Magnetococcus Marinus Research Articles

Energy calculations for sodium vs. potassium on a prokaryotic voltage-gated sodium channel: a quantum-chemical study

The selectivity of the sodium channel has been the subject of numerous experimental and theoretical studies. In this work, this problem is approached from a theoretical point of view based on a model built from the Selective Filter (SF) of the open structure of the voltage-activated channel of the bacterium Magnetococcus marinus. This approach has allowed us to calculate the interaction energies of the system (cation-water-SF-fragment), both for the sodium cation and the potassium cation. The results have highlighted the importance of differential dehydration of cations, as well as the environment where it occurs. Semi-empirical and ab initio methods have been applied to analyze and quantify the interaction energies when the cations are in the SF of the sodium channel, with the DFT (ab initio) methods giving us the key to the distribution of the interaction energies and therefore how dehydration occurs.

MAb-Functionalized Biomimetic MamC-Mediated-Magnetoliposomes as Drug Delivery Systems for Cancer Therapy.

In cancer therapy, new therapeutic nanoformulations able to mediate targeted chemotherapy are required. Recently, biomimetic magnetic nanoparticles (BMNPs) mediated by MamC, a magnetosome protein from Magnetococcus marinus MC-1, have proven, in vitro and in vivo, to be effective drug nanocarriers (following the application of an external gradient magnetic field) and to allow combination with hyperthermia. However, these nanoassemblies require further optimization to improve cytocompatibility, stability and active targeting ability. Herein, we describe the production of the magnetoliposomes (LP) embedding BMNPs functionalized (or not) with doxorubicin (DOXO), [LP(+/-DOXO-BMNPs)], and their surface modification with the DO-24 mAb, which targets the human Met/HGF receptor's ectodomain (overexpressed in many cancers). Nanoformulations were extensively characterized using TEM, DLS, FTIR and when tested in vitro, the lipid coating increased the colloidal stability and their biocompatibility, favoring the cellular uptake in cells overexpressing the cognate receptor. Indeed, the magnetoliposomes mAb-LP(+/-DOXO-BMNPs) exerted a specific active targeting ability by the presence of the mAb that preserved its immunocompetence. Both LP(BMNPs) and mAb-LP(BMNPs) were not toxic to cells, while +/-mAb-LP(DOXO-BMNPs) nanoformulations were indeed cytotoxic. Therefore, this study represents a proof of concept for the development of promising drug carriers for cancer therapy based on local chemotherapy directed by mAbs.

Self-transport of swimming bacteria is impaired by porous microstructure

Motility is a fundamental survival strategy of bacteria to navigate porous environments, where they mediate essential biogeochemical processes in quiescent wetlands and sediments. However, a comprehensive understanding of the mechanisms regulating self-transport in the confined interstices of porous media is lacking, and determining the interactions between cells and surfaces of the solid matrix becomes paramount. Here, we precisely track the movement of bacteria (Magnetococcus marinus) through a series of microfluidic porous media with broadly varying geometries and show how successive scattering events from solid surfaces decorrelate cell motion. Ordered versus disordered media impact the cells’ motility over short ranges, but their large-scale transport properties are regulated by the cutoff of their persistent motility. An effective mean free path is established as the key geometrical parameter controlling cell transport, and we implement a theoretical model that universally predicts the effective cell diffusion for the diverse geometries studied here. These results aid in our understanding of the physical ecology of swimming cells, and their role in environmental and health hazards in stagnant porous media.

