Structure of Thiocyanate Hydrolase: A New Nitrile Hydratase Family Protein with a Novel Five-coordinate Cobalt(III) Center

Development of (NO)Fe(N2S2) as a Metallodithiolate Spin Probe Ligand: A Case Study Approach

ConspectusThe ubiquity of sulfur-metal connections in nature inspires the design of bi- and multimetallic systems in synthetic inorganic chemistry. Common motifs for biocatalysts developed in evolutionary biology include the placement of metals in close proximity with flexible sulfur bridges as well as the presence of π-acidic/delocalizing ligands. This Account will delve into the development of a (NO)Fe(N2S2) metallodithiolate ligand that harnesses these principles. The Fe(NO) unit is the centroid of a N2S2 donor field, which as a whole is capable of serving as a redox-active, bidentate S-donor ligand. Its paramagnetism as well as the ν(NO) vibrational monitor can be exploited in the development of new classes of heterobimetallic complexes. We offer four examples in which the unpaired electron on the {Fe(NO)}7 unit is spin-paired with adjacent paramagnets in proximal and distal positions.First, the exceptional stability of the (NO)Fe(N2S2)-Fe(NO)2 platform, which permits its isolation and structural characterization at three distinct redox levels, is linked to the charge delocalization occurring on both the Fe(NO) and the Fe(NO)2 supports. This accommodates the formation of a rare nonheme {Fe(NO)}8 triplet state, with a linear configuration. A subsequent FeNi complex, featuring redox-active ligands on both metals (NO on iron and dithiolene on nickel), displayed unexpected physical properties. Our research showed good reversibility in two redox processes, allowing isolation in reduced and oxidized forms. Various spectroscopic and crystallographic analyses confirmed these states, and Mössbauer data supported the redox change at the iron site upon reduction. Oxidation of the complex produced a dimeric dication, revealing an intriguing magnetic behavior. The monomer appears as a spin-coupled diradical between {Fe(NO)}7 and the nickel dithiolene monoradical, while dimerization couples the latter radical units via a Ni2S2 rhomb. Magnetic data (SQUID) on the dimer dication found a singlet ground state with a thermally accessible triplet state that is responsible for magnetism. A theoretical model built on an H4 chain explains this unexpected ferromagnetic low-energy triplet state arising from the antiferromagnetic coupling of a four-radical molecular conglomerate. For comparison, two (NO)Fe(N2S2) were connected through diamagnetic group 10 cations producing diradical trimetallic complexes. Antiferromagnetic coupling is observed between {Fe(NO)}7 units, with exchange coupling constants (J) of -3, -23, and -124 cm-1 for NiII, PdII, and PtII, respectively. This trend is explained by the enhanced covalency and polarizability of sulfur-dense metallodithiolate ligands. A central paramagnetic trans-Cr(NO)(MeCN) receiver unit core results in a cissoid structural topology, influenced by the stereoactivity of the lone pair(s) on the sulfur donors. This {Cr(NO)}5 radical bridge, unlike all previous cases, finds the coupling between the distal Fe(NO) radicals to be ferromagnetic (J = 24 cm-1).The stability and predictability of this S = 1/2 moiety and the steric/electronic properties of the bridging thiolate sulfurs suggest it to be a likely candidate for the development of novel molecular (magnetic) compounds and possibly materials. The role of synthetic inorganic chemistry in designing synthons that permit connections of the (NO)Fe(N2S2) metalloligand is highlighted as well as the properties of the heterobi- and polymetallic complexes derived therefrom.

Metabolic engineering of Oryza sativa for complete biodegradation of thiocyanate

Industrial thiocyanate (SCN^-) waste streams from gold mining and coal coking have caused serious environmental pollution worldwide. Phytoremediation is an efficient technology in treating hazardous wastes from the environment. However, the phytoremediation efficiency of thiocyanate is very low due to the fact that plants lack thiocyanate degradation enzymes. In this study, the thiocyanate hydrolase module was assembled correctly in rice seedlings and showed thiocyanate hydrolase activity. Rice seedlings engineered to express thiocyanate degrading activity were able to completely remove thiocyanate from coking wastewater. Our findings suggest that transforming the thiocyanate hydrolase module into plants is an efficient strategy for rapid phytoremediation of thiocyanate in the environment. Moreover, the rice seedlings expressing apoplastic or cytoplasmic targeted thiocyanate hydrolase module were constructed to compare the phytoremediation efficiency of secretory/intracellular recombinant thiocyanate hydrolase. The most obvious finding from this study is that the apoplastic expression system is more efficient than the cytoplasm expression system in the phytoremediation of thiocyanate. At last, this research also shows that the secreted thiocyanate hydrolase from engineered rice plants does not influence rhizosphere bacterial community composition.

