Secondary transporters for nickel and cobalt ions: theme and variations

Comparative genomic analysis of nickel homeostasis in cable bacteria

BACKGROUND

Cable bacteria are filamentous members of the Desulfobulbaceae family that are capable of performing centimetre‑scale electron transport in marine and freshwater sediments. This long‑distance electron transport is mediated by a network of parallel conductive fibres embedded in the cell envelope. This fibre network efficiently transports electrical currents along the entire length of the centimetre‑long filament. Recent analyses show that these fibres consist of metalloproteins that harbour a novel nickel‑containing cofactor, which indicates that cable bacteria have evolved a unique form of biological electron transport. This nickel‑dependent conduction mechanism suggests that cable bacteria are strongly dependent on nickel as a biosynthetic resource. Here, we performed a comprehensive comparative genomic analysis of the genes linked to nickel homeostasis. We compared the genome‑encoded adaptation to nickel of cable bacteria to related members of the Desulfobulbaceae family and other members of the Desulfobulbales order.

RESULTS

Presently, four closed genomes are available for the monophyletic cable bacteria clade that consists of the genera Candidatus Electrothrix and Candidatus Electronema. To increase the phylogenomic coverage, we additionally generated two closed genomes of cable bacteria: Candidatus Electrothrix gigas strain HY10‑6 and Candidatus Electrothrix antwerpensis strain GW3‑4, which are the first closed genomes of their respective species. Nickel homeostasis genes were identified in a database of 38 cable bacteria genomes (including 6 closed genomes). Gene prevalence was compared to 19 genomes of related strains, residing within the Desulfobulbales order but outside of the cable bacteria clade, revealing several genome‑encoded adaptations to nickel homeostasis in cable bacteria. Phylogenetic analysis indicates that nickel importers, nickel‑binding enzymes and nickel chaperones of cable bacteria are affiliated to organisms outside the Desulfobulbaceae family, with several proteins showing affiliation to organisms outside of the Desulfobacterota phylum. Conspicuously, cable bacteria encode a unique periplasmic nickel export protein RcnA, which possesses a putative cytoplasmic histidine‑rich loop that has been largely expanded compared to RcnA homologs in other organisms.

CONCLUSION

Cable bacteria genomes show a clear genetic adaptation for nickel utilization when compared to closely related genera. This fully aligns with the nickel‑dependent conduction mechanism that is uniquely found in cable bacteria.

Cytotoxic effects and comparative analysis of Ni ion uptake by osteoarthritic and physiological osteoblasts

Nickel(Ni)-containing materials have been widely used in a wide range of medical applications, including orthopaedics. Despite their excellent properties, there is still a problem with the release of nickel ions into the patient's body, which can cause changes in the behaviour of surrounding cells and tissues. This study aims to evaluate the effects of Ni on bone cells with an emphasis on the determination of Ni localization in cellular compartments in time. For these purposes, one of the most suitable models for studying the effects induced by metal implants was used-the patient's osteoarthritic cells. Thanks to this it was possible to simulate the pathophysiological conditions in the patient's body, as well as to evaluate the response of the cells which come into direct contact with the material after the implantation of the joint replacement. The largest differences in cell viability, proliferation and cell cycle changes occurred between Ni 0.5 mM and 1 mM concentrations. Time-dependent localization of Ni in cells showed that there is a continuous transport of Ni ions between the nucleus and the cytoplasm, as well as between the cell and the environment. Moreover, osteoarthritic osteoblasts showed faster changes in concentration and ability to accumulate more Ni, especially in the nucleus, than physiological osteoblasts. The differences in Ni accumulation process explains the higher sensitivity of patient osteoblasts to Ni and may be crucial in further studies of implant-derived cytotoxic effects.

Metal selectivity and translocation mechanism characterization in proteoliposomes of the transmembrane NiCoT transporter NixA from Helicobacter pylori

Essential trace metals play key roles in the survival, replication, and virulence of bacterial pathogens. Helicobacter pylori (H. pylori), the main bacterial cause of gastric ulcers, requires Ni(ii) to colonize and persist in the acidic environment inside the stomach, exploiting the nickel-containing enzyme urease to catalyze the hydrolysis of urea to ammonia and bicarbonate and create a pH-buffered microenvironment. Urease utilizes Ni(ii) as a catalytic cofactor for its activity. In ureolytic bacteria, unique transmembrane (TM) transporters evolved to guarantee the selective uptake and efflux of Ni(ii) across cellular membranes to meet the cellular requirements. NixA is an essential Ni(ii) transporter expressed by H. pylori when the extracellular environment experiences a drop in pH. This Class I nickel-cobalt transporter of the NiCoT family catalyzes the uptake of Ni(ii) across the inner membrane from the periplasm. In this study, we characterized NixA using a platform whereby, for the first time on a NiCoT transporter, recombinantly expressed and purified NixA and key mutants in the translocation pathway have been reconstituted in artificial lipid bilayer vesicles (proteoliposomes). Fluorescent sensors responsive to Ni(ii) transport (Fluozin-3-Zn(ii)), luminal pH changes (pyranine), and membrane potential (oxonol VI) were encapsulated in the proteoliposomes lumen to monitor, in real-time, NixA transport properties and translocation mechanism. Kinetic transport analysis revealed that NixA is highly selective for Ni(ii) with no substrate promiscuity towards Co(ii), the other putative metal substrate of the NiCoT family, nor Zn(ii). NixA-mediated Ni(ii) transport exhibited a Michaelis-Menten-type saturable substrate concentration dependence, with an experimental KM, Ni(ii) = 31.0 ± 1.2 μM. Ni(ii) transport by NixA was demonstrated to be electrogenic, and metal translocation did not require a proton motive force, resulting in the generation of a positive-inside transmembrane potential in the proteoliposome lumen. Mutation analysis characterized key transmembrane residues for substrate recognition, binding, and/or transport, suggesting the presence of a three-step transmembrane translocation conduit. Taken together, these investigations reveal that NixA is a Ni(ii)-selective Class I NiCoT electrogenic uniporter. The work also provides an in vitro approach to characterize the transport properties of metal transporters responsible for Ni(ii) acquisition and extrusion in prokaryotes.

Iron transport mechanisms and their evolution focusing on chloroplasts

Iron (Fe) is an essential element for photosynthetic organisms, required for several vital biological functions. Photosynthesis, which takes place in the chloroplasts of higher plants, is the major Fe consumer. Although the components of the root Fe uptake system in dicotyledonous and monocotyledonous plants have been extensively studied, the Fe transport mechanisms of chloroplasts in these two groups of plants have received little attention. This review focuses on the comparative analysis of Fe transport processes in the evolutionary ancestors of chloroplasts (cyanobacteria) with the processes in embryophytes and green algae (Viridiplantae). The aim is to summarize how chloroplasts are integrated into cellular Fe homeostasis and how Fe transporters and Fe transport mechanisms have been modified by evolution.

Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn

Infectious diseases caused by pathogenic bacteria severely threaten human health. Traditional Chinese herbs are potential sources of new or alternative medicine. In this study, we analyzed for the first time antibacterial substances in the methanol-phase extract from a traditional Chinese herb-Commelina communis Linn-which showed an inhibition rate of 58.33% against 24 species of common pathogenic bacteria. The extract was further purified using preparative high-performance liquid chromatography (Prep-HPLC), which generated four single fragments (Fragments 1 to 4). The results revealed that Fragment 1 significantly increased bacterial cell surface hydrophobicity and membrane permeability and decreased membrane fluidity, showing disruptive effects on cell integrity of Gram-positive and Gram-negative bacteria, such as Bacillus cereus, Enterococcus faecalis, Staphylococcus aureus, and Salmonella enterica subsp., compared to the control groups (p < 0.05). In sum, 65 compounds with known functions in Fragment 1 were identified using liquid chromatography and mass spectrometry (LC-MS), of which quercetin-3-o-glucuronide was predominant (19.35%). Comparative transcriptomic analysis revealed multiple altered metabolic pathways mediated by Fragment 1, such as inhibited ABC transporters, ribosome, citrate cycle and oxidative phosphorylation, and upregulated nitrogen metabolism and purine metabolism, thereby resulting in the repressed bacterial growth and even death (p < 0.05). Overall, the results of this study demonstrate that Fragment 1 from C. communis Linn is a promising candidate against common pathogenic bacteria.

The Key Element Role of Metallophores in the Pathogenicity and Virulence of Staphylococcus aureus: A Review

The ubiquitous bacterium Staphylococcus aureus causes many diseases that sometimes can be fatal due to its high pathogenicity. The latter is caused by the ability of this pathogen to secrete secondary metabolites, enabling it to colonize inside the host causing infection through various processes. Metallophores are secondary metabolites that enable bacteria to sequester metal ions from the surrounding environment since the availability of metal ions is crucial for bacterial metabolism and virulence. The uptake of iron and other metal ions such as nickel and zinc is one of these essential mechanisms that gives this germ its virulence properties and allow it to overcome the host immune system. Additionally, extensive interactions occur between this pathogen and other bacteria as they compete for resources. Staphylococcus aureus has high-affinity metal import pathways including metal ions acquisition, recruitment and metal-chelate complex import. These characteristics give this bacterium the ability to intake metallophores synthesized by other bacteria, thus enabling it to compete with other microorganisms for the limited nutrients. In scarce host conditions, free metal ions are extremely low because they are confined to storage and metabolic molecules, so metal ions are sequestered by metallophores produced by this bacterium. Both siderophores (iron chelating molecules) and staphylopine (wide- spectrum metallophore) are secreted by Staphylococcus aureus giving it infectious properties. The genetic regulation of the synthesis and export together with the import of metal loaded metallophores are well established and are all covered in this review.

A NiCoT family metal transporter of Mycobacterium tuberculosis (Rv2856/NicT) behaves as a drug efflux pump that facilitates cross-resistance to antibiotics

Metals often act as a facilitator in the proliferation and persistence of antibiotic resistance. Efflux pumps play key roles in the co-selection of metal and antibiotic resistance. Here, we report the ability of a putative nickel/cobalt transporter (NiCoT family), Rv2856 or NicT of Mycobacterium tuberculosis (Mtb), to transport metal and antibiotics and identified some key amino acid residues that are important for its function. Ectopic expression of NicT in Escherichia coli CS109 resulted in the increase of intracellular nickel uptake. Additionally, enhanced tolerance towards several antibiotics (norfloxacin, sparfloxacin, ofloxacin, gentamicin, nalidixic acid and isoniazid) was observed with NicT overexpression in E. coli and Mycobacterium smegmatis. A comparatively lower intracellular accumulation of norfloxacin upon NicT overexpression than that of the cells without NicT indicated the involvement of NicT in an active efflux process. Although expression of NicT did not alter the sensitivity towards kanamycin, doxycycline, tetracycline, apramycin, neomycin and ethambutol, the presence of a sub-inhibitory dose of Ni²⁺ resulted in the manifestation of low-level tolerance towards these drugs. Further, substitution of four residues (H77I, D82I, H83L and D227I) in the conserved regions of NicT by isoleucine and leucine resulted in reduced to nearly complete loss of the transport function for both metals and antimicrobials. Therefore, the study suggests that nickel transporter Rv2856/NicT may actively export different drugs and the presence of nickel might drive the cross-resistance to some of the antibiotics.

Nickel stress-tolerance in plant-bacterial associations

Nickel (Ni) is an essential element for plant growth and is a constituent of several metalloenzymes, such as urease, Ni-Fe hydrogenase, Ni-superoxide dismutase. However, in high concentrations, Ni is toxic and hazardous to plants, humans and animals. High levels of Ni inhibit plant germination, reduce chlorophyll content, and cause osmotic imbalance and oxidative stress. Sustainable plant-bacterial native associations are formed under Ni-stress, such as Ni hyperaccumulator plants and rhizobacteria showed tolerance to high levels of Ni. Both partners (plants and bacteria) are capable to reduce the Ni toxicity and developed different mechanisms and strategies which they manifest in plant-bacterial associations. In addition to physical barriers, such as plants cell walls, thick cuticles and trichomes, which reduce the elevated levels of Ni entrance, plants are mitigating the Ni toxicity using their own antioxidant defense mechanisms including enzymes and other antioxidants. Bacteria in its turn effectively protect plants from Ni stress and can be used in phytoremediation. PGPR (plant growth promotion rhizobacteria) possess various mechanisms of biological protection of plants at both whole population and single cell levels. In this review, we highlighted the current understanding of the bacterial induced protective mechanisms in plant-bacterial associations under Ni stress.

Genome Analysis of Acinetobacter lwoffii Strains Isolated from Permafrost Soils Aged from 15 Thousand to 1.8 Million Years Revealed Their Close Relationships with Present-Day Environmental and Clinical Isolates

Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. Acinetobacter lwoffii is a typical soil bacterium that has been increasingly reported as hospital pathogens associated with bacteremia. In order to identify the specific genetic characteristics of ancient permafrost-conserved strains of A. lwoffii and their differences from present-day clinical isolates, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not identify chromosomal genetic determinants that distinguish permafrost strains from clinical A. lwoffii isolates and strains from other natural habitats. Phylogenetic analysis based on whole genome sequences showed that permafrost strains do not form a separate cluster and some of them are most closely related to clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal transfer of genetic material. Comparison of plasmids of modern and permafrost strains showed that plasmids from the modern strains are enriched with antibiotic resistance genes, while the content of genes for resistance to heavy metals and arsenic is nearly the same. The thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter.

Nickel in terrestrial biota: Comprehensive review on contamination, toxicity, tolerance and its remediation approaches

Nickel (Ni) has been a subject of interest for environmental, physiological, biological scientists due to its dual effect (toxicity and essentiality) in terrestrial biota. In general, the safer limit of Ni is 1.5 μg g^-1 in plants and 75-150 μg g^-1 in soil. Litreature review indicates that Ni concentrations have been estimated up to 26 g kg^-1 in terrestrial, and 0.2 mg L^-1 in aquatic resources. In case of vegetables and fruits, mean Ni content has been reported in the range of 0.08-0.26 and 0.03-0.16 mg kg^-1. Considering, Ni toxicity and its potential health hazards, there is an urgent need to find out the suitable remedial approaches. Plant vascular (>80%) and cortical (<20%) tissues are the major sequestration site (cation exchange) of absorbed Ni. Deciphering molecular mechanisms in transgenic plants have immense potential for enhancing Ni phytoremediation and microbial remediation efficiency. Further, it has been suggested that integrated bioremediation approaches have a potential futuristic path for Ni decontamination in natural resources. This systematic review provides insight on Ni effects on terrestrial biota including human and further explores its transportation, bioaccumulation through food chain contamination, human health hazards, and possible Ni remediation approaches.

