Selective leaching of indium from spent LCD screens by siderophore desferrioxamine E

Given the criticality of indium (In) in high-tech applications, spent LCD screens can represent a viable secondary In resource. In this work, an innovative and alternative technology to selectively leach In from spent LCD screens using a microbial chelating agent, desferrioxamine E (DFOE), was developed. Indium was concentrated from spent LCD screens by implementing an adapted pre-treatment procedure, allowing the isolation of an indium-rich glassy fraction. During leaching, the competition between aluminum (Al) and In for complexation with DFOE leads to the precipitation of In(OH)3 at low DFOE concentrations (12-240 µM). After adjusting the optimal conditions (fraction size: 0-36 μM, pH: 5.5, S/L ratio: 1 g/L, 25 °C), the In leaching yield reached 32%, ten times higher than Al over 90 days with 5 mM DFOE. Thus, achieving high In recovery is possible through i) prolonging leaching durations, ii) selective leaching, and iii) minimizing Al interference. This is the first attempt to selectively leach In using a selected siderophore from end-of-life products with high concentrations of non-targeted elements (i.e. Al, Si, and Ca). This study demonstrates the potential of generating indium-rich leachates, which can be subsequently processed through the GaLIophore technology for In refining.

Identification of yttrium oxide-specific peptides for future recycling of rare earth elements from electronic scrap

Yttrium is a heavy rare earth element (REE) that acquires remarkable characteristics when it is in oxide form and doped with other REEs. Owing to these characteristics Y2 O3 can be used in the manufacture of several products. However, a supply deficit of this mineral is expected in the coming years, contributing to its price fluctuation. Thus, developing an efficient, cost-effective, and eco-friendly process to recover Y2 O3 from secondary sources has become necessary. In this study, we used phage surface display to screen peptides with high specificity for Y2 O3 particles. After three rounds of enrichment, a phage expressing the peptide TRTGCHVPRCNTLS (DM39) from the random pVIII phage peptide library Cys4 was found to bind specifically to Y2 O3 , being 531.6-fold more efficient than the wild-type phage. The phage DM39 contains two arginines in the polar side chains, which may have contributed to the interaction between the mineral targets. Immunofluorescence assays identified that the peptide's affinity was strong for Y2 O3 and negligible to LaPO4 :Ce3+ ,Tb3+ . The identification of a peptide with high specificity and affinity for Y2 O3 provides a potentially new strategic approach to recycle this type of material from secondary sources, especially from electronic scrap.

Graphene oxide and bacteria interactions: what is known and what should we expect?

Graphene oxide (GO) and graphene-based materials (GBMs) have gained over the last two decades considerable attention due to their intrinsic physicochemical properties and their applications. Besides, a lot of concern regarding the potential toxicity of GBMs has emerged. One of the aspects of concern is the interactions between GBMs and different environmental compartments, especially indigenous microbial and, in particular, bacterial communities. Recent research showed that GO and GBMs impacted bacterial pure culture or bacterial communities; therefore, these interactions have to be further studied to better understand and assess the fate of these materials in the environment. Here, we present our opinion and hypotheses related to possible degradation mechanisms of GO that can be used by environmental bacteria. This work is the first attempt to deduce and summarize plausible degradation pathways of GO, from structurally similar recalcitrant and toxic compounds, such as polyaromatic hydrocarbons.

Halomonas gemina sp. nov. and Halomonas llamarensis sp. nov., two siderophore-producing organisms isolated from high-altitude salars of the Atacama Desert

Introduction

This study aimed to identify and characterize novel siderophore-producing organisms capable of secreting high quantities of the iron-binding compounds. In the course of this, two not yet reported halophilic strains designated ATCHA^T and ATCH28^T were isolated from hypersaline, alkaline surface waters of Salar de Llamará and Laguna Lejía, respectively. The alkaline environment limits iron bioavailability, suggesting that native organisms produce abundant siderophores to sequester iron.

Methods

Both strains were characterized by polyphasic approach. Comparative analysis of the 16S rRNA gene sequences revealed their affiliation with the genus Halomonas. ATCHA^T showed close similarity to Halomonas salicampi and Halomonas vilamensis, while ATCH28^T was related closest to Halomonas ventosae and Halomonas salina. The ability of both strains to secrete siderophores was initially assessed using the chromeazurol S (CAS) liquid assay and subsequently further investigated through genomic analysis and NMR. Furthermore, the effect of various media components on the siderophore secretion by strain ATCH28^T was explored.