A New Bis(thioether)-Dipyrrin N2S2 Ligand and Its Coordination Behaviors to Nickel, Copper and Zinc

Tetradentate N2S2 coordination platforms are widespread in biological system and have endowed the metalloenzymes and metalloproteins with abundant reactivities and functions. However, there have only three types of N2S2 scaffolds...

Self-Assembled Nickel-4 Supramolecular Squares and Assays for HER Electrocatalysts Derived Therefrom

Solid-state structures find a self-assembled tetrameric nickel cage with carboxylate linkages, [Ni(N₂S'O)I(CH₃CN)]₄ ([Ni-I]₄⁰), resulting from sulfur acetylation by sodium iodoacetate of an [NiN₂S]₂²⁺ dimer in acetonitrile. Various synthetic routes to the tetramer, best described from XRD as a molecular square, were discovered to generate the hexacoordinate nickel units ligated by N₂S_thioether, iodide, and two carboxylate oxygens, one of which is the bridge from the adjacent nickel unit in [Ni-I]₄⁰. Removal of the four iodides by silver ion precipitation yields an analogous species but with an additional vacant coordination site, [Ni-Solv]⁺, a cation but with coordinated solvent molecules. This also recrystallizes as the tetramer [Ni-Solv]₄⁴⁺. In solution, dissociation into the (presumed) monomer occurs, with coordinating solvents occupying the vacant site [Ni(N₂S'O)I(solv)]⁰, ([Ni-I]⁰). Hydrodynamic radii determined from ¹H DOSY NMR data suggest that monomeric units are present as well in CD₂Cl₂. Evans method magnetism values are consistent with triplet spin states in polar solvents; however, in CD₂Cl₂ solutions no paramagnetism is evident. The abilities of [Ni-I]₄⁰ and [Ni-Solv]₄⁴⁺ to serve as sources of electrocatalysts, or precatalysts, for the hydrogen evolution reaction (HER) were explored. Cyclic voltammetry responses and bulk coulometry with gas chromatographic analysis demonstrated that a stronger acid, trifluoroacetic acid, as a proton source resulted in H₂ production from both electroprecatalysts; however, electrocatalysis developed primarily from uncharacterized deposits on the electrode. With acetic acid as a proton source, the major contribution to the HER is from homogeneous electrocatalysis. Overpotentials of 490 mV were obtained for both the solution-phase [Ni-I]⁰ and [Ni-Solv]⁺. While the electrocatalyst derived from [Ni-Solv]⁺ has a substantially higher TOF (102 s^-1) than [Ni-I]⁰ (19 s^-1), it has a shorter catalytically active lifespan (4 h) in comparison to [Ni-I]⁰ (>18 h).

The roles of chalcogenides in O2 protection of H2ase active sites

At some point, all HER (Hydrogen Evolution Reaction) catalysts, important in sustainable H2O splitting technology, will encounter O2 and O2-damage. The [NiFeSe]-H2ases and some of the [NiFeS]-H2ases, biocatalysts for reversible H2 production from protons and electrons, are exemplars of oxygen tolerant HER catalysts in nature. In the hydrogenase active sites oxygen damage may be extensive (irreversible) as it is for the [FeFe]-H2ase or moderate (reversible) for the [NiFe]-H2ases. The affinity of oxygen for sulfur, in [NiFeS]-H2ase, and selenium, in [NiFeSe]-H2ase, yielding oxygenated chalcogens results in maintenance of the core NiFe unit, and myriad observable but inactive states, which can be reductively repaired. In contrast, the [FeFe]-H2ase active site has less possibilities for chalcogen-oxygen uptake and a greater chance for O2-attack on iron. Exposure to O2 typically leads to irreversible damage. Despite the evidence of S/Se-oxygenation in the active sites of hydrogenases, there are limited reported synthetic models. This perspective will give an overview of the studies of O2 reactions with the hydrogenases and biomimetics with focus on our recent studies that compare sulfur and selenium containing synthetic analogues of the [NiFe]-H2ase active sites.

