A Compass To Boost Navigation: Cell Biology of Bacterial Magnetotaxis

Trapping and scattering of a multiflagellated bacterium by a hard surface

Thiovulum majus, which is one of the fastest known bacteria, swims using hundreds of flagella. Unlike typical pusher cells, which swim in circular paths over hard surfaces, T. majus localize near hard boundaries by turning their flagella to exert a net force normal to the surface. To probe the torques that stabilize this hydrodynamically bound state, the trajectories of several thousand collisions between a T. majus cell and a wall of a quasi-two-dimensional microfluidic chamber are analyzed. Measuring the fraction of cells escaping the wall either to the left or to the right of the point of contact-and how this probability varies with incident angle and time spent in contact with the surface-maps the scattering dynamics onto a first passage problem. These measurements are compared to the prediction of a Fokker-Planck equation to fit the angular velocity of a cell in contact with a hard surface. This analysis reveals a bound state with a narrow basin of attraction in which cells orient their flagella normal to the surface. The escape angle predicted by matching these near field dynamics with the far-field hydrodynamics is consistent with observation. We discuss the significance of these results for the ecology of T. majus and their self-organization into active chiral crystals.

Magnetosomes as Potential Nanocarriers for Cancer Treatment

Magnetotactic bacteria (MTBs) and their organelles, magnetosomes, are intriguing options that might fulfill the criteria of using bacterial magnetosomes (BMs). The ferromagnetic crystals contained in BMs can condition the magnetotaxis of MTBs, which is common in water storage facilities. This review provides an overview of the feasibility of using MTBs and BMs as nanocarriers in cancer treatment. More evidence suggests that MTBs and BMs can be used as natural nanocarriers for conventional anticancer medicines, antibodies, vaccine DNA, and siRNA. In addition to improving the stability of chemotherapeutics, their usage as transporters opens the possibilities for the targeted delivery of single ligands or combinations of ligands to malignant tumors. Magnetosome magnetite crystals are different from chemically made magnetite nanoparticles (NPs) because they are strong single-magnetic domains that stay magnetized even at room temperature. They also have a narrow size range and a uniform crystal morphology. These chemical and physical properties are essential for their usage in biotechnology and nanomedicine. Bioremediation, cell separation, DNA or antigen regeneration, therapeutic agents, enzyme immobilization, magnetic hyperthermia, and contrast enhancement of magnetic resonance are just a few examples of the many uses for magnetite-producing MTB, magnetite magnetosomes, and magnetosome magnetite crystals. From 2004 to 2022, data mining of the Scopus and Web of Science databases showed that most research using magnetite from MTB was carried out for biological reasons, such as in magnetic hyperthermia and drug delivery.

Phenomic and transcriptomic analyses reveal the sequential synthesis of Fe3O4 nanoparticles in Acidithiobacillus ferrooxidans BYM

IMPORTANCE

As the most important non-magnetotactic magnetosome-producing bacteria, Acidithiobacillus ferrooxidans only requires very mild conditions to produce Fe3O4 nanoparticles, thus conferring greater flexibility and potential application in biomagnetic nanoparticle production. However, the available information cannot explain the mechanism of Fe3O4 nanoparticle formation in A. ferrooxidans. In this study, we applied phenomic and transcriptomic analyses to reveal this mechanism. We found that different treatment condition factors notably affect the phenomic data of Fe3O4 nanoparticle in A. ferrooxidans. Using transcriptomic analyses, the gene network controlling/regulating Fe3O4 nanoparticle biogenesis in A. ferrooxidans was proposed, excavating the candidate hub genes for Fe3O4 nanoparticle formation in A. ferrooxidans. Based on this information, a sequential model for Fe3O4 nanoparticle synthesis in A. ferrooxidans was hypothesized. It lays the groundwork for further clarifying the feature of Fe3O4 nanoparticle synthesis.