Results

The CAS assay confirmed the ability of both strains to produce iron-binding compounds. Genomic analysis of strain ATCHA^T revealed the presence of a not yet reported NRPS-dependant gene cluster responsible for the secretion of siderophore. However, as only small amounts of siderophore were secreted, further investigations did not lie within the scope of this study. Via NMR and genomic analysis, strain ATCH28^T has been determined to produce desferrioxamine E (DFOE). Although this siderophore is common in various terrestrial microorganisms, it has not yet been reported to occur within Halomonas, making strain ATCH28^T the first member of the genus to produce a non-amphiphilic siderophore. By means of media optimization, the produced quantity of DFOE could be increased to more than 1000 µM.

Discussion

Phenotypic and genotypic characteristics clearly differentiated both strains from other members of the genus Halomonas. Average nucleotide identity (ANI) values and DNA-DNA relatedness indicated that the strains represented two novel species. Therefore, both species should be added as new representatives of the genus Halomonas, for which the designations Halomonas llamarensis sp. nov. (type strain ATCHA^T = DSM 114476 = LMG 32709) and Halomonas gemina sp. nov. (type strain ATCH28^T = DSM 114418 = LMG 32708) are proposed.

Review on machine learning-based bioprocess optimization, monitoring, and control systems

Machine Learning is quickly becoming an impending game changer for transforming big data thrust from the bioprocessing industry into actionable output. However, the complex data set from bioprocess, lagging cyber-integrated sensor system, and issues with storage scalability limit machine learning real-time application. Hence, it is imperative to know the state of technology to address prevailing issues. This review first gives an insight into the basic understanding of the machine learning domain and discusses its complexities for more comprehensive applications. Followed by an outline of how relevant machine learning models are for statistical and logical analysis of the enormous datasets generated to control bioprocess operations. Then this review critically discusses the current knowledge, its limitations, and future aspects in different subfields of the bioprocessing industry. Further, this review discusses the prospects of adopting a hybrid method to dovetail different modeling strategies, cyber-networking, and integrated sensors to develop new digital biotechnologies.

Gallium-binding peptides as a tool for the sustainable treatment of industrial waste streams

Here we provide a proof of principle for an application-oriented concept for the peptide-based recovery of gallium in industrial wastewater, which was supported by biosorption studies with a real wastewater sample. We investigated the interaction of the gallium-binding peptides TMHHAAIAHPPH, NYLPHQSSSPSR, SQALSTSRQDLR, HTQHIQSDDHLA, and NDLQRHRLTAGP with gallium and arsenic through different experimental and computational approaches. Data obtained from isothermal titration microcalorimetry indicated a competitive influence by the presence of acetate ions with an exothermic contribution to the otherwise endothermic peptide gallium interactions. For peptide HTQHIQSDDHLA, a stabilizing influence of acetate ions on the metal peptide interaction was found. Peptide NYLPHQSSSPSR showed the highest affinity for gallium in ITC studies. Computational modeling of peptide NYLPHQSSSPSR was used to determine interaction parameters and to explain a possible binding mechanism. Furthermore, the peptides were immobilized on polystyrene beads. Thus, we created a novel and exceptionally robust peptide-based material for the biosorption of gallium from an aqueous solution. Data obtained from isothermal titration microcalorimetry indicated a competitive influence by the presence of acetate ions with an exothermic contribution to the otherwise endothermic peptide gallium interactions. For peptide HTQHIQSDDHLA, a stabilizing influence of acetate ions on the metal peptide interaction was found. Peptide NYLPHQSSSPSR showed the highest affinity for gallium in ITC studies. Computational modeling of peptide NYLPHQSSSPSR was used to determine interaction parameters and to explain a possible binding mechanism. Furthermore, the peptides were immobilized on polystyrene beads. Thus, we created a novel and exceptionally robust peptide-based material for the biosorption of gallium from an aqueous solution.

Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

Next generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material research. However, limitations of traditional phage display hinder the identification process. Growth-based library biases and target-unrelated peptides often result in the dominance of parasitic sequences and the collapse of library diversity. This study describes the effective enrichment of specific peptide motifs potentially binding to arsenic as proof-of-concept using the combination of PSD and NGS. Arsenic is an environmental toxin, which is applied in various semiconductors as gallium arsenide and selective recovery of this element is crucial for recycling and remediation. The development of biomolecules as specific arsenic-binding sorbents is a new approach for its recovery. Usage of NGS for all biopanning fractions allowed for evaluation of motif enrichment, in-depth insight into the selection process and the discrimination of biopanning artefacts, e.g., the amplification-induced library-wide reduction in hydrophobic amino acid proportion. Application of bioinformatics tools led to the identification of an SxHS and a carboxy-terminal QxQ motif, which are potentially involved in the binding of arsenic. To the best of our knowledge, this is the first report of PSD combined with NGS of all relevant biopanning fractions.

