Magnetite biomineralization and geomagnetic sensitivity in higher animals: an update and recommendations for future study

Magnetite, the only known biogenic material with ferromagnetic properties, has been identified as a biochemical precipitate in three of the five kingdoms of living organisms, with a fossil record that now extends back nearly 2 billion years. In the magnetotactic bacteria, protoctists, and fish, single-domain crystals of magnetite are arranged in membrane-bound linear structures called magnetosomes, which function as biological bar magnets. Magnetosomes in all three of these groups bear an overall structural similarity to each other, which includes alignment of the individual crystallographic [111] directions parallel to the long axis. Although the magnetosomes represent only a small volume fraction in higher organisms, enough of these highly energetic structures are present to provide sensitivity to extremely small fluctuations and gradients in the background geomagnetic field. Previous experiments with elasmobranch fish are reexamined to test the hypothesis that gradients played a role in their successful geomagnetic conditioning, and a variety of four-turn coil designs are considered that could be used to test the various hypotheses proposed for them.     

Gender-enriched transcription of activation associated secreted proteins in Ostertagia ostertagi

Activation associated secreted proteins (ASP) are members of a nematode-specific protein family belonging to the SCP/Tpx-1/Ag5/PR-1/Sc7 family. Three different types of molecules have been identified in this family: two-domain ASPs and single-domain ASPs showing homology to either the C-terminal or N-terminal domain of the two-domain ASP. The function of these proteins is still unclear, but a role in transition to parasitism and a role as allergen are often suggested. Here we report that the abomasal cattle parasite Ostertagia ostertagi produces at least 15 ASPs, including two-domain and C- and N-type single-domain ASPs. Ten of these are highly transcribed in the L4 stage, whereas others are highly enriched in adult male worms. The latter was especially the case for the N-type single-domain ASPs Oo-ASP1 and Oo-ASP2 and also for Oo-ASP3, which is homologous with the Haemonchus contortus and Ancylostoma caninum C-type single-domain ASPs. Immunohistochemistry showed that Oo-ASP3 was localised in the oesophagus. Oo-ASP1 and Oo-ASP2 on the other hand were localised in the reproductive tract of both male and female worms, suggesting a role in reproduction or in the development of the reproductive tract.     

Specificity of reversible ADP-ribosylation and regulation of cellular processes

Proper and timely regulation of cellular processes is fundamental to the overall health and viability of organisms across all kingdoms of life. Thus, organisms have evolved multiple highly dynamic and complex biochemical signaling cascades in order to adapt and survive diverse challenges. One such method of conferring rapid adaptation is the addition or removal of reversible modifications of different chemical groups onto macromolecules which in turn induce the appropriate downstream outcome. ADP-ribosylation, the addition of ADP-ribose (ADPr) groups, represents one of these highly conserved signaling chemicals. Herein we outline the writers, erasers and readers of ADP-ribosylation and dip into the multitude of cellular processes they have been implicated in. We also review what we currently know on how specificity of activity is ensured for this important modification.     

Algal Visual Proteins: An Evolutionary Point of View

Light is a major environmental signal controlling most life processes; hence, light perception is absolutely necessary for organisms that rely on light. In order to detect light, organisms evolved photoreceptors, which are found throughout all the kingdoms with enormous structural variations. Yet, the nature of the photoreceptor pigment is highly conserved, probably for the stringent conditions it has to satisfy. In prokaryotes such as the archaebacteria Halobacterium halobium and Natronobacterium pharaonis, the cell membrane provides an extensive surface on which membrane-spanning light-sensitive proteins are spread with a fixed bidimensional orientation for maximal effectiveness in photon capturing. In unicellular algae, a similar pigment-containing patch probably exists in the Chlorophyta, whereas more complex photoreceptors, such as three-dimensional crystals of membrane-spanning proteins, for example, may occur in the Euglenophyta and Chrysophyta. The superfamily of the seven membrane-spanning domains proteins is responsible for reception roles (chemoreception, mechanoreception, photoreception), and one of these proteins (i.e., rhodopsin) is responsible for photoreception and vision. Therefore, we could reasonably expect it or its homologues to be found in any group of living organisms that manifests photobehavior. Indications of the presence of rhodopsin in all the domains are emerging; therefore, we consider experimental evidence that bears out this theory on organisms other than algae and then provide a more exhaustive examination of the visual pigments present in algal phyla.     