Nanoscale battery cathode materials induce DNA damage in bacteria

The increasing use of nanoscale lithium nickel manganese cobalt oxide (Li x Ni y Mn z Co1-y-z O2, NMC) as a cathode material in lithium-ion batteries poses risk to the environment. Learning toxicity mechanisms on molecular levels is critical to promote proactive risk assessment of these complex nanomaterials and inform their sustainable development. We focused on DNA damage as a toxicity mechanism and profiled in depth chemical and biological changes linked to DNA damage in two environmentally relevant bacteria upon nano-NMC exposure. DNA damage occurred in both bacteria, characterized by double-strand breakage and increased levels of many putative chemical modifications on bacterial DNA bases related to direct oxidative stress and lipid peroxidation, measured by cutting-edge DNA adductomic techniques. Chemical probes indicated elevated intracellular reactive oxygen species and transition metal ions, in agreement with DNA adductomics and gene expression analysis. By integrating multi-dimensional datasets from chemical and biological measurements, we present rich mechanistic insights on nano-NMC-induced DNA damage in bacteria, providing targets for biomarkers in the risk assessment of reactive materials that may be extrapolated to other nano-bio interactions.

Bioinformatics of Metalloproteins and Metalloproteomes

Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.

Dynamics and conformational propensities of staphylococcal CntA

Enzymes use transition metals as co-factors for catalytic roles in biological processes. Notably, manganese, iron, cobalt, nickel, copper and zinc are abundantly used. Staphylococcus aureus, a commensal bacterium asymptomatically, lies on the human body causing variety of infections. S. aureus is equipped by advanced virulence-regulatory circuits of metal acquisition like Cnt that acquires metals at infection sites by utilizing a nicotianamine-like metallophore staphylopine. Despite significant growth in structural studies, how CntA of Cnt system transmits conformational signal upon staphylopine recognition remains elusive. Here, we analyzed the structural changes adopted by CntA during close-to-open transition by computational approaches. CntA uses a bi-domain architectural form of domain II which performed 37° rigid body rotation and 1.1 Å translation assisted by inter-domain hinge cluster residues. Important clustered communities were found regulating the conformational changes in CntA where communities 4 and 5 are found crucial. Besides open and close states, the fluctuating regions sampled two additional intermediate states which were considered close or open previously. CntA prefers fluctuating the non-conserved regions rather than conserved where domain II turned out to be rigid and maintains a stable fold. Overall, the CntA system is a potential target for structural biologist to hamper such conformational behaviors at family level.Communicated by Ramaswamy H. Sarma.

The developmental and iron nutritional pattern of PIC1 and NiCo does not support their interdependent and exclusive collaboration in chloroplast iron transport in Brassica napus

The accumulation of NiCo following the termination of the accumulation of iron in chloroplast suggests that NiCo is not solely involved in iron uptake processes of chloroplasts. Chloroplast iron (Fe) uptake is thought to be operated by a complex containing permease in chloroplast 1 (PIC1) and nickel-cobalt transporter (NiCo) proteins, whereas the role of other Fe homeostasis-related transporters such as multiple antibiotic resistance protein 1 (MAR1) is less characterized. Although pieces of information exist on the regulation of chloroplast Fe uptake, including the effect of plant Fe homeostasis, the whole system has not been revealed in detail yet. Thus, we aimed to follow leaf development-scale changes in the chloroplast Fe uptake components PIC1, NiCo and MAR1 under deficient, optimal and supraoptimal Fe nutrition using Brassica napus as model. Fe deficiency decreased both the photosynthetic activity and the Fe content of plastids. Supraoptimal Fe nutrition caused neither Fe accumulation in chloroplasts nor any toxic effects, thus only fully saturated the need for Fe in the leaves. In parallel with the increasing Fe supply of plants and ageing of the leaves, the expression of BnPIC1 was tendentiously repressed. Though transcript and protein amount of BnNiCo tendentiously increased during leaf development, it was even markedly upregulated in ageing leaves. The relative transcript amount of BnMAR1 increased mainly in ageing leaves facing Fe deficiency. Taken together chloroplast physiology, Fe content and transcript amount data, the exclusive participation of NiCo in the chloroplast Fe uptake is not supported. Saturation of the Fe requirement of chloroplasts seems to be linked to the delay of decomposing the photosynthetic apparatus and keeping chloroplast Fe homeostasis in a rather constant status together with a supressed Fe uptake machinery.

Acute and Chronic Toxicity of Cobalt to Freshwater Organisms: Using a Species Sensitivity Distribution Approach to Establish International Water Quality Standards

Water quality standards for cobalt (Co) have not been developed for the European Union or United States. The objective of the present study was to produce freshwater Co toxicity data that could be used by both the European Union and the United States to develop appropriate regulatory standards (i.e., environmental quality standards or predicted-no-effect concentrations in Europe and ambient water quality criteria or state water quality standards in the United States). Eleven species, including algae, an aquatic plant, and several invertebrate and fish species, were used in the performance of acute and chronic Co toxicity tests. Acute median lethal or median effective concentration (LC50 or EC50) values ranged from 90.1 µg Co/L for duckweed (Lemna minor) to 157 000 µg Co/L for midges (Chironomus tentans). Chronic 10% effect concentration (EC10) values ranged from 4.9 µg Co/L for duckweed to 2170 µg Co/L for rainbow trout (Oncorhynchus mykiss). Chronic 20% effect concentration (EC20) values ranged from 11.1 µg Co/L for water flea (Ceriodaphnia dubia) to 2495 µg Co/L for O. mykiss. Results indicated that invertebrate and algae/plant species are more sensitive to chronic Co exposures than fish. Acute-to-chronic ratios (derived as acute LC50s divided by chronic EC20s) were lowest for juvenile O. mykiss (0.6) and highest for the snail Lymnaea stagnalis (2670). Following the European-based approach and using EC10 values, species sensitivity distributions (SSDs) were developed and a median hazardous concentration for 5% of the organisms of 1.80 µg Co/L was derived. Chronic EC20 values were used, also in an SSD approach, to derive a US Environmental Protection Agency-style final chronic value of 7.13 µg Co/L. Environ Toxicol Chem 2020;39:799-811. © 2020 SETAC.

The influence of cobalt manganese ferrite nanoparticles (Co0.5Mn0.5Fe2O4) on reduction of hazardous effects of vanadate in adult rats

Effect of cobalt manganese ferrite nanoparticles (M-NPs) (Co0.5Mn0.5Fe2O4) on vanadium hazards was assessment in the present study. Four groups of adult male albino rats [control group and three variably treated groups with ammonium metavanadate accompanied with or without cobalt M-NPs] were studied. The oral administration of ammonium metavanadate (Am.V) (20 mg/kg b.wt.) demonstrated the facility of vanadium to distribute and accumulate in the distinctive body organs and ordered as kidney > liver > lung > brain > spleen. Also, Am.V administration induce a significant disturbance in many physiological parameters (RBS, cholesterol, triglyceride, aspartate transaminase, alanine transaminase, Alb., bilirubin, Alk.Ph., urea, creat., Hb%, red blood cell count and packed cell volume) which might be expected to the liberation of free radicals according to the vanadium intoxication or its ability to disturb many body metabolisms. On the other hand, the intraperitoneal administration of 5% M-NPs in parallel with Am.V orally administration showed the ability of M-NPs to reduce Am.V dangerous impacts, which might be resulted from the essentiality of M-NPs metals to the body metabolism and to its free radicals scavenging properties. So, M-NPs could reduce Am.V hazardous effects.

Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions

In the current study, we aimed to elucidate the plant growth-promoting characteristics of Pseudomonas psychrotolerans CS51 under heavy metal stress conditions (Zn, Cu, and Cd) and determine the genetic makeup of the CS51 genome using the single-molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that inoculation with CS51 induced endogenous indole-3-acetic acid (IAA) and gibberellins (GAs), which significantly enhanced cucumber growth (root shoot length) and increased the heavy metal tolerance of cucumber plants. Moreover, genomic analysis revealed that the CS51 genome consisted of a circular chromosome of 5,364,174 base pairs with an average G+C content of 64.71%. There were around 4774 predicted protein-coding sequences (CDSs) in 4859 genes, 15 rRNA genes, and 67 tRNA genes. Around 3950 protein-coding genes with function prediction and 733 genes without function prediction were identified. Furthermore, functional analyses predicted that the CS51 genome could encode genes required for auxin biosynthesis, nitrate and nitrite ammonification, the phosphate-specific transport system, and the sulfate transport system, which are beneficial for plant growth promotion. The heavy metal resistance of CS51 was confirmed by the presence of genes responsible for cobalt-zinc-cadmium resistance, nickel transport, and copper homeostasis in the CS51 genome. The extrapolation of the curve showed that the core genome contained a minimum of 2122 genes (95% confidence interval = 2034.24 to 2080.215). Our findings indicated that the genome sequence of CS51 may be used as an eco-friendly bioresource to promote plant growth in heavy metal-contaminated areas.

Dynamic interactions of CbiN and CbiM trigger activity of a cobalt energy-coupling-factor transporter

Energy-coupling factor (ECF) transporters for uptake of vitamins and transition-metal ions into prokaryotic cells share a common architecture consisting of a substrate-specific integral membrane protein (S), a transmembrane coupling protein (T) and two cytoplasmic ATP-binding-cassette-family ATPases. S components rotate within the membrane to expose their binding pockets alternately to the exterior and the cytoplasm. In contrast to vitamin transporters, metal-specific systems rely on additional proteins with essential but poorly understood functions. CbiN, a membrane protein composed of two transmembrane helices tethered by an extracytoplasmic loop of 37 amino-acid residues represents the auxiliary component that temporarily interacts with the CbiMQO₂ Co²⁺ transporter. CbiN was previously shown to induce significant Co²⁺ transport activity in the absence of CbiQO₂ in cells producing the S component CbiM plus CbiN or a Cbi(MN) fusion. Here we analyzed the mode of interaction between the two protein domains. Any deletion in the CbiN loop abolished transport activity. In silico predicted protein-protein contacts between segments of the CbiN loop and loops in CbiM were confirmed by cysteine-scanning mutagenesis and crosslinking. Likewise, an ordered structure of the CbiN loop was observed by electron paramagnetic resonance analysis after site-directed spin labeling. The N-terminal loop of CbiM containing three of four metal ligands was partially immobilized in wild-type Cbi(MN) but completely immobile in inactive variants with CbiN loop deletions. Decreased dynamics of the inactive form was also detected by solid-state nuclear magnetic resonance of isotope-labeled protein in proteoliposomes. In conclusion, CbiM-CbiN loop-loop interactions facilitate metal insertion into the binding pocket.

How Plants Handle Trivalent (+3) Elements

Plant development and fitness largely depend on the adequate availability of mineral elements in the soil. Most essential nutrients are available and can be membrane transported either as mono or divalent cations or as mono- or divalent anions. Trivalent cations are highly toxic to membranes, and plants have evolved different mechanisms to handle +3 elements in a safe way. The essential functional role of a few metal ions, with the possibility to gain a trivalent state, mainly resides in the ion's redox activity; examples are iron (Fe) and manganese. Among the required nutrients, the only element with +3 as a unique oxidation state is the non-metal, boron. However, plants also can take up non-essential trivalent elements that occur in biologically relevant concentrations in soils. Examples are, among others, aluminum (Al), chromium (Cr), arsenic (As), and antimony (Sb). Plants have evolved different mechanisms to take up and tolerate these potentially toxic elements. This review considers recent studies describing the transporters, and specific and unspecific channels in different cell compartments and tissues, thereby providing a global vision of trivalent element homeostasis in plants.

ECF-type ABC transporters for uptake of vitamins and transition metal ions into prokaryotic cells

Energy-coupling factor (ECF) transporters mediate the uptake of micronutrients in prokaryotes. They consist of two ATP-binding-cassette family ATPases, a transmembrane coupling protein (T component) and a substrate-binding membrane protein (S component). ECF transporters for Co²⁺ and Ni²⁺ ions have one or two additional proteins with extracytoplasmic regions but poorly understood function. Homologs of T components with a predicted localization in plastids are widespread in plants but their physiological role is unclear. S components in eukaryotes are very rare and restricted to biotin-specific variants. Apart from a potential contribution to the export of flavins to serve the assembly of extracytoplasmic electron transfer chains, ECF transporters function as importers.

Multimetal tolerance mechanisms in bacteria: The resistance strategies acquired by bacteria that can be exploited to 'clean-up' heavy metal contaminants from water

Heavy metal pollution is one of the major environmental concerns worldwide. Toxic heavy metals when untreated get accumulated in environment and can pose severe threats to living organisms. It is well known that metals play a major role either directly or indirectly in different metabolic processes of bacteria. This allows bacterial cells to grow even in the presence of some toxic heavy metals. Microbial biotechnology has thus emerged as an effective and eco friendly solution in recent years for bioremediation of heavy metals. Therefore, this review is focused on summarising bacterial adaptation mechanisms for various heavy metals. It also shares some applications of have metal tolerant bacteria in bioremediation. Bacteria have evolved a number of processes for heavy metal tolerance viz., transportation across cell membrane, accumulation on cell wall, intra as well as extracellular entrapment, formation of complexes and redox reactions which form the basis of different bioremediation strategies. The genetic determinants for most of these resistances are located on plasmids however some may be chromosomal as well. Bacterial cells can uptake heavy by both ATP dependent and ATP independent processes. Bacterial cell wall also plays a very important role in accumulating heavy metals by bacterial cells. Gram-positive bacteria accumulate much higher concentrations of heavy metals on their cell walls than that of metals gram -ve bacteria. The role of bacterial metallothioneins (MTs) in heavy metal has also been reported. Thus, heavy metal tolerant bacteria are important for bioremediation of heavy metal pollutants from areas containing high concentrations of particular heavy metals.