Recovery of gallium from wafer fabrication industry wastewaters by Desferrioxamine B and E using reversed-phase chromatography approach

Gallium (Ga) is a critical element in developing renewable energy generation and energy efficient systems. The supply of Ga is at risk and needed recycling technologies for its availability in future. This study demonstrated the recovery of Ga³⁺ from low gallium concentrated wafer fabrication industry wastewaters using the siderophores desferrioxamine B (DFOB) and desferrioxamine E (DFOE). The complexation of Ga³⁺ by DFOB and DFOE was through hydroxamate group as demonstrated by infrared spectroscopy, nuclear magnetic resonance and density functional theory calculations. The high selectivity of DFOB/E towards Ga³⁺ was observed due to the formation of highly stable complex. Indeed, due to the formation of such high stability complex, the DFOB and DFOE were able to successfully complex 100% Ga in the two different process water from wafer fabrication industry. For the recovery of the siderophores, a high rate of decomplexation of Ga (>90%) was achieved upon addition of 6 times excess of ethylenediaminetetraacetic acid (EDTA) at pH of 3.5. More than 95% of Ga-DFOB and Ga-DFOE complex were recovered with purity (% of Ga moles in comparison to total moles of metals) of 69.8 and 92.9%, respectively by application of a C18 reversed-phase chromatography column. This study, for the first time, demonstrated a technical solution to the recovery of Ga³⁺ from the low concentrated wastewater based on siderophores and reversed-phase chromatography. A German patent application had been filed for this technology.

Directed Evolution and Engineering of Gallium-Binding Phage Clones-A Preliminary Study

The phage surface display technology is a useful tool to screen and to extend the spectrum of metal-binding protein structures provided by nature. The directed evolution approach allows identifying specific peptide ligands for metals that are less abundant in the biosphere. Such peptides are attractive molecules in resource technology. For example, gallium-binding peptides could be applied to recover gallium from low concentrated industrial wastewater. In this study, we investigated the affinity and selectivity of five bacteriophage clones displaying different gallium-binding peptides towards gallium and arsenic in independent biosorption experiments. The displayed peptides were highly selective towards Ga³⁺ whereby long linear peptides showed a lower affinity and specificity than those with a more rigid structure. Cysteine scanning was performed to determine the relationship between secondary peptide structure and gallium sorption. By site-directed mutagenesis, the amino acids of a preselected peptide sequence are systematically replaced by cysteines. The resulting disulphide bridge considerably reduces the flexibility of linear peptides. Subsequent biosorption experiments carried out with the mutants obtained from cysteine scanning demonstrated, depending on the position of the cysteines in the peptide, either a considerable increase in the affinity of gallium compared to arsenic or an increase in the affinity for arsenic compared to gallium. This study shows the impressive effect on peptide–target interaction based on peptide structure and amino acid position and composition via the newly established systematic cysteine scanning approach.

Chromatopanning for the identification of gallium binding peptides

This study is concerned with a chromatography-based approach (Immobilized Metal Ion Affinity Chromatography) for the recovery of gallium binding peptide sequences from a recombinant phage display library. The here described methods apply the fundamental knowledge and methods of separation science and meet thereby the key requirement of the phage display technique of precise separation of target-binding bacteriophage clones from non-interacting bacteriophage during the biopanning. During the chromatopanning called process, a total of 101 bacteriophage clones were identified of which in subsequent binding experiments, phage clones expressing the peptide sequences TMHHAAIAHPPH, SQALSTSRQDLR and HTQHIQSDDHLA were characterized to bind >10 fold better to a target that presents immobilized gallium ions than control phage, displaying no peptide sequence. The performance of biopanning experiments in chromatographic systems is particularly suitable for demanding targets such as trivalent metal ions. We found, that the selection process benefits immensely from the stable immobilization of the target metal ions during the entire biopanning process as well as the complete recovery of well interacting bacteriophage clones. Among others, this was possible due to an enhanced monitoring of process conditions and fractionation of eluates.

Screening and selection of technologically applicable microorganisms for recovery of rare earth elements from fluorescent powder

Rare Earth Elements (REE) are essential elements in many new technology products. Up to now, recycling is poorly established and no environmentally friendly strategies are applied. Modern biotechnologies like bioleaching can contribute to overcome the current limitations. In this study, we investigated bioleaching approaches exemplary for fluorescent phosphor (FP), which is accumulated during the recycling of fluorescent tubes and energy saving bulbs. A broad spectrum of different microorganisms were tested regarding their potential to leach REE from FP. Among them were classical acidophilic microorganisms, as well as various heterotrophic ones, producing organic acids or metal complexing metabolites, or having a high metal tolerance. Larger amounts of REE were leached with the strains Komagataeibacter xylinus, Lactobacillus casei, and Yarrowia lipolytica. Besides the COOH-functionality, also other biotic processes contribute to metal leaching, as comparison with indirect leaching approaches showed. Among the different REE components of the FP preferably the oxidic red dye yttrium europium oxide (YOE) that contain the critical REE yttrium and europium was leached. The results provide the basis for the development of an environmentally friendly recycling process for REE from waste materials.