A numerical method for the locomotion of bi-flagellated bacteria in viscous fluid

Flagellated bacteria propel themselves by rotating flexible flagella driven by independent motors. Depending on the rotation direction of the motors and the handedness of the helical filaments, the flagella either pull or push the cell body. Motivated by experimental observations of Magnetococcus marinus, we develop an elastohydrodynamic model to study the locomotion of a bi-flagellated bacterium with one puller flagellum and one pusher flagellum. In this model, the boundary integral technique and Kirchhoff rod model are employed respectively to calculate the hydrodynamic forces on the swimmer and model the elastic deformations of the flagella. Our numerical results demonstrate that the model bacterium travels along a double helical trajectory, which is consistent with the experimental observations. Varying the stiffness, orientations or positions of the flagella significantly changes the swimming characteristics. Notably, when either the applied torque is higher than a critical value or the flagellum stiffness is lower than a critical stiffness, the pusher flagellum exhibits overwhirling motion, resulting in a more complicated swimming style and a lower swimming speed. For a moderate flagellum stiffness, the swimming speed is insensitive to the rest configuration orientation over a wide range of orientation angles as the flagella deform to maintain alignment with the swimming direction.

Open state of bacterial sodium channel: insights from molecular dynamics simulations

Voltage gated sodium channels are membrane proteins that play an important role in propagating action potentials in excitable cells. In response to changes in the potential difference across the membrane, these channels cycle through three main functional states - resting, open and inactivated state. Thanks to advances in structural biology, the structures of the bacterial sodium channel from Magnetococcus marinus (NavMS) and Arcobacter butzleri (NavAB) have been captured in different functional states.

Selective Photoinduced Dimerization and Slow Recovery of a BLUF Domain of EB1.

The EAL-BLUF fragment from Magnetococcus marinus BldP1 (EB1) light-dependently hydrolyzes c-di-GMP. Herein, the photoreaction of the BLUF domain of EB1 (eBLUF) is studied. It is found for the first time that a monomeric BLUF domain forms a dimer upon illumination and its dark recovery is very slow. The dimer of light- and dark-state protomers (LD-dimer) is much more stable than that of two light-state protomers (LL-dimer), and the dark recovery of the LD-dimer is approximately 20 times slower than that of the LL-dimer, which is suitable for optogenetic tools. The secondary structure of the L-monomer is different from those of the D-monomer and the LD-dimer. The transient grating measurements reveal that this conformational change occurs simultaneously with dimerization. Although the W91A mutant exhibits a spectral red shift, it forms a heterodimer with the L-monomer of wild-type eBLUF with similar stability to the LD-dimer. This suggests that the conformation of the dimerization site of W91A is similar to that of the dark state (dark-mimic mutant); that is, the light-induced structural changes in the chromophore cavity are not transferred to the other part of the protein. The selective photoinduced dimerization of eBLUF is potentially useful to control interprotein interactions between two different effector domains bound to these proteins.

An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing asparagine

Voltage-gated sodium (Nav) channels play critical roles in propagating action potentials and otherwise manipulating ionic gradients in excitable cells. These channels open in response to membrane depolarization, selectively permeating sodium ions until rapidly inactivating. Structural characterization of the gating cycle in this channel family has proved challenging, particularly due to the transient nature of the open state. A structure from the bacterium Magnetococcus marinus Nav (NavMs) was initially proposed to be open, based on its pore diameter and voltage-sensor conformation. However, the functional annotation of this model, and the structural details of the open state, remain disputed. In this work, we used molecular modeling and simulations to test possible open-state models of NavMs. The full-length experimental structure, termed here the α-model, was consistently dehydrated at the activation gate, indicating an inability to conduct ions. Based on a spontaneous transition observed in extended simulations, and sequence/structure comparison to other Nav channels, we built an alternative π-model featuring a helix transition and the rotation of a conserved asparagine residue into the activation gate. Pore hydration, ion permeation, and state-dependent drug binding in this model were consistent with an open functional state. This work thus offers both a functional annotation of the full-length NavMs structure and a detailed model for a stable Nav open state, with potential conservation in diverse ion-channel families.