MMS6 protein regulates crystal morphology during nano-sized magnetite biomineralization in vivo

Biomineralization, the process by which minerals are deposited by organisms, has attracted considerable attention because this mechanism has shown great potential to inspire bottom-up material syntheses. To understand the mechanism for morphological regulation that occurs during biomineralization, many regulatory proteins have been isolated from various biominerals. However, the molecular mechanisms that regulate the morphology of biominerals remain unclear because there is a lack of in vivo evidence. Magnetotactic bacteria synthesize intracellular magnetosomes that comprise membrane-enveloped single crystalline magnetite (Fe(3)O(4)). These nano-sized magnetite crystals (<100 nm) are bacterial species dependent in shape and size. Mms6 is a protein that is tightly associated with magnetite crystals. Based on in vitro experiments, this protein was first implicated in morphological regulation during nano-sized magnetite biomineralization. In this study, we analyzed the mms6 gene deletion mutant (Δmms6) of Magnetospirillum magneticum (M. magneticum) AMB-1. Surprisingly, the Δmms6 strain was found to synthesize the smaller magnetite crystals with uncommon crystal faces, while the wild-type and complementation strains synthesized highly ordered cubo-octahedral crystals. Furthermore, deletion of mms6 gene led to drastic changes in the profiles of the proteins tightly bound to magnetite crystals. It was found that Mms6 plays a role in the in vivo regulation of the crystal structure to impart the cubo-octahedral morphology to the crystals during biomineralization in magnetotactic bacteria. Magnetotactic bacteria synthesize magnetite crystals under ambient conditions via a highly controlled morphological regulation system that uses biological molecules.     

Competitive interactions shape offspring performance in relation to seasonal timing of emergence in Atlantic salmon

1.?Timing of birth/hatching may have strong effects on offspring fitness. Breeding time is generally considered to have evolved to match offspring arrival with optimal seasonal environmental conditions, though this is rarely tested experimentally and factors shaping the relations between timing of birth and reproductive success are often poorly understood. 2.?By manipulating incubation temperature of Atlantic salmon embryos, and hence controlling for maternal and genetic effects, we obtained offspring emerging from nests prior to (accelerated), during and after (decelerated) normal emergence times, and accordingly experienced widely different seasonal environmental conditions at emergence (stream temperature range 4-16 °C). The accelerated group emerged at temperatures that are generally considered to be highly sub-optimal for growth and likely imposes strong constraints on feeding and activity, and during a peak in water discharge which is expected to negatively influence habitat availability. 3.?In the wild, overall mortality during the period after emergence was 79%, and was significantly affected by both release density and emergence timing. Accelerated offspring, which emerged earliest and experienced the harshest environmental conditions, had both highest survival and largest final body size. The effect was particularly strong at the high density release site, where survival of accelerated offspring was significantly higher than both the normal and decelerated groups. 4.?In more controlled semi-natural environments, all developmental groups were able to perform well, but accelerated offspring had a relatively better performance than the later emerging offspring when density was high. Furthermore, the relative performance of the different groups was not sensitive to water discharge regimes (temporally stable vs. fluctuating). 5.?These results suggest that the performance of offspring in relation to seasonal timing of emergence is highly affected by competitive interactions in Atlantic salmon. Although a match between phenology and optimal seasonal environmental conditions may be highly important for organisms depending on specific resources that are only available during a limited period of the season, such resources may be available in variable amounts year around for many organisms. For these, offspring success may to a larger degree be shaped by the timing of their hatching/birth relative to each other, and particularly so under high population densities.     

Biogenic magnetite as a basis for magnetic field detection in animals

Bacteria, sharks, honey bees, and homing pigeons as well as other organisms seem to detect the direction of the earth's magnetic field. Indirect but reproducible evidence suggests that the bees and birds can also respond to very minute changes in its intensity. The mechanisms behind this sensitivity are not known. Naturally magnetic, biologically precipitated magnetite (Fe₃O₄) has been found in chitons, magnetotactic bacteria, honey bees, homing pigeons, and dolphins. Its mineralization in localized areas may be associated with the ability of these animals to respond to the direction and intensity of the earth's magnetic field. The presence of large numbers (～10⁸) of superparamagnetic magnetite crystals in honey bees and similar numbers of single-domain magnetite grains in pigeons suggests that there may be at least two basic types of ferrimagnetic magnetoreceptive organelles. Theoretical calculations show that ferrimagnetic organs using either type of grain when integrated by the nervous system are capable of accounting for even the most extreme magnetic field sensitivities reported. Indirect evidence suggests that organic magnetite may be a common biological component, and may account for the results of numerous high field and electromagnetic experiments on animals.     

Giardia: highly evolved parasite or early branching eukaryote?