Leaching of rare earth elements from fluorescent powder using the tea fungus Kombucha

In most modern technologies such as flat screens, highly effective magnets and lasers, as well as luminescence phosphors, Rare Earth Elements (REE) are used. Unfortunately no environmentally friendly recycling process exists so far. In comparison to other elements the interaction of microorganisms with REE has been studied to a less extent. However, as REE are ubiquitously present in nature it can be assumed that microorganisms play an important role in the biogeochemistry of REE. This study investigates the potential of organic acid-producing microbes for extracting REE from industrial waste. In Germany, 175 tons of fluorescent phosphor (FP) are collected per year as a distinct fraction from the recycling of compact fluorescent lamps. Because the FP contains about 10% of REE-oxides bound in the so-called triband dyes it is a readily accessible secondary resource of REE. Using the symbiotic mixed culture Kombucha, consisting of yeasts and acetic acid bacteria, REE were leached at a significant rate. The highest leaching-rates were observed in shake cultures using the entire Kombucha-consortium or its supernatant as leaching agent compared to experiments using the isolates Zygosaccharomyces lentus and Komagataeibacter hansenii as leaching organisms. During the cultivation, the pH decreased as a result of organic acid production (mainly acetic and gluconic acid). Thus, the underlying mechanism of the triband dye solubilisation is probably linked to the carboxyl-functionality or a proton excess. In accordance with the higher solubility of REE-oxides compared to REE-phosphates and -aluminates, the red dye Y₂O₃:Eu²⁺ containing relatively expensive REE was shown to be preferentially solubilized. These results show that it is possible to dissolve the REE-compounds of FP with the help of microbial processes. Moreover, they provide the basis for the development of an eco-friendly alternative to the currently applied methods that use strong inorganic acids or toxic chemicals.

Au-Interaction of Slp1 Polymers and Monolayer from Lysinibacillus sphaericus JG-B53 - QCM-D, ICP-MS and AFM as Tools for Biomolecule-metal Studies

In this publication the gold sorption behavior of surface layer (S-layer) proteins (Slp1) of Lysinibacillus sphaericus JG-B53 is described. These biomolecules arrange in paracrystalline two-dimensional arrays on surfaces, bind metals, and are thus interesting for several biotechnical applications, such as biosorptive materials for the removal or recovery of different elements from the environment and industrial processes. The deposition of Au(0) nanoparticles on S-layers, either by S-layer directed synthesis or adsorption of nanoparticles, opens new possibilities for diverse sensory applications. Although numerous studies have described the biosorptive properties of S-layers, a deeper understanding of protein-protein and protein-metal interaction still remains challenging. In the following study, inductively coupled mass spectrometry (ICP-MS) was used for the detection of metal sorption by suspended S-layers. This was correlated to measurements of quartz crystal microbalance with dissipation monitoring (QCM-D), which allows the online detection of proteinaceous monolayer formation and metal deposition, and thus, a more detailed understanding on metal binding. The ICP-MS results indicated that the binding of Au(III) to the suspended S-layer polymers is pH dependent. The maximum binding of Au(III) was obtained at pH 4.0. The QCM-D investigations enabled the detection of Au(III) sorption as well as the deposition of Au(0)-NPs in real-time during the in situ experiments. Further, this method allowed studying the influence of metal binding on the protein lattice stability of Slp1. Structural properties and protein layer stability could be visualized directly after QCM-D experiment using atomic force microscopy (AFM). In conclusion, the combination of these different methods provides a deeper understanding of metal binding by bacterial S-layer proteins in suspension or as monolayers on either bacterial cells or recrystallized surfaces.

S-Layer-Based Nanocomposites for Industrial Applications

This chapter covers the fundamental aspects of bacterial S-layers: what are S-layers, what is known about them, and what are their main features that makes them so interesting for the production of nanostructures. After a detailed introduction of the paracrystalline protein lattices formed by S-layer systems in nature the chapter explores the engineering of S-layer-based materials. How can S-layers be used to produce "industry-ready" nanoscale bio-composite materials, and which kinds of nanomaterials are possible (e.g., nanoparticle synthesis, nanoparticle immobilization, and multifunctional coatings)? What are the advantages and disadvantages of S-layer-based composite materials? Finally, the chapter highlights the potential of these innovative bacterial biomolecules for future technologies in the fields of metal filtration, catalysis, and bio-functionalization.