Patterns of bacterial motility in microfluidics-confining environments

Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures (Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic environments presenting various levels of confinement and geometrical complexity, in the absence of external flow and concentration gradients. When the confinement is moderate, such as in quasi-open spaces with only one limiting wall, and in wide channels, the motility behavior of bacteria with complex flagellar architectures approximately follows the hydrodynamics-based predictions developed for simple monotrichous bacteria. Specifically, V. natriegens and V. fischeri moved parallel to the wall and P. putida and E. coli presented a stable movement parallel to the wall but with incidental wall escape events, while M. marinus exhibited frequent flipping between wall accumulator and wall escaper regimes. Conversely, in tighter confining environments, the motility is governed by the steric interactions between bacteria and the surrounding walls. In mesoscale regions, where the impacts of hydrodynamics and steric interactions overlap, these mechanisms can either push bacteria in the same directions in linear channels, leading to smooth bacterial movement, or they could be oppositional (e.g., in mesoscale-sized meandered channels), leading to chaotic movement and subsequent bacterial trapping. The study provides a methodological template for the design of microfluidic devices for single-cell genomic screening, bacterial entrapment for diagnostics, or biocomputation.

Improving the Cellular Uptake of Biomimetic Magnetic Nanoparticles.

Magnetococcus marinus magnetosome-associated protein MamC, expressed as recombinant, has been proven to mediate the formation of novel biomimetic magnetic nanoparticles (BMNPs) that are successful drug nanocarriers for targeted chemotherapy and hyperthermia agents. These BMNPs present several advantages over inorganic magnetic nanoparticles, such as larger sizes that allow the former to have larger magnetic moment per particle, and an isoelectric point at acidic pH values, which allows both the stable functionalization of BMNPs at physiological pH value and the molecule release at acidic (tumor) environments, simply based on electrostatic interactions. However, difficulties for BMNPs cell internalization still hold back the efficiency of these nanoparticles as drug nanocarriers and hyperthermia agents. In the present study we explore the enhanced BMNPs internalization following upon their encapsulation by poly (lactic-co-glycolic) acid (PLGA), a Food and Drug Administration (FDA) approved molecule. Internalization is further optimized by the functionalization of the nanoformulation with the cell-penetrating TAT peptide (TATp). Our results evidence that cells treated with the nanoformulation [TAT-PLGA(BMNPs)] show up to 80% more iron internalized (after 72 h) compared to that of cells treated with BMNPs (40%), without any significant decrease in cell viability. This nanoformulation showing optimal internalization is further characterized. In particular, the present manuscript demonstrates that neither its magnetic properties nor its performance as a hyperthermia agent are significantly altered due to the encapsulation. In vitro experiments demonstrate that, following upon the application of an alternating magnetic field on U87MG cells treated with BMNPs and TAT-PLGA(BMNPs), the cytotoxic effect of BMNPs was not affected by the TAT-PLGA enveloping. Based on that, difficulties shown in previous studies related to poor cell uptake of BMNPs can be overcome by the novel nanoassembly described here.

Light-driven carbon−carbon bond formation via CO2 reduction catalyzed by complexes of CdS nanorods and a 2-oxoacid oxidoreductase

Redox enzymes are capable of catalyzing a vast array of useful reactions, but they require redox partners that donate or accept electrons. Semiconductor nanocrystals provide a mechanism to convert absorbed photon energy into redox equivalents for enzyme catalysis. Here, we describe a system for photochemical carbon-carbon bond formation to make 2-oxoglutarate by coupling CO2 with a succinyl group. Photoexcited electrons from cadmium sulfide nanorods (CdS NRs) transfer to 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus MC-1 (MmOGOR), which catalyzes a carbon-carbon bond formation reaction. We thereby decouple MmOGOR from its native role in the reductive tricarboxylic acid cycle and drive it directly with light. We examine the dependence of 2-oxoglutarate formation on a variety of factors and, using ultrafast transient absorption spectroscopy, elucidate the critical role of electron transfer (ET) from CdS NRs to MmOGOR. We find that the efficiency of this ET depends strongly on whether the succinyl CoA (SCoA) cosubstrate is bound at the MmOGOR active site. We hypothesize that the conformational changes due to SCoA binding impact the CdS NR-MmOGOR interaction in a manner that decreases ET efficiency compared to the enzyme with no cosubstrate bound. Our work reveals structural considerations for the nano-bio interfaces involved in light-driven enzyme catalysis and points to the competing factors of enzyme catalysis and ET efficiency that may arise when complex enzyme reactions are driven by artificial light absorbers.