Experimental analysis of diverse actin-like proteins from various magnetotactic bacteria by functional expression in Magnetospirillum gryphiswaldense

IMPORTANCE

To efficiently navigate within the geomagnetic field, magnetotactic bacteria (MTB) align their magnetosome organelles into chains, which are organized by the actin-like MamK protein. Although MamK is the most highly conserved magnetosome protein common to all MTB, its analysis has been confined to a small subgroup owing to the inaccessibility of most MTB. Our study takes advantage of a genetically tractable host where expression of diverse MamK orthologs together with a resurrected MamK LUCA and uncharacterized actin-like Mad28 proteins from deep-branching MTB resulted in gradual restoration of magnetosome chains in various mutants. Our results further indicate the existence of species-specific MamK interactors and shed light on the evolutionary relationships of one of the key proteins associated with bacterial magnetotaxis.

Renaissance for magnetotactic bacteria in astrobiology

Capable of forming magnetofossils similar to some magnetite nanocrystals observed in the Martian meteorite ALH84001, magnetotactic bacteria (MTB) once occupied a special position in the field of astrobiology during the 1990s and 2000s. This flourish of interest in putative Martian magnetofossils faded from all but the experts studying magnetosome formation, based on claims that abiotic processes could produce magnetosome-like magnetite crystals. Recently, the rapid growth in our knowledge of the extreme environments in which MTB thrive and their phylogenic heritage, leads us to advocate for a renaissance of MTB in astrobiology. In recent decades, magnetotactic members have been discovered alive in natural extreme environments with wide ranges of salinity (up to 90 g L-1), pH (1-10), and temperature (0-70 °C). Additionally, some MTB populations are found to be able to survive irradiated, desiccated, metal-rich, hypomagnetic, or microgravity conditions, and are capable of utilizing simple inorganic compounds such as sulfate and nitrate. Moreover, MTB likely emerged quite early in Earth's history, coinciding with a period when the Martian surface was covered with liquid water as well as a strong magnetic field. MTB are commonly discovered in suboxic or oxic-anoxic interfaces in aquatic environments or sediments similar to ancient crater lakes on Mars, such as Gale crater and Jezero crater. Taken together, MTB can be exemplary model microorganisms in astrobiology research, and putative ancient Martian life, if it ever occurred, could plausibly have included magnetotactic microorganisms. Furthermore, we summarize multiple typical biosignatures that can be applied for the detection of ancient MTB on Earth and extraterrestrial MTB-like life. We suggest transporting MTB to space stations and simulation chambers to further investigate their tolerance potential and distinctive biosignatures to aid in understanding the evolutionary history of MTB and the potential of magnetofossils as an extraterrestrial biomarker.

Functional expression of foreign magnetosome genes in the alphaproteobacterium Magnetospirillum gryphiswaldense

Magnetosomes of magnetotactic bacteria (MTB) consist of structurally perfect, nano-sized magnetic crystals enclosed within vesicles of a proteo-lipid membrane. In species of Magnetospirillum, biosynthesis of their cubo-octahedral-shaped magnetosomes was recently demonstrated to be a complex process, governed by about 30 specific genes that are comprised within compact magnetosome gene clusters (MGCs). Similar, yet distinct gene clusters were also identified in diverse MTB that biomineralize magnetosome crystals with different, genetically encoded morphologies. However, since most representatives of these groups are inaccessible by genetic and biochemical approaches, their analysis will require the functional expression of magnetosome genes in foreign hosts. Here, we studied whether conserved essential magnetosome genes from closely and remotely related MTB can be functionally expressed by rescue of their respective mutants in the tractable model Magnetospirillum gryphiswaldense of the Alphaproteobacteria. Upon chromosomal integration, single orthologues from other magnetotactic Alphaproteobacteria restored magnetosome biosynthesis to different degrees, while orthologues from distantly related Magnetococcia and Deltaproteobacteria were found to be expressed but failed to re-induce magnetosome biosynthesis, possibly due to poor interaction with their cognate partners within multiprotein magnetosome organelle of the host. Indeed, co-expression of the known interactors MamB and MamM from the alphaproteobacterium Magnetovibrio blakemorei increased functional complementation. Furthermore, a compact and portable version of the entire MGCs of M. magneticum was assembled by transformation-associated recombination cloning, and it restored the ability to biomineralize magnetite both in deletion mutants of the native donor and M. gryphiswaldense, while co-expression of gene clusters from both M. gryphiswaldense and M. magneticum resulted in overproduction of magnetosomes. IMPORTANCE We provide proof of principle that Magnetospirillum gryphiswaldense is a suitable surrogate host for the functional expression of foreign magnetosome genes and extended the transformation-associated recombination cloning platform for the assembly of entire large magnetosome gene cluster, which could then be transplanted to different magnetotactic bacteria. The reconstruction, transfer, and analysis of gene sets or entire magnetosome clusters will be also promising for engineering the biomineralization of magnetite crystals with different morphologies that would be valuable for biotechnical applications.

Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium

Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.

Live-Cell Fluorescence Imaging of Magnetosome Organelle for Magnetotaxis Motility

The assessment of intracellular dynamics is crucial for understanding the function and formation process of bacterial organelle, just as it is for the inquisition of their eukaryotic counterparts. The methods for imaging magnetosome organelles in a magnetotactic bacterial cell using live-cell fluorescence imaging by highly inclined and laminated optical sheet (HILO) microscopy are presented in this chapter. Furthermore, we introduce methods for pH imaging in magnetosome lumen as an application of fluorescence magnetosome imaging.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

The Magnetosome Protein, Mms6 from Magnetospirillum magneticum Strain AMB-1, Is a Lipid-Activated Ferric Reductase

Magnetosomes of magnetotactic bacteria consist of magnetic nanocrystals with defined morphologies enclosed in vesicles originated from cytoplasmic membrane invaginations. Although many proteins are involved in creating magnetosomes, a single magnetosome protein, Mms6 from Magnetospirillum magneticum strain AMB-1, can direct the crystallization of magnetite nanoparticles in vitro. The in vivo role of Mms6 in magnetosome formation is debated, and the observation that Mms6 binds Fe³⁺ more tightly than Fe²⁺ raises the question of how, in a magnetosome environment dominated by Fe³⁺, Mms6 promotes the crystallization of magnetite, which contains both Fe³⁺ and Fe²⁺. Here we show that Mms6 is a ferric reductase that reduces Fe³⁺ to Fe²⁺ using NADH and FAD as electron donor and cofactor, respectively. Reductase activity is elevated when Mms6 is integrated into either liposomes or bicelles. Analysis of Mms6 mutants suggests that the C-terminal domain binds iron and the N-terminal domain contains the catalytic site. Although Mms6 forms multimers that involve C-terminal and N-terminal domain interactions, a fusion protein with ubiquitin remains a monomer and displays reductase activity, which suggests that the catalytic site is fully in the monomer. However, the quaternary structure of Mms6 appears to alter the iron binding characteristics of the C-terminal domain. These results are consistent with a hypothesis that Mms6, a membrane protein, promotes the formation of magnetite in vivo by a mechanism that involves reducing iron.

Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals

Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.

Magnetic Particle Imaging of Magnetotactic Bacteria as Living Contrast Agents Is Improved by Altering Magnetosome Arrangement

Superparamagnetic iron oxide nanoparticles (SPIONs) can be used as imaging agents to differentiate between normal and diseased tissue or track cell movement. Magnetic particle imaging (MPI) detects the magnetic properties of SPIONs, providing quantitative and sensitive image data. MPI performance depends on the size, structure, and composition of nanoparticles. Magnetotactic bacteria produce magnetosomes with properties similar to those of synthetic nanoparticles, and these can be modified by mutating biosynthetic genes. The use of Magnetospirillum gryphiswaldense, MSR-1 with a mamJ deletion, containing clustered magnetosomes instead of typical linear chains, resulted in improved MPI signal and resolution. Bioluminescent MSR-1 with the mamJ deletion were administered into tumor-bearing and healthy mice. In vivo bioluminescence imaging revealed the viability of MSR-1, and MPI detected signals in livers and tumors. The development of living contrast agents offers opportunities for imaging and therapy with multimodality imaging guiding development of these agents by tracking the location, viability, and resulting biological effects.