Immobilization of microorganisms for AFM studies in liquids

Reproducible immobilization method even for living eukaryotes and prokaryotes on polyelectrolyte coated surfaces for high resolution AFM imaging in liquids.

Development of functionalised polyelectrolyte capsules using filamentous Escherichia coli cells

Background

Escherichia coli is one of the best studied microorganisms and finds multiple applications especially as tool in the heterologous production of interesting proteins of other organisms. The heterologous expression of special surface (S-) layer proteins caused the formation of extremely long E. coli cells which leave transparent tubes when they divide into single E. coli cells. Such natural structures are of high value as bio-templates for the development of bio-inorganic composites for many applications. In this study we used genetically modified filamentous Escherichia coli cells as template for the design of polyelectrolyte tubes that can be used as carrier for functional molecules or particles. Diversity of structures of biogenic materials has the potential to be used to construct inorganic or polymeric superior hybrid materials that reflect the form of the bio-template. Such bio-inspired materials are of great interest in diverse scientific fields like Biology, Chemistry and Material Science and can find application for the construction of functional materials or the bio-inspired synthesis of inorganic nanoparticles.

Results

Genetically modified filamentous E. coli cells were fixed in 2% glutaraldehyde and coated with alternating six layers of the polyanion polyelectrolyte poly(sodium-4styrenesulfonate) (PSS) and polycation polyelectrolyte poly(allylamine-hydrochloride) (PAH). Afterwards we dissolved the E. coli cells with 1.2% sodium hypochlorite, thus obtaining hollow polyelectrolyte tubes of 0.7 μm in diameter and 5–50 μm in length. For functionalisation the polyelectrolyte tubes were coated with S-layer protein polymers followed by metallisation with Pd(0) particles. These assemblies were analysed with light microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy and transmission electron microscopy.

Conclusion

The thus constructed new material offers possibilities for diverse applications like novel catalysts or metal nanowires for electrical devices. The novelty of this work is the use of filamentous E. coli templates and the use of S-layer proteins in a new material construct.

Biosensing for the environment and defence: aqueous uranyl detection using bacterial surface layer proteins

The fabrication of novel uranyl (UO(2)(2+)) binding protein based sensors is reported. The new biosensor responds to picomolar levels of aqueous uranyl ions within minutes using Lysinibacillus sphaericus JG-A12 S-layer protein tethered to gold electrodes. In comparison to traditional self assembled monolayer based biosensors the porous bioconjugated layer gave greater stability, longer electrode life span and a denser protein layer. Biosensors responded specifically to UO(2)(2+) ions and showed minor interference from Ni(2+), Cs(+), Cd(2+) and Co(2+). Chemical modification of JG-A12 protein phosphate and carboxyl groups prevented UO(2)(2+) binding, showing that both moieties are involved in the recognition to UO(2)(2+).

Construction of an S-layer protein exhibiting modified self-assembling properties and enhanced metal binding capacities

The functional S-layer protein gene slfB of the uranium mining waste pile isolate Bacillus sphaericus JG-A12 was cloned as a polymerase chain reaction product into the expression vector pET Lic/Ek 30 and heterologously expressed in Escherichia coli Bl21(DE3). The addition of His tags to the N and C termini enabled the purification of the recombinant protein by Ni-chelating chromatography. The Ni binding capacity of the His-tagged recombinant S-layer protein was compared with that of the wild-type S layer. The inductively coupled plasma mass spectrometry analyses demonstrate a significantly enhanced Ni binding capability of the recombinant protein. In addition, the self-assembling properties of the purified modified S-layer proteins were studied by light microscopy and scanning electron microscopy. Whereas the wild-type S-layer proteins re-assembled into regular cylindric structures, the recombinant S-layer proteins reassembled into regular sheets that formed globular agglomerating structures. The nanoporous structure of the protein meshwork, together with its enhanced Ni binding capacity, makes the recombinant S-layer attractive as a novel self-assembling biological template for the fabrication of metal nanoclusters and construction of nanomaterials that are of technical interest.

Manufacturing and characterization of Pd nanoparticles formed on immobilized bacterial cells

AIMS

To fabricate and analyse Pd nanoparticles on immobilized bacterial cells.