Degradation pathway and microbial mechanism of high-concentration thiocyanate in gold mine tailings wastewater

As one of the inorganic pollutants with the highest concentration in the waste water of gold tailings using biohydrometallurgy, thiocyanate (SCN-) was effectively degraded in this research adopting a two-stage activated sludge biological treatment, and the corresponding degradation pathway and microbial community characteristics in this process were also studied. The results showed that SCN- at 1818.00 mg L-1 in the influent decreased to 0.68 mg L-1 after flowing through the two-stage activated sludge units. Raman spectroscopy was used to study the changes of relevant functional groups, finding that SCN- was degraded in the COS pathway. Based on 16S rRNA high-throughput sequencing technology, the microbial diversity in this system was analyzed, and the results indicated that Thiobacillus played a major role in degrading SCN-, of which the abundance in these two activated sludge units was 32.05% and 20.37%, respectively. The results further revealed the biological removal mechanism of SCN- in gold mine tailings wastewater.

Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications

Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.

Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium

Industrial thiocyanate (SCN^-) waste streams from gold mining and coal coking have polluted environments worldwide. Modern SCN^- bioremediation involves use of complex engineered heterotrophic microbiomes; little attention has been given to the ability of a simple environmental autotrophic microbiome to biodegrade SCN^-. Here we present results from a bioreactor experiment inoculated with SCN^- -loaded mine tailings, incubated autotrophically, and subjected to a range of environmentally relevant conditions. Genome-resolved metagenomics revealed that SCN^- hydrolase-encoding, sulphur-oxidizing autotrophic bacteria mediated SCN^- degradation. These microbes supported metabolically-dependent non-SCN^--degrading sulphur-oxidizing autotrophs and non-sulphur oxidizing heterotrophs, and "niche" microbiomes developed spatially (planktonic versus sessile) and temporally (across changing environmental parameters). Bioreactor microbiome structures changed significantly with increasing temperature, shifting from Thiobacilli to a novel SCN^- hydrolase-encoding gammaproteobacteria. Transformation of carbonyl sulphide (COS), a key intermediate in global biogeochemical sulphur cycling, was mediated by plasmid-hosted CS₂ and COS hydrolase genes associated with Thiobacillus, revealing a potential for horizontal transfer of this function. Our work shows that simple native autotrophic microbiomes from mine tailings can be employed for SCN^- bioremediation, thus improving the recycling of ore processing waters and reducing the hydrological footprint of mining.

Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria

Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for highly active biogeochemical cycles. The sulfur cycle is one of the most important of these and bacterial sulfur oxidation is dominated by members of the obligately chemolithoautotrophic genus Thioalkalivibrio. Currently, 10 species have been described in this genus, but over one hundred isolates have been obtained from soda lake samples. The genomes of 75 strains were sequenced and annotated previously, and used in this study to provide a comprehensive picture of the diversity and distribution of genes related to dissimilatory sulfur metabolism in Thioalkalivibrio. Initially, all annotated genes in 75 Thioalkalivibrio genomes were placed in ortholog groups and filtered by bi-directional best BLAST analysis. Investigation of the ortholog groups containing genes related to sulfur oxidation showed that flavocytochrome c (fcc), the truncated sox system, and sulfite:quinone oxidoreductase (soe) are present in all strains, whereas dissimilatory sulfite reductase (dsr; which catalyzes the oxidation of elemental sulfur) was found in only six strains. The heterodisulfide reductase system (hdr), which is proposed to oxidize sulfur to sulfite in strains lacking both dsr and soxCD, was detected in 73 genomes. Hierarchical clustering of strains based on sulfur gene repertoire correlated closely with previous phylogenomic analysis. The phylogenetic analysis of several sulfur oxidation genes showed a complex evolutionary history. All in all, this study presents a comprehensive investigation of sulfur metabolism-related genes in cultivated Thioalkalivibrio strains and provides several avenues for future research.