The phylogeny of the commonest protozoal agent of intestinal disease, Giardia, is unclear. Although recent intensive research suggests this important human parasite is an early branching eukaryote that evolved before the endosymbiotic origin of mitochondria, there is also evidence to suggest that, as a highly evolved parasite, it has lost many of its ancestral characteristics. In this case, these organisms might have arisen much more recently from aerobic free-living flagellates.     

Disruption of magnetic orientation in hatchling loggerhead sea turtles by pulsed magnetic fields

Loggerhead sea turtles (Caretta caretta) derive both directional and positional information from the Earths magnetic field, but the mechanism underlying magnetic field detection in turtles has not been determined. One hypothesis is that crystals of biogenic, single-domain magnetite provide the physical basis of the magnetic sense. As a first step toward determining if magnetite is involved in sea turtle magnetoreception, hatchling loggerheads were exposed to pulsed magnetic fields (40 mT, 4 ms rise time) capable of altering the magnetic dipole moment of biogenic magnetite crystals. A control group of turtles was treated identically but not exposed to the pulsed fields. Both groups of turtles subsequently oriented toward a light source, implying that the pulsed fields did not disrupt the motivation to swim or the ability to maintain a consistent heading. However, when swimming in darkness under conditions in which turtles normally orient magnetically, control turtles oriented significantly toward the offshore migratory direction while those that were exposed to the magnetic pulses did not. These results are consistent with the hypothesis that at least part of the sea turtle magnetoreception system is based on magnetite. In principle, a magnetite-based magnetoreception system might be involved in detecting directional information, positional information, or both.     

MamO Is a Repurposed Serine Protease that Promotes Magnetite Biomineralization through Direct Transition Metal Binding in Magnetotactic Bacteria

Many living organisms transform inorganic atoms into highly ordered crystalline materials. An elegant example of such biomineralization processes is the production of nano-scale magnetic crystals in magnetotactic bacteria. Previous studies implicated the involvement of two putative serine proteases, MamE and MamO, during the early stages of magnetite formation in Magnetospirillum magneticum AMB-1. Here, using genetic analysis and X-ray crystallography, we show that MamO has a degenerate active site, rendering it incapable of protease activity. Instead, MamO promotes magnetosome formation through two genetically distinct, noncatalytic activities: activation of MamE-dependent proteolysis of biomineralization factors and direct binding to transition metal ions. By solving the structure of the protease domain bound to a metal ion, we identify a surface-exposed di-histidine motif in MamO that contributes to metal binding and show that it is required to initiate biomineralization in vivo. Finally, we find that pseudoproteases are widespread in magnetotactic bacteria and that they have evolved independently in three separate taxa. Our results highlight the versatility of protein scaffolds in accommodating new biochemical activities and provide unprecedented insight into the earliest stages of biomineralization.     

Evolution of proton pumping ATPases: Rooting the tree of life

Proton pumping ATPases are found in all groups of present day organisms. The F-ATPases of eubacteria, mitochondria and chloroplasts also function as ATP synthases, i.e., they catalyze the final step that transforms the energy available from reduction/oxidation reactions (e.g., in photosynthesis) into ATP, the usual energy currency of modern cells. The primary structure of these ATPases/ATP synthases was found to be much more conserved between different groups of bacteria than other parts of the photosynthetic machinery, e.g., reaction center proteins and redox carrier complexes.These F-ATPases and the vacuolar type ATPase, which is found on many of the endomembranes of eukaryotic cells, were shown to be homologous to each other; i.e., these two groups of ATPases evolved from the same enzyme present in the common ancestor. (The term eubacteria is used here to denote the phylogenetic group containing all bacteria except the archaebacteria.) Sequences obtained for the plasmamembrane ATPase of various archaebacteria revealed that this ATPase is much more similar to the eukaryotic than to the eubacterial counterpart. The eukaryotic cell of higher organisms evolved from a symbiosis between eubacteria (that evolved into mitochondria and chloroplasts) and a host organism. Using the vacuolar type ATPase as a molecular marker for the cytoplasmic component of the eukaryotic cell reveals that this host organism was a close relative of the archaebacteria.A unique feature of the evolution of the ATPases is the presence of a non-catalytic subunit that is paralogous to the catalytic subunit, i.e., the two types of subunits evolved from a common ancestral gene. Since the gene duplication that gave rise to these two types of subunits had already occurred in the last common ancestor of all living organisms, this non-catalytic subunit can be used to root the tree of life by means of an outgroup; that is, the location of the last common ancestor of the major domains of living organisms (archaebacteria, eubacteria and eukaryotes) can be located in the tree of life without assuming constant or equal rates of change in the different branches.A correlation between structure and function of ATPases has been established for present day organisms. Implications resulting from this correlation for biochemical pathways, especially photosynthesis, that were operative in the last common ancestor and preceding life forms are discussed.     