METHODS AND RESULTS

Biological ceramic composites (biocers) were used as a template to produce Pd(0) nanoparticles. The metal-binding cells of the uranium mining waste pile isolate, Bacillus sphaericus JG-A12 were used as a biological component of the biocers and immobilized by using sol-gel technology. Vegetative cells and surface-layer proteins of this strain are known to bind high amounts of Pd(II) that can be reduced to Pd(0) particles by the addition of a reducing agent. Sorption of Pd(II) by the biocers from a metal complex solution was studied by inductively coupled plasma mass spectroscopy analyses. After embedding into sol-gel ceramics, the cells retained their Pd(II)-binding capability. Pd(0) nanoclusters were produced by the addition of hydrogen as reducing agent after the sorption of Pd(II). The interactions of Pd(0) with the biocers and the formed Pd(0) nanoparticles were investigated by extended X-ray absorption fine structure spectroscopy. The particles had a size of 0.6-0.8 nm.

CONCLUSIONS

Bacterial cells that were immobilized by embedding into sol-gel ceramics were used as a template to produce Pd nanoclusters of a size smaller than 1 nm. These particles possess interesting physical and chemical properties.

SIGNIFICANCE AND IMPACT OF THE STUDY

The use of embedded bacterial cells as template enabled the fabrication of immobilized Pd(0) nanoparticles. These particles are highly interesting for technical applications, such as the development of novel catalysts.

Secondary structure and Pd(II) coordination in S-layer proteins from Bacillus sphaericus studied by infrared and X-ray absorption spectroscopy

The S-layer of Bacillus sphaericus strain JG-A12, isolated from a uranium-mining site, exhibits a high metal-binding capacity, indicating that it may provide a protective function by preventing the cellular uptake of heavy metals and radionuclides. This property has allowed the use of this and other S-layers as self-assembling organic templates for the synthesis of nanosized heavy metal cluster arrays. However, little is known about the molecular basis of the metal-protein interactions and their impact on secondary structure. We have studied the secondary structure, protein stability, and Pd((II)) coordination in S-layers from the B. sphaericus strains JG-A12 and NCTC 9602 to elucidate the molecular basis of their biological function and of the metal nanocluster growth. Fourier transform infrared spectroscopy reveals similar secondary structures, containing approximately 35% beta-sheets and little helical structure. pH-induced infrared absorption changes of the side-chain carboxylates evidence a remarkably low pK < 3 in both strains and a structural stabilization when Pd((II)) is bound. The COO(-)-stretching absorptions reveal a predominant Pd((II)) coordination by chelation/bridging by Asp and Glu residues. This agrees with XANES and EXAFS data revealing oxygens as coordinating atoms to Pd((II)). The additional participation of nitrogen is assigned to side chains rather than to the peptide backbone. The topology of nitrogen- and carboxyl-bearing side chains appears to mediate heavy metal binding to the large number of Asp and Glu in both S-layers at particularly low pH as an adaptation to the environment from which the strain JG-A12 has been isolated. These side chains are thus prime targets for the design of engineered S-layer-based nanoclusters.

Metal binding by bacteria from uranium mining waste piles and its technological applications

Uranium mining waste piles, heavily polluted with radionuclides and other toxic metals, are a reservoir for bacteria that have evolved special strategies to survive in these extreme environments. Understanding the mechanisms of bacterial adaptation may enable the development of novel bioremediation strategies and other technological applications. Cell isolates of Bacillus sphaericus JG-A12 from a uranium mining waste pile in Germany are able to accumulate high amounts of toxic metals such as U, Cu, Pb, Al, and Cd as well as precious metals. Some of these metals, i.e. U, Cu, Pd(II), Pt(II) and Au(III), are also bound by the highly orderd paracrystalline proteinaceous surface layer (S-layer) that envelopes the cells of this strain. These special capabilities of the cells and the S-layer proteins of B. sphaericus JG-A12 are highly interesting for the clean-up of uranium contaminated waste waters, for the recovery of precious metals from electronic wastes, and for the production of metal nanoclusters. The fabricated nanoparticles are promising for the development of novel catalysts. This work reviews the molecular biology of the S-layer of the strain JG-A12 and the S-layer dependent interactions of the bacterial cells with metals. It presents future perspectives for their application in bioremediation and nanotechnology.