Essential and Detrimental - an Update on Intracellular Iron Trafficking and Homeostasis

Chloroplasts, mitochondria and vacuoles represent characteristic organelles of the plant cell, with a predominant function in cellular metabolism. Chloroplasts are the site of photosynthesis and therefore basic and essential for photoautotrophic growth of plants. Mitochondria produce energy during respiration and vacuoles act as internal waste and storage compartments. Moreover, chloroplasts and mitochondria are sites for the biosynthesis of various compounds of primary and secondary metabolism. For photosynthesis and energy generation, the internal membranes of chloroplasts and mitochondria are equipped with electron transport chains. To perform proper electron transfer and several biosynthetic functions, both organelles contain transition metals and here iron is by far the most abundant. Although iron is thus essential for plant growth and development, it becomes toxic when present in excess and/or in its free, ionic form. The harmful effect of the latter is caused by the generation of oxidative stress. As a consequence, iron transport and homeostasis have to be tightly controlled during plant growth and development. In addition to the corresponding transport and homeostasis proteins, the vacuole plays an important role as an intracellular iron storage and release compartment at certain developmental stages. In this review, we will summarize current knowledge on iron transport and homeostasis in chloroplasts, mitochondria and vacuoles. In addition, we aim to integrate the physiological impact of intracellular iron homeostasis on cellular and developmental processes.

Role of Nickel in Microbial Pathogenesis

Nickel is an essential cofactor for some pathogen virulence factors. Due to its low availability in hosts, pathogens must efficiently transport the metal and then balance its ready intracellular availability for enzyme maturation with metal toxicity concerns. The most notable virulence-associated components are the Ni-enzymes hydrogenase and urease. Both enzymes, along with their associated nickel transporters, storage reservoirs, and maturation enzymes have been best-studied in the gastric pathogen Helicobacter pylori, a bacterium which depends heavily on nickel. Molecular hydrogen utilization is associated with efficient host colonization by the Helicobacters, which include both gastric and liver pathogens. Translocation of a H. pylori carcinogenic toxin into host epithelial cells is powered by H2 use. The multiple [NiFe] hydrogenases of Salmonella enterica Typhimurium are important in host colonization, while ureases play important roles in both prokaryotic (Proteus mirabilis and Staphylococcus spp.) and eukaryotic (Cryptoccoccus genus) pathogens associated with urinary tract infections. Other Ni-requiring enzymes, such as Ni-acireductone dioxygenase (ARD), Ni-superoxide dismutase (SOD), and Ni-glyoxalase I (GloI) play important metabolic or detoxifying roles in other pathogens. Nickel-requiring enzymes are likely important for virulence of at least 40 prokaryotic and nine eukaryotic pathogenic species, as described herein. The potential for pathogenic roles of many new Ni-binding components exists, based on recent experimental data and on the key roles that Ni enzymes play in a diverse array of pathogens.

Comparative genomics and metagenomics of the metallomes

Recent achievements and advances in comparative genomic and metagenomic analyses of trace metals were reviewed and discussed.

Sequence Variation of Rare Outer Membrane Protein β-Barrel Domains in Clinical Strains Provides Insights into the Evolution of Treponema pallidum subsp. pallidum, the Syphilis Spirochete

In recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) of Treponema pallidum subspecies pallidum, the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions of tprC, tprD, and bamA in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we used T. pallidum 0548 (tp0548) genotyping and tp0558 sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants in T. pallidum subsp. pallidum reference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. On the basis of structural models, nonconservative amino acid substitutions in predicted transmembrane β-strands of T. pallidum repeat C (TprC) and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures drive T. pallidum subsp. pallidum OMP diversity and that genetic exchange contributes to the evolutionary biology of T. pallidum subsp. pallidum They also set the stage for topology-based analysis of antibody responses to OMPs and help frame strategies for syphilis vaccine development.IMPORTANCE Despite recent progress characterizing outer membrane proteins (OMPs) of Treponema pallidum, little is known about how their surface-exposed, β-barrel-forming domains vary among strains circulating within high-risk populations. In this study, sequences for the β-barrel-encoding regions of three OMP loci, tprC, tprD, and bamA, in T. pallidum subsp. pallidum isolates from a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurs predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function were also noted. Our findings suggest that selection pressures exerted within human populations drive T. pallidum subsp. pallidum OMP diversity and that recombination at OMP loci contributes to the evolutionary biology of syphilis spirochetes. These results also set the stage for topology-based analysis of antibody responses that promote clearance of T. pallidum subsp. pallidum and frame strategies for vaccine development based upon conserved OMP extracellular loops.

Mechanistic insights into staphylopine-mediated metal acquisition

Metal acquisition is vital to pathogens for successful infection within hosts. Staphylopine (StP), a broad-spectrum metallophore biosynthesized by the major human pathogen, Staphylococcus aureus, plays a central role in transition-metal acquisition and bacterial virulence. The StP-like biosynthesis loci are present in various pathogens, and the proteins responsible for StP/metal transportation have been determined. However, the molecular mechanisms of how StP/metal complexes are recognized and transported remain unknown. We report multiple structures of the extracytoplasmic solute-binding protein CntA from the StP/metal transportation system in apo form and in complex with StP and three different metals. We elucidated a sophisticated metal-bound StP recognition mechanism and determined that StP/metal binding triggers a notable interdomain conformational change in CntA. Furthermore, CRISPR/Cas9-mediated single-base substitution mutations and biochemical analysis highlight the importance of StP/metal recognition for StP/metal acquisition. These discoveries provide critical insights into the study of novel metal-acquisition mechanisms in microbes.

Trace metal metabolism in plants

Many trace metals are essential micronutrients, but also potent toxins. Due to natural and anthropogenic causes, vastly different trace metal concentrations occur in various habitats, ranging from deficient to toxic levels. Therefore, one focus of plant research is on the response to trace metals in terms of uptake, transport, sequestration, speciation, physiological use, deficiency, toxicity, and detoxification. In this review, we cover most of these aspects for the essential micronutrients copper, iron, manganese, molybdenum, nickel, and zinc to provide a broader overview than found in other recent reviews, to cross-link aspects of knowledge in this very active research field that are often seen in a separated way. For example, individual processes of metal usage, deficiency, or toxicity often were not mechanistically interconnected. Therefore, this review also aims to stimulate the communication of researchers following different approaches, such as gene expression analysis, biochemistry, or biophysics of metalloproteins. Furthermore, we highlight recent insights, emphasizing data obtained under physiologically and environmentally relevant conditions.

Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation

This research employs draft genome sequence data of Klebsiella pneumoniae AWD5 to explore genes that contribute to the degradation of polyaromatic hydrocarbon (PAH) and stimulate plant growth, for rhizosphere-mediated bioremediation. Annotation analysis suggests that the strain AWD5 not only possess gene clusters for PAH utilization, but also for utilization of benzoate, fluorobenzoate, phenylacetate (paa), hydroxyphenylacetic acid (hpa), 3-hydroxyphenyl propionate (mhp). A comparative genome analysis revealed that the genome of AWD5 was highly similar with genomes of environmental as well as clinical K. pneumoniae isolates. The artemis output confirmed that there are 139 different genes present in AWD5 which were absent in genome of clinical strain K. pneumoniae ATCC BAA-2146, and 25 genes were identified to be present in AWD5 genome but absent in genome of environmental strain K. pneumoniae KP-1. Pathway analyzed using Kyoto Encyclopedia of Genes and Genomes enzyme database revealed the presence of gene clusters that code for enzymes to initiate the opening of aromatic rings. The polyaromatic hydrocarbon and benzoate degradation were found to be metabolized through ortho-cleavage pathway, mineralizing the compounds to TCA cycle intermediates. Genes for plant growth promoting attributes such as Indole acetic acid (IAA) synthesis, siderophore production, and phosphate solubilization were detected in the genome. These attributes were verified in vitro, including IAA (14.75 µg/ml), siderophore production (13.56%), phosphate solubilization (198.28 ng/ml), and ACC deaminase (0.118 mM α-ketobutyrate/mg) in the presence of pyrene, and also compared with results obtained in glucose amended medium. K. pneumoniae AWD5 enhanced the growth of Jatropha curcas in the presence of pyrene-contaminated soil. Moreover, AWD5 harbors heavy metal resistance genes indicating adaptation to contaminants. The study revealed the genomic attributes of K. pneumoniae AWD5 for its catabolic characteristics for different aromatic compounds, which makes it suitable for rhizoremediation of PAH-contaminated soil.

