MamA as a Model Protein for Structure-Based Insight into the Evolutionary Origins of Magnetotactic Bacteria

Gas and light: triggers of c-di-GMP-mediated regulation

The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.

A review of the ecology, genetics, evolution, and magnetosome –induced behaviours of the magnetotactic bacteria

The discovery of magnetosome and magnetotaxis in its most simple form in the magnetotactic bacteria (MTB) had created the tremendous impetus. MTB, spanning multiple phyla, are distributed worldwide, and they form the organelles called magnetosomes for biomineralization. Eight phylotypes of MTB belong to Alphaproteobacteria and Nitrospirae. MTB show preference for specific redox and oxygen concentration. Magnetosome chains function as the internal compass needle and align the bacterial cells passively along the local geomagnetic field (GMF). The nature of magnetosomes produced by MTB and their phylogeny suggest that bullet-shaped magnetites appeared about 3.2 billion years ago with the first magnetosomes. All MTB contains ten genes in conserved mamAB operon for magnetosome chain synthesis of which nine genes are conserved in greigite-producing MTB. Many candidate genes identify the aero-, redox-, and perhaps phototaxis. Among the prokaryotes, the MTB possess the highest number of O2-binding proteins. Magnetofossils serve as an indicator of oxygen and redox levels of the ancient environments. Most descendants of ancestral MTB lost the magnetosome genes in the course of evolution. Environmental conditions initially favored the evolution of MTB and expansion of magnetosome-formation genes. Subsequent changes in atmospheric oxygen concentration have led to changes in the ecology of MTB, loss of magnetosome genes, and evolution of nonMTB.

Expanding magnetic organelle biogenesis in the domain Bacteria

BACKGROUND

The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis.

RESULTS

Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria.

CONCLUSIONS

These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle. Video Abstract.

Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria

The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth's geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria IMPORTANCE A diversity of organisms can sense the geomagnetic field for the purpose of navigation. Magnetotactic bacteria are the most primitive magnetism-sensing organisms known thus far and represent an excellent model system for the study of the origin, evolution, and mechanism of microbial magnetoreception (or magnetotaxis). The present study is the first report focused on magnetosome gene cluster duplication in the Alphaproteobacteria, which suggests the important role of gene duplication in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria A novel scenario for the evolution of magnetotaxis in the Alphaproteobacteria is proposed and may provide new insights into evolution of magnetoreception of higher species.

Diversity and ecology of and biomineralization by magnetotactic bacteria

Magnetotactic bacteria (MTB) biomineralize intracellular, membrane-bounded crystals of magnetite (Fe₃ O₄ ) and/or greigite (Fe₃ S₄ ) called magnetosomes. MTB play important roles in the geochemical cycling of iron, sulfur, nitrogen and carbon. Significantly, they also represent an intriguing model system not just for the study of microbial biomineralization but also for magnetoreception, prokaryotic organelle formation and microbial biogeography. Here we review current knowledge on the ecology of and biomineralization by MTB, with an emphasis on more recent reports of unexpected ecological and phylogenetic findings regarding MTB. In this study, we conducted a search of public metagenomic databases and identified six novel magnetosome gene cluster-containing genomic fragments affiliated with the Deltaproteobacteria and Gammaproteobacteria classes of the Proteobacteria phylum, the Nitrospirae phylum and the Planctomycetes phylum from the deep subseafloor, marine oxygen minimum zone, groundwater biofilm and estuary sediment, thereby extending our knowledge on the diversity and distribution of MTB as well deriving important information as to their ecophysiology. We point out that the increasing availability of sequence data will facilitate researchers to systematically explore the ecology and biomineralization of MTB even further.

Four-stranded mini microtubules formed by Prosthecobacter BtubAB show dynamic instability

Microtubules, the dynamic, yet stiff hollow tubes built from αβ-tubulin protein heterodimers, are thought to be present only in eukaryotic cells. Here, we report a 3.6-Å helical reconstruction electron cryomicroscopy structure of four-stranded mini microtubules formed by bacterial tubulin-like Prosthecobacter dejongeii BtubAB proteins. Despite their much smaller diameter, mini microtubules share many key structural features with eukaryotic microtubules, such as an M-loop, alternating subunits, and a seam that breaks overall helical symmetry. Using in vitro total internal reflection fluorescence microscopy, we show that bacterial mini microtubules treadmill and display dynamic instability, another hallmark of eukaryotic microtubules. The third protein in the btub gene cluster, BtubC, previously known as "bacterial kinesin light chain," binds along protofilaments every 8 nm, inhibits BtubAB mini microtubule catastrophe, and increases rescue. Our work reveals that some bacteria contain regulated and dynamic cytomotive microtubule systems that were once thought to be only useful in much larger and sophisticated eukaryotic cells.