Key Signatures of Magnetofossils Elucidated by Mutant Magnetotactic Bacteria and Micromagnetic Calculations

Magnetotactic bacteria (MTB) produce single-stranded or multi-stranded chains of magnetic nanoparticles that contribute to the magnetization of sediments and rocks. Their magnetic fingerprint can be detected in ancient geological samples and serve as a unique biosignature of microbial life. However, some fossilized assemblages bear contradictory signatures pointing to magnetic components that have distinct origin(s). Here, using micromagnetic simulations and mutant MTB producing looped magnetosome chains, we demonstrate that the observed magnetofossil fingerprints are produced by a mixture of single-stranded and multi-stranded chains, and that diagenetically induced chain collapse, if occurring, must preserve the strong uniaxial anisotropy of native chains. This anisotropy is the key factor for distinguishing magnetofossils from other populations of natural magnetite particles, including those with similar individual crystal characteristics. Furthermore, the detailed properties of magnetofossil signatures depend on the proportion of equant and elongated magnetosomes, as well as on the relative abundances of single-stranded and multi-stranded chains. This work has important paleoclimatic, paleontological, and phylogenetic implications, as it provides reference data to differentiate distinct MTB lineages according to their chain and magnetosome morphologies, which will enable the tracking of the evolution of some of the most ancient biomineralizing organisms in a time-resolved manner. It also enables a more accurate discrimination of different sources of magnetite particles, which is pivotal for gaining better environmental and relative paleointensity reconstructions from sedimentary records.

Current view of iron biomineralization in magnetotactic bacteria

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Iron biomineralization into magnetic nanoparticles by Magnetotactic bacteria (MTB).

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Magnetosome formation mechanism presented in four main steps.

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Magnetosome-associated proteins (MAPs) regulate the biomineralization process.

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Chain arrangement and crystals morphology Variations exist between different MTB.

Biomineralization is the process of mineral formation by living organisms. One notable example of these organisms is magnetotactic bacteria (MTB). MTB are Gram-negative bacteria that can biomineralize iron into magnetic nanoparticles. This ability allows these aquatic microorganisms to orient themselves according to the geomagnetic field. The biomineralization process takes place in a specialized sub-cellular membranous organelle, the magnetosome. The magnetosome contains a defined set of magnetosome-associated proteins (MAPs) that controls the biomineralization environment, including iron concentration, redox, and pH. Magnetite formation is subjected to a tight regulation within the magnetosome that affects the nanoparticle nucleation, size, and shape, leading to well-defined magnetic properties. The formed magnetite nanoparticles have unique characteristics of a stable, single magnetic domain with narrow size distribution and high crystalline structures, which turned MTB into the subject of interest in multidisciplinary research. This graphical review provides a current overview of iron biomineralization in magnetotactic bacteria, focusing on Alphaproteobacteria. To better understand this complex mechanism, we present the four main steps and the main MAPs participating in the process of magnetosome formation.

The Complex Transcriptional Landscape of Magnetosome Gene Clusters in Magnetospirillum gryphiswaldense

Magnetosomes are complex membrane organelles synthesized by magnetotactic bacteria (MTB) for navigation in the Earth’s magnetic field. In the alphaproteobacterium Magnetospirillum gryphiswaldense, all steps of magnetosome formation are tightly controlled by >30 specific genes arranged in several gene clusters. However, the transcriptional organization of the magnetosome gene clusters has remained poorly understood. Here, by applying Cappable-seq and whole-transcriptome shotgun RNA sequencing, we show that mamGFDCop and feoAB1op are transcribed as single transcriptional units, whereas multiple transcription start sites (TSS) are present in mms6op, mamXYop, and the long (>16 kb) mamABop. Using a bioluminescence reporter assay and promoter knockouts, we demonstrate that most of the identified TSS originate from biologically meaningful promoters which mediate production of multiple transcripts and are functionally relevant for proper magnetosome biosynthesis. In addition, we identified a strong promoter in a large intergenic region within mamXYop, which likely drives transcription of a noncoding RNA important for gene expression in this operon. In summary, our data suggest a more complex transcriptional architecture of the magnetosome operons than previously recognized, which is largely conserved in other magnetotactic Magnetospirillum species and, thus, is likely fundamental for magnetosome biosynthesis in these organisms.

IMPORTANCE Magnetosomes have emerged as a model system to study prokaryotic organelles and a source of biocompatible magnetic nanoparticles for various biomedical applications. However, the lack of knowledge about the transcriptional organization of magnetosome gene clusters has severely impeded the engineering, manipulation, and transfer of this highly complex biosynthetic pathway into other organisms. Here, we provide a high-resolution image of the previously unappreciated transcriptional landscape of the magnetosome operons. Our findings are important for further unraveling the complex genetic framework of magnetosome biosynthesis. In addition, they will facilitate the rational reengineering of magnetic bacteria for improved bioproduction of tunable magnetic nanoparticles, as well as transplantation of magnetosome biosynthesis into foreign hosts by synthetic biology approaches. Overall, our study exemplifies how a genetically complex pathway is orchestrated at the transcriptional level to ensure the balanced expression of the numerous constituents required for the proper assembly of one of the most intricate prokaryotic organelles.