Metal interactions with the transmembrane region of HupE Ni2+ transporter explain its efficiency

Efficient nickel transport is crucial for the survival and virulence of various bacteria and fungi, with Ni²⁺ being required for the activity of nine enzymes such as [NiFe] hydrogenase, which catalyzes the reversible oxidation of molecular hydrogen for energy production. This work focuses on a region of transmembrane domain I from the HupE nickel transporter, highly conserved in the HupE/UreJ and NiCoT permease families, analyzing its interactions with native Ni²⁺ and two other metal ions (Cu²⁺ and Zn²⁺), which might interfere with nickel binding. Metal coordination sites are pointed out and thermodynamic parameters are discussed in detail. Their comparison to the previously studied periplasmic metal binding region satisfies our chemical curiosity and allows to draw conclusions about HupE metal specificity. The results of this study explain one of the reasons why HupE is a medium-affinity and low-capacity transporter - its periplasmic region, ₂₂HVGLHADGTLAGLN₃₅, binds Ni²⁺ with much higher affinity than the transmembrane ₃₆HPFSGLDH₄₃ one, which should transport the metal inside the cell. Moreover, the specificity of the transmembrane region is similar to that of the periplasmic one and to that of the full-length HupE - Cu²⁺ ions are able to outcompete Ni²⁺.

A Bacillus paralicheniformis Iron-Containing Urease Reduces Urea Concentrations in Rice Wine

Urease, a nickel-containing metalloenzyme, was the first enzyme to be crystallized and has a prominent position in the history of biochemistry. In the present study, we identified a nickel urease gene cluster, ureABCEFGDH, in Bacillus paralicheniformis ATCC 9945a and characterized it in Escherichia coli Enzymatic assays demonstrate that this oxygen-stable urease is also an iron-containing acid urease. Heterologous expression assays of UreH suggest that this accessory protein is involved in the transmembrane transportation of nickel and iron ions. Moreover, this iron-containing acid urease has a potential application in the degradation of urea in rice wine. The present study not only enhances our understanding of the mechanism of activation of urease but also provides insight into the evolution of metalloenzymes.IMPORTANCE An iron-containing, oxygen-stable acid urease from B. paralicheniformis ATCC 9945a with good enzymatic properties was characterized. This acid urease shows activities toward both urea and ethyl carbamate. After digestion with 6 U/ml urease, approximately 92% of the urea in rice wine was removed, suggesting that this urease has great potential in the food industry.

Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq

Nickel acts as cofactor for a number of enzymes of many bacteria species. Its homeostasis is ensured by proteins working as ion efflux or accumulation systems. These mechanisms are also generally adopted to counteract life-threatening high extra-cellular Ni²⁺ concentrations. Little is known regarding nickel tolerance in the genus Sphingobium. We studied the response of the novel Sphingobium sp. ba1 strain, able to adapt to high Ni²⁺ concentrations. Differential gene expression in cells cultured in 10 mM Ni²⁺, investigated by RNA-seq analysis, identified 118 differentially expressed genes. Among the 90 up-regulated genes, a cluster including genes coding for nickel and other metal ion efflux systems (similar to either cnrCBA, nccCBA or cznABC) and for a NreB-like permease was found. Comparative analyses among thirty genomes of Sphingobium species show that this cluster is conserved only in two cases, while in the other genomes it is partially present or even absent. The differential expression of genes encoding proteins which could also work as Ni²⁺-accumulators (HupE/UreJ-like protein, NreA and components of TonB-associated transport and copper-homeostasis systems) was also detected. The identification of Sphingobium sp. ba1 strain adaptive mechanisms to nickel ions, can foster its possible use for biodegradation of poly-aromatic compounds in metal-rich environments.

Comparative mathematical modelling of a green approach for bioaccumulation of cobalt from wastewater

Cobalt is an essential element, but its wide use in industry generates important environmental and biological problems. The present study explores theoretical and empirical models of a green process for cobalt {Co²⁺} bioaccumulation from aqueous solutions. Two Gram-positive Bacillus subtilis species, strains CECT 4522 and LMM (the latter a former laboratory isolate from wastewater samples, which was phylogenetically characterized for the present work), were selected among others as the best Co²⁺ accumulation systems. Mathematical models representing kinetic and steady-state conditions for discrete and large amounts of bacterial biomass were expanded. In this way, it was possible to theoretically calculate the amount of Co²⁺ retained on the outer cell wall layer and incorporated inside the cell at any time. Theoretical and empirical hyperbolic-type models were suitable to fit the experimental bioaccumulation data for discrete amounts of bacteria biomass. In addition, kinetic relationships between the amount of Co²⁺ accumulated and the time before (or after) reaching steady state were established for large amounts of bacterial biomass. Other kinetic approaches were also satisfactorily tested. The two Gram-positive bacteria assayed are promising agents for developing heavy metal removal systems from industrial waste.

Importance of the C-terminal histidine residues of Helicobacter pylori GroES for Toll-like receptor 4 binding and interleukin-8 cytokine production

Helicobacter pylori infection is associated with the development of gastric and duodenal ulcers as well as gastric cancer. GroES of H. pylori (HpGroES) was previously identified as a gastric cancer-associated virulence factor. Our group showed that HpGroES induces interleukin-8 (IL-8) cytokine release via a Toll-like receptor 4 (TLR4)-dependent mechanism and domain B of the protein is crucial for interactions with TLR4. In the present study, we investigated the importance of the histidine residues in domain B. To this end, a series of point mutants were expressed in Escherichia coli, and the corresponding proteins purified. Interestingly, H96, H104 and H115 were not essential, whereas H100, H102, H108, H113 and H118 were crucial for IL-8 production and TLR4 interactions in KATO-III cells. These residues were involved in nickel binding. Four of five residues, H102, H108, H113 and H118 induced certain conformation changes in extended domain B structure, which is essential for interactions with TLR4 and consequent IL-8 production. We conclude that interactions of nickel ions with histidine residues in domain B help to maintain the conformation of the C-terminal region to conserve the integrity of the HpGroES structure and modulate IL-8 release.