Novel surface layer protein genes in Bacillus sphaericus associated with unusual insertion elements

The surface layer (S-layer) protein genes of the uranium mining waste pile isolate Bacillus sphaericus JG-A12 and of its relative B. sphaericus NCTC 9602 were analysed. The almost identical N-termini of the two S-layer proteins possess a unique structure, comprising three N-terminal S-layer homologous (SLH) domains. The central parts of the proteins share a high homology and are related to the S-layer proteins of B. sphaericus CCM 2177 and P-1. In contrast, the C-terminal parts of the S-layer proteins of JG-A12 and NCTC 9602 differ significantly between each other. Surprisingly, the C-terminal part of the S-layer protein of JG-A12 shares a high identity with that of the S-layer protein of B. sphaericus CCM 2177. In both JG-A12 and NCTC 9602 the chromosomal S-layer protein genes are followed by a newly identified putative insertion element comprising three ORFs, which encode a putative transposase, a putative integrase/recombinase and a putative protein containing a DNA binding helix-turn-helix motif, and the S-layer-protein-like gene copies sllA (9602) or sllB (JG-A12). Interestingly, both B. sphaericus strains studied were found to contain an additional, plasmid-located and silent S-layer protein gene with the same sequence as sllA and sllB. The primary structures of the corresponding putative proteins are almost identical in both strains. The N-terminal and central parts of these S-layer proteins share a high identity with those of the chromosomally encoded functional S-layer proteins. Their C-terminal parts, however, differ significantly. These results strongly suggest that the S-layer protein genes have evolved via horizontal transfer of genetic information followed by DNA rearrangements mediated by mobile elements.

Chloromethylmuconolactones as critical metabolites in the degradation of chloromethylcatechols: recalcitrance of 2-chlorotoluene

To elucidate possible reasons for the recalcitrance of 2-chlorotoluene, the metabolism of chloromethylcatechols, formed after dioxygenation and dehydrogenation by Ralstonia sp. strain PS12 tetrachlorobenzene dioxygenase and chlorobenzene dihydrodiol dehydrogenase, was monitored using chlorocatechol dioxygenases and chloromuconate cycloisomerases partly purified from Ralstonia sp. strain PS12 and Wautersia eutropha JMP134. Two chloromethylcatechols, 3-chloro-4-methylcatechol and 4-chloro-3-methylcatechol, were formed from 2-chlorotoluene. 3-Chloro-4-methylcatechol was transformed into 5-chloro-4-methylmuconolactone and 2-chloro-3-methylmuconolactone. For mechanistic reasons neither of these cycloisomerization products can be dehalogenated by chloromuconate cycloisomerases, with the result that 3-chloro-4-methylcatechol cannot be mineralized by reaction sequences related to catechol ortho-cleavage pathways known thus far. 4-Chloro-3-methylcatechol is only poorly dehalogenated during enzymatic processing due to the kinetic properties of the chloromuconate cycloisomerases. Thus, degradation of 2-chlorotoluene via a dioxygenolytic pathway is evidently problematic. In contrast, 5-chloro-3-methylcatechol, the major dioxygenation product formed from 3-chlorotoluene, is subject to quantitative dehalogenation after successive transformation by chlorocatechol 1,2-dioxygenase and chloromuconate cycloisomerase, resulting in the formation of 2-methyldienelactone. 3-Chloro-5-methylcatechol is transformed to 2-chloro-4-methylmuconolactone.

Rational engineering of the regioselectivity of TecA tetrachlorobenzene dioxygenase for the transformation of chlorinated toluenes

The tetrachlorobenzene dioxygenase (TecA) of Ralstonia sp. PS12 carries out the first step in the aerobic biodegradation of chlorinated toluenes. Besides dioxygenation of the aromatic ring of 4-chloro-, 2,4-, 2,5- and 3,4-dichlorotoluene as the main reaction, it also catalyses mono-oxygenation of the methyl groups of 2,3-, 2,6-, 3,5-di- and 2,4,5-trichlorotoluene as the main reactions, channelling these compounds into dead-end pathways. Based on the crystal structure of the homologous naphthalene dioxygenase (NDO) and alignment of the alpha-subunits of NDO and TecA, the substrate pocket of TecA was modelled. Recently, for NDO and the homologous 2-nitrotoluene dioxygenase (2NTDO), two amino acids (Phe(352) of NDO and Asn(258) of 2NTDO) were identified which control the regioselectivity of these enzymes. The corresponding amino acids at Phe(366) and Leu(272) of TecA were substituted to change the regioselectivity and to expand the product spectrum. Position 366 was shown to control regioselectivity of the enzyme, although mutations resulted in decreased or lost activity. Amino acid substitutions at Leu(272) had little or no effect on the regioselectivity of TecA, but had significant effects on the product formation rate. Substitutions at both positions changed the site of oxidation of 2,4,5-trichlorotoluene slightly. As new products, 3,4,6-trichloro-1-methyl-1,2-dihydroxy-1,2-dihydrocyclohexan-3,5-diene, 4,6-dichloro-3-methylcatechol, 3,6-dichloro-4-methylcatechol and 3,4-dichloro-6-methylcatechol were identified.