Biomimetic heterobimetallic architecture of Ni(ii) and Fe(ii) for CO2 hydrogenation in aqueous media. A DFT study

In this work, density functional theory has been employed to design a heterobimetallic catalyst of Ni(ii) and Fe(ii) for the effective CO₂ hydrogenation to HCOOH. Based on computational results, our newly designed catalyst is found to be effective for such conversion reactions with free energy as low as 14.13 kcal mol⁻¹ for the rate determining step. Such a low value of free energy indicates that the NiFe heterobimetallic catalyst can prove to be very efficient for the above said conversion. Moreover, the effects of ligand substitutions at the active metal center and the effects due to various spin states are also explored, and can serve as a great tool for the rational design of NiFe catalyst for CO₂ hydrogenation.

The hydrogenation of CO₂ by our newly designed [NiFe] heterobimetallic catalyst inspired by the active site of [NiFe] hydrogenase.

Emerging Roles of Carbonyl Sulfide in Chemical Biology: Sulfide Transporter or Gasotransmitter?

SIGNIFICANCE

Carbonyl sulfide (COS) is the most prevalent sulfur-containing gas in the Earth's atmosphere, and it plays important roles in the global sulfur cycle. COS has been implicated in origin of life peptide ligation, is the primary energy source for certain bacteria, and has been detected in mammalian systems. Despite this long and intertwined history with terrestrial biology, limited attention has focused on potential roles of COS as a biological mediator. Recent Advances: Although bacterial COS production is well documented, definitive sources of mammalian COS production have not been confirmed. Enzymatic COS consumption in mammals, however, is well documented and occurs primarily by carbonic anhydrase (CA)-mediated conversion to hydrogen sulfide (H2S). COS has been detected in ex vivo mammalian tissue culture, as well as in exhaled breath as a potential biomarker for different disease pathologies, including cystic fibrosis and organ rejection. Recently, chemical tools for COS delivery have emerged and are poised to advance future investigations into the role of COS in different biological contexts.

CRITICAL ISSUES

Possible roles of COS as an important biomolecule, gasotransmitter, or sulfide transport intermediate remain to be determined. Key advances in both biological and chemical tools for COS research are needed to further investigate these questions.

FUTURE DIRECTIONS

Further evaluation of the biological roles of COS and disentangling the chemical biology of COS from that of H2S are needed to further elucidate these interactions. Chemical tools for COS delivery and modulation may provide a first avenue of investigative tools to answer many of these questions. Antioxid. Redox Signal. 28, 1516-1532.

Overexpression and characterization of two types of nitrile hydratases from Rhodococcus rhodochrous J1

Nitrile hydratase (NHase) from Rhodococcus rhodochrous J1 is widely used for industrial production of acrylamide and nicotinamide. However, the two types of NHases (L-NHase and H-NHase) from R. rhodochrous J1 were only slightly expressed in E. coli by routine methods, which limits the comprehensive and systematic characterization of the enzyme properties. We successfully expressed the two types of recombinant NHases in E. coli by codon-optimization, engineering of Ribosome Binding Site (RBS) and spacer sequences. The specific activity of the purified L-NHase and H-NHase were 400 U/mg and 234 U/mg, respectively. The molecular mass of L-NHase and H-NHase was identified to be 94 kDa and 504 kDa, respectively, indicating that the quaternary structure of the two types of NHases was the same as those in R. rhodochrous J1. H-NHase exhibited higher substrate and product tolerance than L-NHase. Moreover, higher activity and shorter culture time were achieved in recombinant E. coli, and the whole cell catalyst of recombinant E. coli harboring H-NHase has equivalent efficiency in tolerance to the high-concentration product relative to that in R. rhodochrous J1. These results indicate that biotransformation of nitrile by R. rhodochrous J1 represents a potential alternative to NHase-producing E. coli.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN^-), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN^- loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN^-. A second reactor was fed ammonium sulfate to mimic breakdown products of SCN^-. Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN^- reactor, Thiobacillus strains capable of SCN^- degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN^- reactor expressed proteins involved in SCN^- degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings

Thiocyanate (SCN⁻) is a toxic compound that forms when cyanide (CN⁻), used to recover gold, reacts with sulfur species. SCN⁻‐degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory‐based reactors operated without suspended solids. Despite minor upsets during the acclimation period, the SCN⁻ degradation performance was largely unchanged under stable operating conditions. Here, we characterized the microbial community in the SCN⁻ degrading bioreactor that included solid particulate tailings and determined how it differed from the biofilm‐based communities in solids‐free reactor systems inoculated from the same source. Genome‐based analysis revealed that the presence of solids decreased microbial diversity, selected for different strains, suppressed growth of thiobacilli inferred to be primarily responsible for SCN⁻ degradation, and promoted growth of Trupera, an organism not detected in the reactors without solids. In the solids reactor community, heterotrophy and aerobic respiration represent the dominant metabolisms. Many organisms have genes for denitrification and sulfur oxidation, but only one Thiobacillus sp. in the solids reactor has SCN⁻ degradation genes. The presence of the solids prevented floc and biofilm formation, leading to the observed reduced microbial diversity. Collectively the presence of the solids and lack of biofilm community may result in a process with reduced resilience to process perturbations, including fluctuations in the influent composition and pH. The results from this investigation have provided novel insights into the community composition of this industrially relevant community, giving potential for improved process control and operation through ongoing process monitoring.

The ligand unwrapping/rewrapping pathway that exchanges metals in S-acetylated, hexacoordinate N2S2O2 complexes

The effect of S-acetylation in MN₂S₂ complexes on metal exchange reactivity was examined in a series of MN₂S₂O₂ complexes.

The effect of S-acetylation in MN₂S₂ complexes on metal exchange reactivity was examined in a series of MN₂S₂O₂ complexes. While clean exchange processes do not occur for the MN₂S₂ derivatives where formation of S-bridged aggregates predominate, acetylation permits the metal exchange with hierarchy that follows the Irving–Williams series of stability for first row transition metals: Fe²⁺ < Co²⁺ < Ni²⁺ < Cu²⁺ > Zn²⁺. The rate determining step consistent with kinetic parameters depends on both M and M′, supporting a mechanism of exchange that involves ligand unwrapping/rewrapping process as earlier defined by Margerum et al. for M(EDTA) systems. The enhanced metal exchange deriving from S-acetylation is of significance to probes and detection of cysteine-S metallo-proteins and metallo-enzyme active sites, and highlights a new role for S-acetylation.

A Semisynthetic Strategy Leads to Alteration of the Backbone Amidate Ligand in the NiSOD Active Site

Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategy that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ∼1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ∼11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. (14)N-hyperfine is observed on gz, confirming the addition of the apical histidine ligand in the Ni(III) complex. The altered electronic properties and implications for redox catalysis are discussed in light of predictions based on synthetic and computational models.

Iridium-mediated C–S bond activation and transformation: organoiridium(iii) thioether, thiolato, sulfinato and thiyl radical compounds. Synthesis, mechanistic, spectral, electrochemical and theoretical aspects

The iridium-mediated C–S bond scission by an uncommon SET reductive process: exploration of S-centered reactivity of iridium(iii) thiolato complex.

The alpha subunit of nitrile hydratase is sufficient for catalytic activity and post-translational modification

Nitrile hydratases (NHases) possess a mononuclear iron or cobalt cofactor whose coordination environment includes rare post-translationally oxidized cysteine sulfenic and sulfinic acid ligands. This cofactor is located in the α-subunit at the interfacial active site of the heterodimeric enzyme. Unlike canonical NHases, toyocamycin nitrile hydratase (TNHase) from Streptomyces rimosus is a unique three-subunit member of this family involved in the biosynthesis of pyrrolopyrimidine antibiotics. The subunits of TNHase are homologous to the α- and β-subunits of prototypical NHases. Herein we report the expression, purification, and characterization of the α-subunit of TNHase. The UV–visible, EPR, and mass spectra of the α-subunit TNHase provide evidence that this subunit alone is capable of synthesizing the active site complex with full post-translational modifications. Remarkably, the isolated post-translationally modified α-subunit is also catalytically active with the natural substrate, toyocamycin, as well as the niacin precursor 3-cyanopyridine. Comparisons of the steady state kinetic parameters of the single subunit variant to the heterotrimeric protein clearly show that the additional subunits impart substrate specificity and catalytic efficiency. We conclude that the α-subunit is the minimal sequence needed for nitrile hydration providing a simplified scaffold to study the mechanism and post-translational modification of this important class of catalysts.