Comparative effects of Ni(II) and Cu(II) ions and their combinations on redox potential and hydrogen photoproduction by Rhodobacter sphaeroides

The aim of the present work was the study of comparative effects of Cu(II) and Ni(II) and their mixture on growth, redox potential, hydrogen (H₂) yield and ATPase activity in phototrophic purple bacteria R. sphaeroides MDC6522 from Jermuk mineral spring in Armenia. It was ascertained, that Cu²⁺ and Ni²⁺ have different effects on bacterial specific growth rate: in the presence of 5μM Cu²⁺ growth rate was ~3.2-fold lower in comparison with control (no addition), and increased ~1.5-fold in medium with 5μM Ni²⁺. These changes may be resulted by action of the ions on redox potential (E_h). Low concentrations of Ni²⁺ had an enhancing effect on the E_h drop and H₂ production. The increase of concentration from 1 to 5μM enhanced the stimulatory effect of Ni²⁺. H₂ yield in R. sphaeroides (72h of growth) was enhanced ~3-fold with 5μM Ni²⁺, whereas in the presence of 5μM Cu²⁺ H₂ yield was ~1.2 fold lower in comparison with control. Cu²⁺+Ni²⁺ combinations effects were differed from the effect when ions used separately. When Cu²⁺ and Ni²⁺ were added together, the Ni²⁺ stimulatory effect disappeared, which indicated that heavy metal ions mixture may have different action mechanisms. Moreover, N,N'-dicyclohexylcarbodiimide-sensitive ATPase activity of R. sphaeroides membrane vesicles has been increased in the presence of both ions, but in the presence of Сu²⁺ the influence was feebly marked in comparison with Ni²⁺. The results suggest an interaction between these ions and the F_OF₁-ATPase. Thus, the results obtained point out discrimination between Cu²⁺ and Ni²⁺ and their combinations effects and reveal new regulatory pathways to enhance H₂ yield in R. sphaeroides.

Stimulation and Inhibition of Anaerobic Digestion by Nickel and Cobalt: A Rapid Assessment Using the Resazurin Reduction Assay

Stimulation of anaerobic digestion by essential trace metals is beneficial from a practical point of view to enhance the biodegradability and degradation rate of wastes. Hence, a quick method to determine which metal species, and at what concentration, can optimize anaerobic digestion is of great interest to both researchers and operators. In this present study, we investigated the effect of nickel(II), cobalt(II), and their mixture, on the anaerobic digestion of synthetic municipal wastewater. Using a volumetric method, that is, measuring methane production over time, revealed that anaerobic digestion was stimulated by the addition of 5 mg L^-1 nickel(II), and cobalt(II), and their mixture in day(s). However, using a novel resazurin reduction assay, and based on its change in rate over time, we evaluated both inhibition at 250 mg L^-1 nickel(II) and cobalt(II), and also the stimulatory effect of 5 mg L^-1 nickel(II), and cobalt(II), and their mixture, in just 6 h. By investigating the dynamic distribution of these metals in the liquid phase of the anaerobic system and kinetics of resazurin reduction by nickel spiked anaerobic sludge, the concentration of nickel(II) on anaerobic digestion performance was profiled. Three critical concentrations were determined; stimulation starting (around 1 mg L^-1), stimulation ending (around 100 mg L^-1) and stimulation maximizing (around 10 mg L^-1). Hence, we propose that the resazurin reduction assay is a novel and quick protocol for studying the stimulation of anaerobic bioprocesses by bioavailable essential trace metals.

An overview of the biological metal uptake pathways in Pseudomonas aeruginosa

Biological metal ions, including Co, Cu, Fe, Mg, Mn, Mo, Ni and Zn ions, are necessary for the survival and the growth of all microorganisms. Their biological functions are linked to their particular chemical properties: they play a role in structuring macromolecules and/or act as co-factors catalyzing diverse biochemical reactions. These metal ions are also essential for microbial pathogens during infection: they are involved in bacterial metabolism and various virulence factor functions. Therefore, during infection, bacteria need to acquire biological metal ions from the host such that there is competition for these ions between the bacterium and the host. Evidence is increasingly emerging of "nutritional immunity" against pathogens in the hosts; this includes strategies making access to metals difficult for infecting bacteria. It is clear that biological metals play key roles during infection and in the battle between the pathogens and the host. Here, we summarize current knowledge about the strategies used by Pseudomonas aeruginosa to access the various biological metals it requires. P. aeruginosa is a medically significant Gram-negative bacterial opportunistic pathogen that can cause severe chronic lung infections in cystic fibrosis patients and that is responsible for nosocomial infections worldwide.

Novel insights into nickel import in Staphylococcus aureus: the positive role of free histidine and structural characterization of a new thiazolidine-type nickel chelator

Staphylococcus aureus possesses two canonical ABC-importers dedicated to nickel acquisition: the NikABCDE and the CntABCDF systems, active under different growth conditions. This study reports on the extracytoplasmic nickel-binding components SaNikA and SaCntA. We showed by protein crystallography that SaNikA is able to bind either a Ni-(l-His)2 complex or a Ni-(l-His) (2-methyl-thiazolidine dicarboxylate) complex, depending on their availability in culture supernatants. Native mass spectrometry experiments on SaCntA revealed that it binds the Ni(ii) ion via a different histidine-dependent chelator but it cannot bind Ni-(l-His)2. In vitro experiments are consistent with in vivo nickel content measurements that showed that l-histidine has a high positive impact on nickel import via the Cnt system. These results suggest that although both systems may require free histidine, they use different strategies to import nickel.

Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies

Heterotrophic bacteria in the SAR11 and Roseobacter lineages shape the marine carbon, nitrogen, phosphorous, and sulfur cycles, yet they do so having adopted divergent ecological strategies. Currently, it is unknown whether these globally significant groups partition into specific niches with respect to micronutrients (e.g., trace metals) and how that may affect marine trace metal cycling. Here, we used comparative genomics to identify diverse iron, cobalt, nickel, copper, and zinc uptake capabilities in SAR11 and Roseobacter genomes and uncover surprising unevenness within and between lineages. The strongest predictors for the extent of the metal uptake gene content are the total number of transporters per genome, genome size, total metal transporters, and GC content, but numerous exceptions exist in both groups. Taken together, our results suggest that SAR11 have strongly minimized their trace metal uptake versatility, with high-affinity zinc uptake being a unique exception. The larger Roseobacter genomes have greater trace metal uptake versatility on average, but they also appear to have greater plasticity, resulting in phylogenetically similar genomes having largely different capabilities. Ultimately, phylogeny is predictive of the diversity and extent of 20 to 33% of all metal uptake systems, suggesting that specialization in metal utilization mostly occurred independently from overall lineage diversification in both SAR11 and Roseobacter. We interpret these results as reflecting relatively recent trace metal niche partitioning in both lineages, suggesting that concentrations and chemical forms of metals in the marine environment are important factors shaping the gene content of marine heterotrophic Alphaproteobacteria of the SAR11 and Roseobacter lineages.

Chloroplast Iron Transport Proteins - Function and Impact on Plant Physiology

Chloroplasts originated about three billion years ago by endosymbiosis of an ancestor of today's cyanobacteria with a mitochondria-containing host cell. During evolution chloroplasts of higher plants established as the site for photosynthesis and thus became the basis for all life dependent on oxygen and carbohydrate supply. To fulfill this task, plastid organelles are loaded with the transition metals iron, copper, and manganese, which due to their redox properties are essential for photosynthetic electron transport. In consequence, chloroplasts for example represent the iron-richest system in plant cells. However, improvement of oxygenic photosynthesis in turn required adaptation of metal transport and homeostasis since metal-catalyzed generation of reactive oxygen species (ROS) causes oxidative damage. This is most acute in chloroplasts, where radicals and transition metals are side by side and ROS-production is a usual feature of photosynthetic electron transport. Thus, on the one hand when bound by proteins, chloroplast-intrinsic metals are a prerequisite for photoautotrophic life, but on the other hand become toxic when present in their highly reactive, radical generating, free ionic forms. In consequence, transport, storage and cofactor-assembly of metal ions in plastids have to be tightly controlled and are crucial throughout plant growth and development. In the recent years, proteins for iron transport have been isolated from chloroplast envelope membranes. Here, we discuss their putative functions and impact on cellular metal homeostasis as well as photosynthetic performance and plant metabolism. We further consider the potential of proteomic analyses to identify new players in the field.