Magnetoliposomes of mixed biomimetic and inorganic magnetic nanoparticles as enhanced hyperthermia agents

Recently, liposomes have been explored as a potential solution to improve the biocompatibility and the colloidal stability of magnetic nanoparticles. Protocols have been developed for producing magnetoliposomes of magnetite nanoparticles obtained inorganically (MNPs). However, the biomimetic synthesis of magnetite using heterologous proteins from magnetotactic bacteria has become a real alternative to produce novel biomimetic magnetic nanoparticles (BMNPs). Among these, the BMNPs obtained in presence of MamC protein from Magnetococcus marinus MC-1 have been proposed as excellent candidates to be potentially used as drug nanocarriers and as hyperthermia agents. However, their colloidal stability still needs to be improved while maintaining their magnetic properties intact. One possibility explored in this manuscript is to form magnetoliposomes that contain BMNPs. Indeed, the protocols developed for producing magnetoliposomes of MNPs need to be tested and modified to be able to include BMNPs. In this context, a protocol has been developed to produce both magnetoliposomes filled with MNPs and/or BMNPs and their potential as hyperthermia agents was tested. In fact, for the first time, these two types of nanoparticles were mixed in different proportions to test the composition that would optimize such as behaviour as hyperthermia agents. Interestingly, it was observed that the hyperthermia behaviour of the magnetoliposomes greatly improved if they were filled with a mixture of MNPs and BMNPs. These results indicate that these magnetoliposomes display optimal characteristics to become a potential agent for hyperthermia and that the opening of those liposomes could be externally controlled by applying an alternate magnetic field.

Tuning properties of biomimetic magnetic nanoparticles by combining magnetosome associated proteins

The role of magnetosome associated proteins on the in vitro synthesis of magnetite nanoparticles has gained interest, both to obtain a better understanding of the magnetosome biomineralization process and to be able to produce novel magnetosome-like biomimetic nanoparticles. Up to now, only one recombinant protein has been used at the time to in vitro form biomimetic magnetite precipitates, being that a scenario far enough from what probably occurs in the magnetosome. In the present study, both Mms6 and MamC from Magnetococcus marinus MC-1 have been used to in vitro form biomimetic magnetites. Our results show that MamC and Mms6 have different, but complementary, effects on in vitro magnetite nucleation and growth. MamC seems to control the kinetics of magnetite nucleation while Mms6 seems to preferably control the kinetics for crystal growth. Our results from the present study also indicate that it is possible to combine both proteins to tune the properties of the resulting biomimetic magnetites. In particular, by changing the relative ratio of these proteins, better faceted and/or larger magnetite crystals with, consequently, different magnetic moment per particle could be obtained. This study provides with tools to obtain new biomimetic nanoparticles with a potential utility for biotechnological applications.

A Reverse TCA Cycle 2-Oxoacid:Ferredoxin Oxidoreductase that Makes C-C Bonds from CO2

2-oxoglutarate:ferredoxin oxidoreductase (OGOR) is a thiamine pyrophosphate (TPP) and [4Fe-4S] cluster-dependent enzyme from the reductive tricarboxylic acid (rTCA) cycle that fixes CO2 to succinyl-CoA, forming 2-oxoglutarate and CoA. Here we report an OGOR from the rTCA cycle of Magnetococcus marinus MC-1, along with all three potential ferredoxin (Fd) redox partners. We demonstrate MmOGOR operates bidirectionally (both CO2-fixing and 2-oxoglutarate oxidizing), and that only one Fd (MmFd1) supports efficient catalysis. Our 1.94-Å and 2.80-Å resolution crystal structures of native and substrate-bound forms of MmOGOR reveal the determinants of substrate specificity and CoA-binding in an OGOR, and illuminate the [4Fe-4S] cluster environment, portraying the electronic conduit allowing MmFd1 to be wired to the bound-TPP. Structural and biochemical data further identify Glu45α as a mobile residue that impacts catalytic bias toward CO2-fixation although it makes no direct contact with TPP-bound intermediates, indicating that reaction directionality can be tuned by second layer interactions. (149 of 150 words limit).