Yield cultivation of magnetotactic bacteria and magnetosomes: A review

Magnetotactic bacteria (MTB) have started to be employed for the biosynthesis of magnetic nanoparticles, due to the rapidly increasing demand for nanoparticles in biomedical, biotechnology and environmental protection. MBT are the group of prokaryotes that have the ability to produce bio-magnetic minerals or bio-magnetic crystals of either magnetite (Fe₃ O₄ ) or greigite (Fe₃ S₄ ) in numerous shapes and size ranges, known as magnetosomes (MS). MS compel MTB to respond to the applied external magnetic field. However, it is extremely difficult to grow MTB and produce high yield of MS under artificial environmental conditions, thus creating a major hurdle to relocate MTB technology from laboratory scale to industrial or commercial level. Therefore, to best of our knowledge this review is the first attempt to highlight existing research developments about the laboratory scale and mass production of MS by MTB. Moreover, the optimum culture media and environmental conditions used for the cultivation of MTB were also considered. Finally, future research is encouraged for the improvement of MS yield which will result in the development of advanced nanotechnology/magnetotechnology.

Origin of microbial biomineralization and magnetotaxis during the Archean

Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth's dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

A Look into the Biochemistry of Magnetosome Biosynthesis in Magnetotactic Bacteria

Magnetosomes are protein-rich membrane organelles that encapsulate magnetite or greigite and whose chain alignment enables magnetotactic bacteria (MTB) to sense the geomagnetic field. As these bacteria synthesize uniform magnetic particles, their biomineralization mechanism is of great interest among researchers from different fields, from material engineering to medicine. Both magnetosome formation and magnetic particle synthesis are highly controlled processes that can be divided into several crucial steps: membrane invagination from the inner-cell membrane, protein sorting, the magnetosomes' arrangement into chains, iron transport, chemical environment regulation of the magnetosome lumen, magnetic particle nucleation, and finally crystal growth, size, and morphology control. This complex system involves an ensemble of unique proteins that participate in different stages during magnetosome formation, some of which were extensively studied in recent years. Here, we present the current knowledge on magnetosome biosynthesis with a focus on the different proteins and the main biochemical pathways along this process.

A protein-protein interaction in magnetosomes: TPR protein MamA interacts with an Mms6 protein

Magnetosomes are membrane-enveloped bacterial organelles containing nano-sized magnetic particles, and function as a cellular magnetic sensor, which assist the cells to navigate and swim along the geomagnetic field. Localized with each magnetosome is a suite of proteins involved in the synthesis, maintenance and functionalization of the organelle, however the detailed molecular organization of the proteins in magnetosomes is unresolved. MamA is one of the most abundant magnetosome-associated proteins and is anchored to the magnetosome vesicles through protein-protein interactions, but the identity of the protein that interacts with MamA is undetermined. In this study, we found that MamA binds to a magnetosome membrane protein Mms6. Two different molecular masses of Mms6, 14.5-kDa and 6.0-kDa, were associated with the magnetosomes. Using affinity chromatography, we identified that the 14.5-kDa Mms6 interacts with MamA, and the interaction was further confirmed by pull-down, immunoprecipitation and size-exclusion chromatography assays. Prior to this, Mms6 was assumed to be strictly involved with biomineralizing magnetite; however, these results suggest that Mms6 has an additional responsibility, binding to MamA.

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New advance in the 20-year history of MamA.

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Two types of Mms6 exist in the magnetosome membrane, 14.5-kDa and 6.0-kDa versions.

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Mms6 is the binding partner of a TPR protein (MamA) in magnetosome.

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Describes a new role for Mms6 in magnetotactic bacteria.

From invagination to navigation: The story of magnetosome-associated proteins in magnetotactic bacteria

Magnetotactic bacteria (MTB) are a group of Gram-negative microorganisms that are able to sense and change their orientation in accordance with the geomagnetic field. This unique capability is due to the presence of a special suborganelle called the magnetosome, composed of either a magnetite or gregite crystal surrounded by a lipid membrane. MTB were first detected in 1975 and since then numerous efforts have been made to clarify the special mechanism of magnetosome formation at the molecular level. Magnetosome formation can be divided into several steps, beginning with vesicle invagination from the cell membrane, through protein sorting, followed by the combined steps of iron transportation, biomineralization, and the alignment of magnetosomes into a chain. The magnetosome-chain enables the sensing of the magnetic field, and thus, allows the MTB to navigate. It is known that magnetosome formation is tightly controlled by a distinctive set of magnetosome-associated proteins that are encoded mainly in a genomically conserved region within MTB called the magnetosome island (MAI). Most of these proteins were shown to have an impact on the magnetism of MTB. Here, we describe the process in which the magnetosome is formed with an emphasis on the different proteins that participate in each stage of the magnetosome formation scheme.