Three-dimensional domain swapping in nitrollin, a single-domain betagamma-crystallin from Nitrosospira multiformis, controls protein conformation and stability but not dimerization

The betagamma-crystallin superfamily has a well-characterized protein fold, with several members found in both prokaryotic and eukaryotic worlds. A majority of them contain two betagamma-crystallin domains. A few examples, such as ciona crystallin and spherulin 3a exist that represent the eukaryotic single-domain proteins of this superfamily. This study reports the high-resolution crystal structure of a single-domain betagamma-crystallin protein, nitrollin, from the ammonium-oxidizing soil bacterium Nitrosospira multiformis. The structure retains the characteristic betagamma-crystallin fold despite a very low sequence identity. The protein exhibits a unique case of homodimerization in betagamma-crystallins by employing its N-terminal extension to undergo three-dimensional (3D) domain swapping with its partner. Removal of the swapped strand results in partial loss of structure and stability but not dimerization per se as determined using gel filtration and equilibrium unfolding studies. Overall, nitrollin represents a distinct single-domain prokaryotic member that has evolved a specialized mode of dimerization hitherto unknown in the realm of betagamma-crystallins.     

Green algae in alpine biological soil crust communities: acclimation strategies against ultraviolet radiation and dehydration

Green algae are major components of biological soil crusts in alpine habitats. Together with cyanobacteria, fungi and lichens, green algae form a pioneer community important for the organisms that will succeed them. In their high altitudinal habitat these algae are exposed to harsh and strongly fluctuating environmental conditions, mainly intense irradiation, including ultraviolet radiation, and lack of water leading to desiccation. Therefore, green algae surviving in these environments must have evolved with either avoidance or protective strategies, as well as repair mechanisms for damage. In this review we have highlighted these mechanisms, which include photoprotection, photochemical quenching, and high osmotic values to avoid water loss, and in some groups flexibility of secondary cell walls to maintain turgor pressure even in water-limited situations. These highly specialized green algae will serve as good model organisms to study desiccation tolerance or photoprotective mechanisms, due to their natural capacity to withstand unfavorable conditions. We point out the urgent need for modern phylogenetic approaches in characterizing these organisms, and molecular methods for analyzing the metabolic changes involved in their adaptive strategies.     

Seed storage proteins of spermatophytes share a common ancestor with desiccation proteins of fungi

The legumin- and vicilin-like seed storage globulins of spermatophytes are specifically accumulated during embryogenesis and seed development. Previous studies have shown that a precursor common to both legumin and vicilin genes might have evolved by duplication from a single-domain ancestral gene. We here report that amino acid sequences of legumin and vicilin domains share statistically significant similarity to the germination-specific germins of wheat as well as to the spherulation-specific spherulins of myxomycetes. This conclusion is further supported by the derived intron-exon structure of a spherulin gene. Spherulins are thought to be involved in tissue desiccation or hydration. It is suggested that the present-day seed globulins of spermatophytes have evolved from a group of ancient proteins functional in cellular desiccation/hydration processes. Correspondence to: H. Bäumlein     

Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formation

Bacterial flagellar rod structure is built across the peptidoglycan (PG) layer. A Salmonella enterica flagellar protein FlgJ is believed to consist of two functional domains, the N-terminal half acting as a scaffold or cap essential for rod assembly and the C-terminal half acting as a PG hydrolase (PGase) that makes a hole in the PG layer to facilitate rod penetration. In this study, molecular data analyses were conducted on FlgJ data sets sampled from a variety of bacterial species, and three types of FlgJ homologs were identified: (i) "canonical dual-domain" type found in beta- and gamma-proteobacteria that has a domain for one of the PGases, acetylmuramidase (Acm), at the C terminus, (ii) "non-canonical dual-domain" type found in the genus Desulfovibrio (delta-proteobacteria) that bears a domain for another PGase, M23/M37-family peptidase (Pep), at the C terminus and (iii) "single-domain" type found in phylogenetically diverged lineages that lacks the Acm or Pep domain. FlgJ phylogeny, together with the domain architecture, suggested that the single-domain type was the original form of FlgJ and the canonical dual-domain type had evolved from the single-domain type by fusion of the Acm domain to its C terminus in the common ancestor of beta- and gamma-proteobacteria. The non-canonical dual-domain type may have been formed by fusion of the Pep domain to the single-domain type in the ancestor of Desulfovibrio. In some lineages of gamma-proteobacteria, the Acm domain appeared to be lost secondarily from the dual-domain type FlgJ to yield again a single-domain type one. To rationalize the underlying mechanism that gave rise to the two different types of dual-domain FlgJ homologs, we propose a model assuming the lineage-specific co-option of flagellum-specific PGase from diverged housekeeping PGases in bacteria.     