Diversity of bacterial communities in the rhizosphere of the endangered plant, Paeonia jishanensis

The microbial community in the rhizosphere is thought to provide plants with a second set of genomes, which plays a pivotal role in plant growth. In the present study, soil samples were collected from the rhizosphere of an endangered plant, Paeonia jishanensis. The plants were divided into three groups: well-growing plants, poor-growing plants and dead plants. Metagenomic DNA was isolated from rhizosphere soil samples of these plants and 16S rRNA genes were sequenced by the PacBio-RS II system. The results of taxonomic analysis showed that the dominant phyla were Proteobacteria, Acidobacteria, Planctomycetes, Bacteroidetes and Actinobacteria in all three sample types. Linear discriminate analysis Effect Size (LEfSe) showed that 5 species, Hirschia baltica, Arcobacter aquimarinus, Gimesia maris, Magnetococcus marinus and Pseudoxanthobactor soli, were significantly enriched in the rhizosphere of well-growing plants. Additionally, the results of PCA, MDS and clustering analysis indicated that the bacterial community in the rhizosphere of living P. jishanensis plants was similar. With the death of plants, the bacterial community changed considerably. These findings suggest that the abundance of many beneficial rhizospheric microbes declined with the death of P. jishanensis. This is a potential way to preserve endangered plants by inoculating declining species with beneficial microbes.

PH-Dependent Adsorption Release of Doxorubicin on MamC-Biomimetic Magnetite Nanoparticles.

New biomimetic magnetite nanoparticles (hereafter BMNPs) with sizes larger than most common superparamagnetic nanoparticles were produced in the presence of the recombinant MamC protein from Magnetococcus marinus MC-1 and functionalized with doxorubicin (DOXO) intended as potential drug nanocarriers. Unlike inorganic magnetite nanoparticles, in BMNPs the MamC protein controls their size and morphology, providing them with magnetic properties consistent with a large magnetic moment per particle; moreover, it provides the nanoparticles with novel surface properties. BMNPs display the isoelectric point at pH 4.4, being strongly negatively charged at physiological pH (pH 7.4). This allows both (i) their functionalization with DOXO, which is positively charged at pH 7.4, and (ii) the stability of the DOXO-surface bond and DOXO release to be pH dependent and governed by electrostatic interactions. DOXO adsorption follows a Langmuir-Freundlich model, and the coupling of DOXO to BMNPs (binary biomimetic nanoparticles) is very stable at physiological pH (maximum release of 5% of the drug adsorbed). Conversely, when pH decreases, these electrostatic interactions weaken, and at pH 5, DOXO is released up to ∼35% of the amount initially adsorbed. The DOXO-BMNPs display cytotoxicity on the GTL-16 human gastric carcinoma cell line in a dose-dependent manner, reaching about ∼70% of mortality at the maximum amount tested, while the nonloaded BMNPs are fully cytocompatible. The present data suggest that BMNPs could be useful as potential drug nanocarriers with a drug adsorption-release governed by changes in local pH values.

Comparisons of voltage-gated sodium channel structures with open and closed gates and implications for state-dependent drug design.

Voltage-gated sodium channels (Navs) are responsible for the initiation of the action potential in excitable cells. Several prokaryotic sodium channels, most notably NavMs from Magnetococcus marinus and NavAb from Arcobacter butzleri, have been shown to be good models for human sodium channels based on their sequence homologies and high levels of functional similarities, including ion flux, and functional consequences of critical mutations. The complete full-length crystal structures of these prokaryotic sodium channels captured in different functional states have now revealed the molecular natures of changes associated with the gating process. These include the structures of the intracellular gate, the selectivity filter, the voltage sensors, the intra-membrane fenestrations, and the transmembrane (TM) pore. Here we have identified for the first time how changes in the fenestrations in the hydrophobic TM region associated with the opening of the intracellular gate could modulate the state-dependent ingress and binding of drugs in the TM cavity, in a way that could be exploited for rational drug design.

