylhydrazone (CCCP). Inactivation abolished Hg(II) methylation, but the cells continued taking up Hg(II), likely through competitive binding or ligand exchange of Hg(II) by intracellular proteins or thiol-containing cellular components. Similarly, treatment with CCCP impaired the ability of spheroplasts to methylate Hg(II) but did not stop Hg(II) uptake. Spheroplasts showed a greater capacity to adsorb Hg(II) than whole cells, and the level of cytoplasmic membrane-bound Hg(II) correlated well with MeHg production, as Hg(II) methylation is associated with cytoplasmic HgcAB. Our results indicate that active metabolism is not required for cellular Hg(II) uptake, thereby providing an improved understanding of Hg(II) bioavailability for methylation.

Molecular Dynamics Simulations of Membrane Permeability

This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.

Methylmercury's chemistry: From the environment to the mammalian brain

Methylmercury is a neurotoxicant that is found in fish and rice. MeHg's toxicity is mediated by blockage of -SH and -SeH groups of proteins. However, the identification of MeHg's targets is elusive. Here we focus on the chemistry of MeHg in the abiotic and biotic environment. The toxicological chemistry of MeHg is complex in metazoans, but at the atomic level it can be explained by exchange reactions of MeHg bound to -S(e)H with another free -S(e)H group (R¹S(e)-HgMe + R²-S(e)H ↔ R¹S(e)H + R²-S(e)-HgMe). This reaction was first studied by professor Rabenstein and here it is referred as the "Rabenstein's Reaction". The absorption, distribution, and excretion of MeHg in the environment and in the body of animals will be dictated by Rabenstein's reactions. The affinity of MeHg by thiol and selenol groups and the exchange of MeHg by Rabenstein's Reaction (which is a diffusion controlled reaction) dictates MeHg's neurotoxicity. However, it is important to emphasize that the MeHg exchange reaction velocity with different types of thiol- and selenol-containing proteins will also depend on protein-specific structural and thermodynamical factors. New experimental approaches and detailed studies about the Rabenstein's reaction between MeHg with low molecular mass thiol (LMM-SH) molecules (cysteine, GSH, acetyl-CoA, lipoate, homocysteine) with abundant high molecular mass thiol (HMM-SH) molecules (albumin, hemoglobin) and HMM-SeH (GPxs, Selenoprotein P, TrxR1-3) are needed. The study of MeHg migration from -S(e)-Hg- bonds to free -S(e)H groups (Rabenstein's Reaction) in pure chemical systems and neural cells (with special emphasis to the LMM-SH and HMM-S(e)H molecules cited above) will be critical to developing realistic constants to be used in silico models that will predict the distribution of MeHg in humans.

Microbial Mercury Methylation in Aquatic Environments: A Critical Review of Published Field and Laboratory Studies

Methylmercury (MeHg) is an environmental contaminant of concern because it biomagnifies in aquatic food webs and poses a health hazard to aquatic biota, piscivorous wildlife and humans. The dominant source of MeHg to freshwater systems is the methylation of inorganic Hg (IHg) by anaerobic microorganisms; and it is widely agreed that in situ rates of Hg methylation depend on two general factors: the activity of Hg methylators and their uptake of IHg. A large body of research has focused on the biogeochemical processes that regulate these two factors in nature; and studies conducted within the past ten years have made substantial progress in identifying the genetic basis for intracellular methylation and defining the processes that govern the cellular uptake of IHg. Current evidence indicates that all Hg methylating anaerobes possess the gene pair hgcAB that encodes proteins essential for Hg methylation. These genes are found in a large variety of anaerobes, including iron reducers and methanogens; but sulfate reduction is the metabolic process most often reported to show strong links to MeHg production. The uptake of Hg substrate prior to methylation may occur by passive or active transport, or by a combination of both. Competitive inhibition of Hg uptake by Zn speaks in favor of active transport and suggests that essential metal transporters are involved. Shortly after its formation, MeHg is typically released from cells, but the efflux mechanisms are unknown. Although methylation facilitates Hg depuration from the cell, evidence suggests that the hgcAB genes are not induced or favored by Hg contamination. Instead, high MeHg production can be linked to high Hg bioavailability as a result of the formation of Hg(SH)₂, HgS nanoparticles, and Hg-thiol complexes. It is also possible that sulfidic conditions require strong essential metal uptake systems that inadvertently bring Hg into the cytoplasm of Hg methylating microbes. In comparison with freshwaters, Hg methylation in open ocean waters appears less restricted to anoxic environments. It does seem to occur mainly in oxygen deficient zones (ODZs), and possibly within anaerobic microzones of settling organic matter, but MeHg (CH₃Hg⁺) and Me₂Hg ((CH₃)₂Hg) have been shown to form also in surface water samples from the euphotic zone. Future studies may disclose whether several different pathways lead to Hg methylation in marine waters and explain why Me₂Hg is a significant Hg species in oceans but seemingly not in most freshwaters.