Chloroplast Iron Transport Proteins - Function and Impact on Plant Physiology

Chloroplasts originated about three billion years ago by endosymbiosis of an ancestor of today's cyanobacteria with a mitochondria-containing host cell. During evolution chloroplasts of higher plants established as the site for photosynthesis and thus became the basis for all life dependent on oxygen and carbohydrate supply. To fulfill this task, plastid organelles are loaded with the transition metals iron, copper, and manganese, which due to their redox properties are essential for photosynthetic electron transport. In consequence, chloroplasts for example represent the iron-richest system in plant cells. However, improvement of oxygenic photosynthesis in turn required adaptation of metal transport and homeostasis since metal-catalyzed generation of reactive oxygen species (ROS) causes oxidative damage. This is most acute in chloroplasts, where radicals and transition metals are side by side and ROS-production is a usual feature of photosynthetic electron transport. Thus, on the one hand when bound by proteins, chloroplast-intrinsic metals are a prerequisite for photoautotrophic life, but on the other hand become toxic when present in their highly reactive, radical generating, free ionic forms. In consequence, transport, storage and cofactor-assembly of metal ions in plastids have to be tightly controlled and are crucial throughout plant growth and development. In the recent years, proteins for iron transport have been isolated from chloroplast envelope membranes. Here, we discuss their putative functions and impact on cellular metal homeostasis as well as photosynthetic performance and plant metabolism. We further consider the potential of proteomic analyses to identify new players in the field.

Transition Metal Homeostasis

This chapter focuses on transition metals. All transition metal cations are toxic-those that are essential for Escherichia coli and belong to the first transition period of the periodic system of the element and also the "toxic-only" metals with higher atomic numbers. Common themes are visible in the metabolism of these ions. First, there is transport. High-rate but low-affinity uptake systems provide a variety of cations and anions to the cells. Control of the respective systems seems to be mainly through regulation of transport activity (flux control), with control of gene expression playing only a minor role. If these systems do not provide sufficient amounts of a needed ion to the cell, genes for ATP-hydrolyzing high-affinity but low-rate uptake systems are induced, e.g., ABC transport systems or P-type ATPases. On the other hand, if the amount of an ion is in surplus, genes for efflux systems are induced. By combining different kinds of uptake and efflux systems with regulation at the levels of gene expression and transport activity, the concentration of a single ion in the cytoplasm and the composition of the cellular ion "bouquet" can be rapidly adjusted and carefully controlled. The toxicity threshold of an ion is defined by its ability to produce radicals (copper, iron, chromate), to bind to sulfide and thiol groups (copper, zinc, all cations of the second and third transition period), or to interfere with the metabolism of other ions. Iron poses an exceptional metabolic problem due its metabolic importance and the low solubility of Fe(III) compounds, combined with the ability to cause dangerous Fenton reactions. This dilemma for the cells led to the evolution of sophisticated multi-channel iron uptake and storage pathways to prevent the occurrence of unbound iron in the cytoplasm. Toxic metals like Cd2+ bind to thiols and sulfide, preventing assembly of iron complexes and releasing the metal from iron-sulfur clusters. In the unique case of mercury, the cation can be reduced to the volatile metallic form. Interference of nickel and cobalt with iron is prevented by the low abundance of these metals in the cytoplasm and their sequestration by metal chaperones, in the case of nickel, or by B12 and its derivatives, in the case of cobalt. The most dangerous metal, copper, catalyzes Fenton-like reactions, binds to thiol groups, and interferes with iron metabolism. E. coli solves this problem probably by preventing copper uptake, combined with rapid efflux if the metal happens to enter the cytoplasm.

The importance of iron in the biosynthesis and assembly of [NiFe]-hydrogenases

[NiFe]-hydrogenases (Hyd) are redox-active metalloenzymes that catalyze the reversible oxidation of molecular hydrogen to protons and electrons. These enzymes are frequently heterodimeric and have a unique bimetallic active site in their catalytic large subunit and possess a complement of iron sulfur (Fe-S) clusters for electron transfer in the small subunit. Depending on environmental and metabolic requirements, the Fe-S cluster relay shows considerable variation among the Hyd, even employing high potential [4Fe-3S] clusters for improved oxygen tolerance. The general iron sulfur cluster (Isc) machinery is required for small subunit maturation, possibly providing standard [4Fe-4S], which are then modified as required in situ. The [NiFe] cofactor in the active site also has an iron ion to which one CO and two CN- diatomic ligands are attached. Specific accessory proteins synthesize these ligands and insert the cofactor into the apo-hydrogenase large subunit. Carbamoyl phosphate is the precursor of the CN- ligands, and recent experimental evidence suggests that endogenously generated CO2 might be one precursor of CO. Recent advances also indicate how the machineries responsible for cofactor generation obtain iron. Several transport systems for iron into bacterial cells exist; however, in Escherichia coli, it is mainly the ferrous iron transporter Feo and the ferric-citrate siderphore system Fec that are involved in delivering the metal for Hyd biosynthesis. Genetic analyses have provided evidence for the existence of key checkpoints during cofactor biosynthesis and enzyme assembly that ensure correct spatiotemporal maturation of these modular oxidoreductases.

Phytotoxicity of cobalt ions on the duckweed Lemna minor - Morphology, ion uptake, and starch accumulation

Cobalt (Co2+) inhibits vegetative growth of Lemna minor gradually from 1 μM to 100 μM. Fronds accumulated up to 21 mg Co2+ g(-1) dry weight at 10 μM external Co2+ indicating hyperaccumulation. Interestingly, accumulation of Co2+ did not decrease the iron (Fe) content in fronds, highlighting L. minor as a suitable system for studying effects of Co2+ undisturbed by Fe deficiency symptoms unlike most other plants. Digital image analysis revealed the size distribution of fronds after Co2+ treatment and also a reduction in pigmentation of newly formed daughter fronds unlike the mother fronds during the 7-day treatment. Neither chlorophyll nor photosystem II fluorescence changed significantly during the initial 4d, indicating effective photosynthesis. During the later phase of the 7-day treatment, however, chlorophyll content and photosynthetic efficiency decreased in the Co2+-treated daughter fronds, indicating that Co2+ inhibits the biosynthesis of chlorophyll rather than leading to the destruction of pre-existing pigment molecules. In addition, during the first 4d of Co2+ treatment starch accumulated in the fronds and led to the transition of chloroplasts to chloro-amyloplasts and amylo-chloroplasts, while starch levels strongly decreased thereafter.

Regulation of a nickel–cobalt efflux system and nickel homeostasis in a soil actinobacterium Streptomyces coelicolor

In nickel-tolerantStreptomyces coelicolor, a highly nickel-sensitive regulator (Nur) for nickel uptake systems and an extremely insensitive regulator (NmtR) for a nickel efflux pump constitute the nickel homeostasis system.

Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake

Functional and topological analysis ofRhizobium leguminosarumHupE, the founding member of the HupE/UreJ family of nickel permeases, provides new hints on how bacteria manage nickel provision for metalloenzyme synthesis.