Cloning and expression of a gene encoding a novel thermostable thiocyanate-degrading enzyme from a mesophilic alphaproteobacteria strain THI201

Strain THI201, a member of the alphaproteobacteria, is a novel thiocyanate (SCN(-))-degrading bacterium isolated from lake water enriched with potassium thiocyanate (KSCN). This bacterium carries the enzyme thiocyanate hydrolase (SCNase) that hydrolyses thiocyanate to carbonyl sulfide and ammonia. Characterization of both native and recombinant SCNase revealed properties different from known SCNases regarding subunit structure and thermostability: SCNase of strain THI201 was composed of a single protein and thermostable. We cloned and sequenced the corresponding gene and determined a protein of 457 amino acids of molecular mass 50 267 Da. Presence of a twin-arginine (Tat) signal sequence of 32 amino acids was found upstream of SCNase. The deduced amino acid sequence of SCNase showed 83% identity to that of a putative uncharacterized protein of Thiobacillus denitrificans ATCC 25259, but no significant identity to those of three subunits of SCNase from Thiobacillus thioparus strain THI115. The specific activities of native and recombinant enzyme were 0.32 and 4-15 µmol min(-1) (mg protein)(-1), respectively. The maximum activity of SCNase was found in the temperature range 30-70 °C. The thiocyanate-hydrolysing activity in both enzymes was decreased by freeze-thawing, although 25-100% of the activity of recombinant protein could be retrieved by treating the enzyme at 60 °C for 15 min. Furthermore, both native and recombinant enzymes retained the activity after pre-treatment of the protein solution at temperatures up to 70 °C.

Strategy for successful expression of the Pseudomonas putida nitrile hydratase activator P14K in Escherichia coli

Background

Activators of Nitrile hydratase (NHase) are essential for functional NHase biosynthesis. However, the activator P14K in P. putida is difficult to heterogeneously express, which retards the clarification of the mechanism of P14K involved in the maturation of NHase. Although a strep tag containing P14K (strep-P14K) was over-expressed, its low expression level and low stability affect the further analysis.

Results

We successfully expressed P14K through genetic modifications according to N-end rule and analyzed the mechanism for its difficult expression. We found that mutation of the second N-terminal amino-acid of the protein from lysine to alanine or truncating the N-terminal 16 amino-acid sequence resulted in successful expression of P14K. Moreover, fusion of a pelB leader and strep tag together (pelB-strep-P14K) at the N-terminus increased P14K expression. In addition, the pelB-strep-P14K was more stable than the strep-P14K.

Conclusions

Our results are not only useful for clarification of the role of P14K involved in the NHase maturation, but also helpful for heterologous expression of other difficult expression proteins.

Sequential oxidations of thiolates and the cobalt metallocenter in a synthetic metallopeptide: implications for the biosynthesis of nitrile hydratase

Cobalt nitrile hydratases (Co-NHase) contain a catalytic cobalt(III) ion coordinated in an N2S3 first coordination sphere composed of two amidate nitrogens and three cysteine-derived sulfur donors: a thiolate (-SR), a sulfenate (-S(R)O(-)), and a sulfinate (-S(R)O2(-)). The sequence of biosynthetic reactions that leads to the post-translational oxidations of the metal and the sulfur ligands is unknown, but the process is believed to be initiated directly by oxygen. Herein we utilize cobalt bound in an N2S2 first coordination sphere by a seven amino acid peptide known as SODA (ACDLPCG) to model this oxidation process. Upon exposure to oxygen, Co-SODA is oxidized in two steps. In the first fast step (seconds), magnetic susceptibility measurements demonstrated that the metallocenter remains paramagnetic, that is, Co(2+), and sulfur K-edge X-ray absorption spectroscopy (XAS) is used to show that one of the thiolates is oxidized to sulfinate. In a second process on a longer time scale (hours), magnetic susceptibility measurements and Co K-edge XAS show that the metal is oxidized to Co(3+). Unlike other model complexes, additional slow oxidation of the second thiolate in Co-SODA is not observed, and a catalytically active complex is never formed. The likely reason is the absence of the axial thiolate ligand. In essence, the reactivity of Co-SODA can be described as between previously described models which either quickly convert to final product or are stable in air, and it offers a first glimpse into a possible oxidation pathway for nitrile hydratase biosynthesis.