Bioinspired Magnetic Nanochains for Medicine

Superparamagnetic iron oxide nanoparticles (SPIONs) have been widely used for medicine, both in therapy and diagnosis. Their guided assembly into anisotropic structures, such as nanochains, has recently opened new research avenues; for instance, targeted drug delivery. Interestingly, magnetic nanochains do occur in nature, and they are thought to be involved in the navigation and geographic orientation of a variety of animals and bacteria, although many open questions on their formation and functioning remain. In this review, we will analyze what is known about the natural formation of magnetic nanochains, as well as the synthetic protocols to produce them in the laboratory, to conclude with an overview of medical applications and an outlook on future opportunities in this exciting research field.

Induction of Axonal Outgrowth in Mouse Hippocampal Neurons via Bacterial Magnetosomes

Magnetosomes are membrane-enclosed iron oxide crystals biosynthesized by magnetotactic bacteria. As the biomineralization of bacterial magnetosomes can be genetically controlled, they have become promising nanomaterials for bionanotechnological applications. In the present paper, we explore a novel application of magnetosomes as nanotool for manipulating axonal outgrowth via stretch-growth (SG). SG refers to the process of stimulation of axonal outgrowth through the application of mechanical forces. Thanks to their superior magnetic properties, magnetosomes have been used to magnetize mouse hippocampal neurons in order to stretch axons under the application of magnetic fields. We found that magnetosomes are avidly internalized by cells. They adhere to the cell membrane, are quickly internalized, and slowly degrade after a few days from the internalization process. Our data show that bacterial magnetosomes are more efficient than synthetic iron oxide nanoparticles in stimulating axonal outgrowth via SG.

Towards a 'chassis' for bacterial magnetosome biosynthesis: genome streamlining of Magnetospirillum gryphiswaldense by multiple deletions

BACKGROUND

Because of its tractability and straightforward cultivation, the magnetic bacterium Magnetospirillum gryphiswaldense has emerged as a model for the analysis of magnetosome biosynthesis and bioproduction. However, its future use as platform for synthetic biology and biotechnology will require methods for large-scale genome editing and streamlining.

RESULTS

We established an approach for combinatory genome reduction and generated a library of strains in which up to 16 regions including large gene clusters, mobile genetic elements and phage-related genes were sequentially removed, equivalent to ~ 227.6 kb and nearly 5.5% of the genome. Finally, the fragmented genomic magnetosome island was replaced by a compact cassette comprising all key magnetosome biosynthetic gene clusters. The prospective 'chassis' revealed wild type-like cell growth and magnetosome biosynthesis under optimal conditions, as well as slightly improved resilience and increased genetic stability.

CONCLUSION

We provide first proof-of-principle for the feasibility of multiple genome reduction and large-scale engineering of magnetotactic bacteria. The library of deletions will be valuable for turning M. gryphiswaldense into a microbial cell factory for synthetic biology and production of magnetic nanoparticles.

Intrinsically Magnetic Cells: A Review on Their Natural Occurrence and Synthetic Generation

The magnetization of non-magnetic cells has great potential to aid various processes in medicine, but also in bioprocess engineering. Current approaches to magnetize cells with magnetic nanoparticles (MNPs) require cellular uptake or adsorption through in vitro manipulation of cells. A relatively new field of research is "magnetogenetics" which focuses on in vivo production and accumulation of magnetic material. Natural intrinsically magnetic cells (IMCs) produce intracellular, MNPs, and are called magnetotactic bacteria (MTB). In recent years, researchers have unraveled function and structure of numerous proteins from MTB. Furthermore, protein engineering studies on such MTB proteins and other potentially magnetic proteins, like ferritins, highlight that in vivo magnetization of non-magnetic hosts is a thriving field of research. This review summarizes current knowledge on recombinant IMC generation and highlights future steps that can be taken to succeed in transforming non-magnetic cells to IMCs.