A folding inhibitor of the HIV-1 protease

Because the human immunodeficiency virus type 1 protease (HIV-1-PR) is an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single-domain proteins, like each of the monomers forming the HIV-1-PR homodimer, is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly conserved, as a rule hydrophobic, amino acids). These LES have evolved over myriad generations to recognize and strongly attract each other, so as to make the protein fold fast and be stable in its native conformation. Consequently, peptides displaying a sequence identical to those segments of the monomers associated with LES are expected to act as competitive inhibitors and thus destabilize the native structure of the enzyme. These inhibitors are unlikely to lead to escape mutants as they bind to the protease monomers through highly conserved amino acids, which play an essential role in the folding process. The properties of one of the most promising inhibitors of the folding of the HIV-1-PR monomers found among these peptides are demonstrated with the help of spectrophotometric assays and circular dichroism spectroscopy.     

A strategy for evaluating the safety of organisms for biological weed control

A strategy for establishing the specificity and safety of an organism as a biological weed control agent is described. A critical first step is to expose to its attack a small group of plants very closely related and exhibiting morphological and biochemical similarities to the weed. To prevent an erroneous negative result tests are also made on selected cultivated plants, including those closely related to the weed, those of which the associated insects and fungi are little known, those that have evolved apart from or been little exposed to the agent, those attacked by closely related organisms and those already recorded as hosts. The circumstances under which the strategy might fail to indicate safety are discussed, i.e. polyphagous organisms attacking plants irregularly distributed throughout many families, organisms highly specific to two alternate hosts, and those attacking two or three phylogenetically widely separated plant groups. The additional crop plant testing, included in the overall strategy to deal with such possible failures, is discussed. It is shown that the strategy would have included Sesamum tndicum in the list of plants challenged by the bug Teleonemia scrupulosa in biological testing for control of Lantana camara, thereby forewarning of the attack that was subsequently observed in Africa.     

Structure of a putative ancestral protein encoded by a single sequence repeat from a multidomain proteinase inhibitor gene from Nicotiana alata.

BACKGROUND: The ornamental tobacco Nicotiana alata produces a series of proteinase inhibitors (PIs) that are derived from a 43 kDa precursor protein, NaProPI. NaProPI contains six highly homologous repeats that fold to generate six separate structural domains, each corresponding to one of the native PIs. An unusual feature of NaProPI is that the structural domains lie across adjacent repeats and that the sixth PI domain is generated from fragments of the first and sixth repeats. Although the homology of the repeats suggests that they may have arisen from gene duplication, the observed folding does not appear to support this. This study of the solution structure of a single NaProPI repeat (aPI1) forms a basis for unravelling the mechanism by which this protein may have evolved. RESULTS: The three-dimensional structure of aPI1 closely resembles the triple-stranded antiparallel beta sheet observed in each of the native PIs. The five-residue sequence Glu-Glu-Lys-Lys-Asn, which forms the linker between the six structural domains in NaProPI, exists as a disordered loop in aPI1. The presence of this loop in aPI1 results in a loss of the characteristically flat and disc-like topography of the native inhibitors. CONCLUSIONS: A single repeat from NaProPI is capable of folding into a compact globular domain that displays native-like PI activity. Consequently, it is possible that a similar single-domain inhibitor represents the ancestral protein from which NaProPI evolved.     

Three-Dimensional Domain Swapping in Nitrollin, a Single-Domain βγ-Crystallin from Nitrosospira multiformis, Controls Protein Conformation and Stability but Not Dimerization

The βγ-crystallin superfamily has a well-characterized protein fold, with several members found in both prokaryotic and eukaryotic worlds. A majority of them contain two βγ-crystallin domains. A few examples, such as ciona crystallin and spherulin 3a exist that represent the eukaryotic single-domain proteins of this superfamily. This study reports the high-resolution crystal structure of a single-domain βγ-crystallin protein, nitrollin, from the ammonium-oxidizing soil bacterium Nitrosospira multiformis. The structure retains the characteristic βγ-crystallin fold despite a very low sequence identity. The protein exhibits a unique case of homodimerization in βγ-crystallins by employing its N-terminal extension to undergo three-dimensional (3D) domain swapping with its partner. Removal of the swapped strand results in partial loss of structure and stability but not dimerization per se as determined using gel filtration and equilibrium unfolding studies. Overall, nitrollin represents a distinct single-domain prokaryotic member that has evolved a specialized mode of dimerization hitherto unknown in the realm of βγ-crystallins.