Effects of exogenous thiocyanate on mineral nutrients, antioxidative responses and free amino acids in rice seedlings

The effects of exogenous thiocyanate (SCN(-)) on amino acids composition, content of mineral nutrients and antioxidative systems in plants were investigated. Young rice seedlings (Oryza sativa L. cv. XZX 45) were grown in nutrient solutions amended with potassium thiocyanate (KSCN). Activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) in plant materials were analyzed in vivo. Mineral nutrients and free amino acids in rice seedlings were also measured to determine metabolic responses to SCN(-) exposure. A significant reduction in transpiration and relative growth was recorded with all treatments (p < 0.05), while changes of total chlorophyll content in leaves was negligible (p > 0.05). SCN-induced toxicity appeared to be more sensitive to activities of POD in shoots and APX activities in roots than the others. The content of nutrient elements in rice seedlings exposed to exogenous SCN(-) was variable, while the effects were more evident at the highest SCN-treatment (p < 0.05). Although the change of total free amino acids in shoots of SCN-exposed seedlings was negligible (p > 0.05), responses of different amino acids to SCN(-) application were quite different. Among fifteen free amino acids detected, serine (Ser), proline (Pro), and methionine (Met) increased, while asparagine (Asp) decreased with an increase of the doses of SCN(-) supplied. Phyto-transport of SCN(-) was apparent and the removal rates were positively correlated to the doses, suggesting that phyto-assimilation of SCN(-) is an enzymatic process through a potentially un-identified degradation pathway.

Self-subunit swapping occurs in another gene type of cobalt nitrile hydratase

Self-subunit swapping is one of the post-translational maturation of the cobalt-containing nitrile hydratase (Co-NHase) family of enzymes. All of these NHases possess a gene organization of <β-subunit> <α-subunit> <activator protein>, which allows the activator protein to easily form a mediatory complex with the α-subunit of the NHase after translation. Here, we discovered that the incorporation of cobalt into another type of Co-NHase, with a gene organization of <α-subunit> <β-subunit> <activator protein>, was also dependent on self-subunit swapping. We successfully isolated a recombinant NHase activator protein (P14K) of Pseudomonas putida NRRL-18668 by adding a Strep-tag N-terminal to the P14K gene. P14K was found to form a complex [α(StrepP14K)₂] with the α-subunit of the NHase. The incorporation of cobalt into the NHase of P. putida was confirmed to be dependent on the α-subunit substitution between the cobalt-containing α(StrepP14K)₂ and the cobalt-free NHase. Cobalt was inserted into cobalt-free α(StrepP14K)₂ but not into cobalt-free NHase, suggesting that P14K functions not only as a self-subunit swapping chaperone but also as a metallochaperone. In addition, NHase from P. putida was also expressed by a mutant gene that was designed with a <β-subunit> <α-subunit> <P14K> order. Our findings expand the general features of self-subunit swapping maturation.

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture

All proteins require physical interactions with other proteins in order to perform their functions. Most of them oligomerize into homomers, and a vast majority of these homomers interact with other proteins, at least part of the time, forming transient or obligate heteromers. In the present paper, we review the structural, biophysical and evolutionary aspects of these protein interactions. We discuss how protein function and stability benefit from oligomerization, as well as evolutionary pathways by which oligomers emerge, mostly from the perspective of homomers. Finally, we emphasize the specificities of heteromeric complexes and their structure and evolution. We also discuss two analytical approaches increasingly being used to study protein structures as well as their interactions. First, we review the use of the biological networks and graph theory for analysis of protein interactions and structure. Secondly, we discuss recent advances in techniques for detecting correlated mutations, with the emphasis on their role in identifying pathways of allosteric communication.