Magnetic Guidance [Microwave Surfing

Examines whether magnetic bacteria will provide a potential role in medicine. Normally, one thinks of bacteria as a source of medical problems, e.g., infections, rather than a part of the solution. But, as a team of researchers from Montreal, Canada, has recently demonstrated, swarms of specialized magnetic bacteria, the Magnetococcus marinus strain MC-1, may someday be harnessed in the battle against cancer. The MC-1 bacteria, found in saltwater estuaries in the northern hemisphere, use their internal “compass needles” and the Earth’s geomagnetic field to point themselves toward deeper hypoxic (low-oxygen-concentration) water, their preferred habitat. It is this affinity for hypoxic environments that makes these bacteria particularly useful in targeting tumors.

Magnetite Nanoparticles Biomineralization in the Presence of the Magnetosome Membrane Protein MamC: Effect of Protein Aggregation and Protein Structure on Magnetite Formation

MamC from Magnetococcus marinus MC-1 has been shown to control the size of magnetite crystals in in vitro experiments, thereby demonstrating its potential as a candidate protein for the production of magnetite nanoparticles possibly useful in medical and other applications. However, the importance of the structure and aggregation state of the protein on the resulting biomimetic nanoparticles has not yet been assessed. One method normally used to prevent the aggregation of integral membrane proteins is the introduction of detergents during protein purification. In this study, results from protein aggregation following the addition of Triton-X100, DDM, and LDAO are presented. Magnetite particles formed in the presence of MamC purified using these three detergents were compared. Our results show that detergents alter the structure of the folded recombinant protein, thus preventing the ability of MamC to control the size of magnetite crystals formed chemically in vitro. Furthermore, we show that the introduct...

Oriented Circular Dichroism Spectroscopy as a Tool for Studying the Gating of Sodium Channels

Voltage Gated Sodium Channels (Navs) are important pharmacological targets as the sight of action for local anaesthetics, anti-arrhythmic and anticonvulsants. While drugs may be used to individually target conditions they have little specificity for the subtypes of different tissues, this is explained by a state-dependant binding. The Nav from Magnetococcus marinus, NavMs, has proven to be a useful model for studying eukaryotic Navs, sharing both homology and relevant pharmacology; furthermore, it can be obtained with a yield and purity required for structural and biophysical studies. While the binding of ligands to both eukaryotic and Navs has been inferred by electrophysiology there is little information on the state or conformation of drug-bound channels. We are developing Oriented Synchrotron Radiation Circular Dichroism (oSRCD) spectroscopy as a method for examining the conformational changes of NavMs that occur upon ligand binding. The spectra of oriented samples of helical membrane proteins are dependent upon the angle the transmembrane helices make relative to the incident light beam. Monitoring changes in their spectra can inform on angular changes of the pore lining helices associated with channel gating as a result of external stimuli such as ligand binding.

The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria.

Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared with other bacterial taxonomic groups remain to be illustrated. Here, we analysed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1. Detailed analyses of the ribosomal proteins and whole proteomes of 390 genomes reveal that, among the Proteobacteria analysed, only MO-1 and MC-1 have coding sequences (CDSs) with a similarly high proportion of origins from Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria and Gammaproteobacteria. Interestingly, a comparative metabolic network analysis with anoxic network enzymes from sequenced MTB and non-MTB successfully allows the eventual prediction of an organism with a metabolic profile compatible for magnetosome production. Altogether, our genomic analysis reveals multiple origins of MO-1 and M. marinus MC-1 genomes and suggests a metabolism-restriction model for explaining whether a bacterium could become an MTB upon acquisition of magnetosome encoding genes.