Metabolism of dichloromethylcatechols as central intermediates in the degradation of dichlorotoluenes by Ralstonia sp. strain PS12

Ralstonia sp. strain PS12 is able to use 2,4-, 2,5-, and 3,4-dichlorotoluene as growth substrates. Dichloromethylcatechols are central intermediates that are formed by TecA tetrachlorobenzene dioxygenase-mediated activation at two adjacent unsubstituted carbon atoms followed by TecB chlorobenzene dihydrodiol dehydrogenase-catalyzed rearomatization and then are channeled into a chlorocatechol ortho cleavage pathway involving a chlorocatechol 1,2-dioxygenase, chloromuconate cycloisomerase, and dienelactone hydrolase. However, completely different metabolic routes were observed for the three dichloromethylcatechols analyzed. Whereas 3,4-dichloro-6-methylcatechol is quantitatively transformed into one dienelactone (5-chloro-2-methyldienelactone) and thus is degraded via a linear pathway, 3,5-dichloro-2-methylmuconate formed from 4,6-dichloro-3-methylcatechol is subject to both 1,4- and 3,6-cycloisomerization and thus is degraded via a branched metabolic route. 3,6-Dichloro-4-methylcatechol, on the first view, is transformed predominantly into one (2-chloro-3-methyl-trans-) dienelactone. In situ (1)H nuclear magnetic resonance analysis revealed the intermediate formation of 2,5-dichloro-4-methylmuconolactone, showing that both 1,4- and 3,6-cycloisomerization occur with this muconate and indicating a degradation of the muconolactone via a reversible cycloisomerization reaction and the dienelactone-forming branch of the pathway. Diastereomeric mixtures of two dichloromethylmuconolactones were prepared chemically to proof such a hypothesis. Chloromuconate cycloisomerase transformed 3,5-dichloro-2-methylmuconolactone into a mixture of 2-chloro-5-methyl-cis- and 3-chloro-2-methyldienelactone, affording evidence for a metabolic route of 3,5-dichloro-2-methylmuconolactone via 3,5-dichloro-2-methylmuconate into 2-chloro-5-methyl-cis-dienelactone. 2,5-Dichloro-3-methylmuconolactone was transformed nearly exclusively into 2-chloro-3-methyl-trans-dienelactone.

Monitoring key reactions in degradation of chloroaromatics by in situ (1)H nuclear magnetic resonance: solution structures of metabolites formed from cis-dienelactone

A (1)H nuclear magnetic resonance ((1)H NMR) assay was used to study the enzymatic transformation of cis-dienelactone, a central intermediate in the degradation of chloroaromatics. It was shown that the product of the cis-dienelactone hydrolase reaction is maleylacetate, in which there is no evidence for the formation of 3-hydroxymuconate. Under acidic conditions, the product structure was 4-carboxymethyl-4-hydroxybut-2-en-4-olide. Maleylacetate was transformed by maleylacetate reductase into 3-oxoadipate, a reaction competing with spontaneous decarboxylation into cis-acetylacrylate. One-dimensional (1)H NMR in (1)H(2)O could thus be shown to be an excellent noninvasive tool for monitoring enzyme activities and assessing the solution structure of substrates and products.

Transformation of chlorinated benzenes and toluenes by Ralstonia sp. strain PS12 tecA (tetrachlorobenzene dioxygenase) and tecB (chlorobenzene dihydrodiol dehydrogenase) gene products

The tecB gene, located downstream of tecA and encoding tetrachlorobenzene dioxygenase, in Ralstonia sp. strain PS12 was cloned into Escherichia coli DH5alpha together with the tecA gene. The identity of the tecB gene product as a chlorobenzene dihydrodiol dehydrogenase was verified by transformation into the respective catechols of chlorobenzene, the three isomeric dichlorobenzenes, as well as 1,2,3- and 1,2,4-trichlorobenzenes, all of which are transformed by TecA into the respective dihydrodihydroxy derivatives. Di- and trichlorotoluenes were either subject to TecA-mediated dioxygenation (the major or sole reaction observed for the 1,2,4-substituted 2,4-, 2,5-, and 3,4-dichlorotoluenes), resulting in the formation of the dihydrodihydroxy derivatives, or to monooxygenation of the methyl substituent (the major or sole reaction observed for 2,3-, 2,6-, and 3,5-dichloro- and 2,4,5-trichlorotoluenes), resulting in formation of the respective benzyl alcohols. All of the chlorotoluenes subject to dioxygenation by TecA were transformed, without intermediate accumulation of dihydrodihydroxy derivatives, into the respective catechols by TecAB, indicating that dehydrogenation is no bottleneck for chlorobenzene or chlorotoluene degradation. However, only those chlorotoluenes subject to a predominant dioxygenation were growth substrates for PS12, confirming that monooxygenation is an unproductive pathway in PS12.