Influence of sequential thiolate oxidation on a nitrile hydratase mimic probed by multiedge X-ray absorption spectroscopy

Nitrile hydratases (NHases) are Fe(III)- and Co(III)-containing hydrolytic enzymes that convert nitriles into amides. The metal-center is contained within an N(2)S(3) coordination motif with two post-translationally modified cysteinates contained in a cis arrangement, which have been converted into a sulfinate (R-SO(2)(-)) and a sulfenate (R-SO(-)) group. Herein, we utilize Ru L-edge and ligand (N-, S-, and P-) K-edge X-ray absorption spectroscopies to probe the influence that these modifications have on the electronic structure of a series of sequentially oxidized thiolate-coordinated Ru(II) complexes ((bmmp-TASN)RuPPh(3), (bmmp-O(2)-TASN)RuPPh(3), and (bmmp-O(3)-TASN)RuPPh(3)). Included is the use of N K-edge spectroscopy, which was used for the first time to extract N-metal covalency parameters. We find that upon oxygenation of the bis-thiolate compound (bmmp-TASN)RuPPh(3) to the sulfenato species (bmmp-O(2)-TASN)RuPPh(3) and then to the mixed sulfenato/sulfinato speices (bmmp-O(3)-TASN)RuPPh(3) the complexes become progressively more ionic, and hence the Ru(II) center becomes a harder Lewis acid. These findings are reinforced by hybrid DFT calculations (B(38HF)P86) using a large quadruple-ζ basis set. The biological implications of these findings in relation to the NHase catalytic cycle are discussed in terms of the creation of a harder Lewis acid, which aids in nitrile hydrolysis.

Phytotoxicity of thiocyanate to rice seedlings

The acute toxicity of potassium thiocyanate (KSCN) and ammonium thiocyanate (NH(4)SCN) to rice seedlings was tested. Hydroponically-grown plants showed different responses to the two species of thiocyanate. NH(4)SCN caused more severe stress to rice seedlings than KSCN. A significant reduction in transpiration and relative growth was observed with all NH(4)SCN treatments (p < 0.01), while the effect of KSCN on rice seedlings was more evident at greater than 100 mg SCN/L (p < 0.01). Both chemicals had a negligible effect on total chlorophyll content in shoots of rice seedlings (p > 0.05). Although phyto-transport of thiocyanate was apparent, rice seedlings showed significantly higher removal potential for NH(4)SCN than KSCN.

Controlled sulfur oxygenation of the ruthenium dithiolate (4,7-bis-(2'-methyl-2'-mercaptopropyl)-1-thia-4,7-diazacyclononane)RuPPh(3) under limiting O(2) conditions yields thiolato/sulfinato, sulfenato/sulfinato, and bis-sulfinato derivatives

The ruthenium(II) dithiolate complex (bmmp-TASN)RuPPh(3) (1) reacts with O(2) under limiting conditions to yield isolable sulfur oxygenated derivatives as a function of reaction time. With this approach, a family of sulfur-oxygenates has been prepared and isolated without the need for O-atom transfer agents or column chromatography. Addition of 5 equiv of O(2) to 1 yields the thiolato/sulfinato complex (bmmp-O(2)-TASN)RuPPh(3) (2) in 70% yield within 5 min. Increasing the reaction time to 12 h yields the sulfenato/sulfinato derivative (bmmp-O(3)-TASN)RuPPh(3) (3) in 82% yield. Longer reaction times and/or additional O(2) exposure yield the bis-sulfinato complex (bmmp-O(4)-TASN)RuPPh(3) (4). All products remain in the Ru(II) oxidation state under the conditions employed. Stoichiometric hydrolysis of acetonitrile to acetamide by 2 and 3 is observed in mixed acetonitrile, methanol, PIPES buffer (pH = 7.0) mixtures. The Ru(III)/(II) reduction potential of -0.85 V (versus ferrocenium/ferrocene) for 1 shifts to -0.39 and -0.26 V for 2 and 3, respectively, because of the decreased donor ability of sulfur upon oxygenation. X-ray diffraction studies reveal a decrease in Ru-S bond distances upon oxygenation by 0.045(1) and 0.158(1) Å for the sulfenato and sulfinato donors, respectively. Conversely, sulfur-oxygenation increases the Ru-P bond distance by 0.061(1) Å from 1 to 2 and an additional 0.027(1) Å from 2 to 3. Density functional theory investigations using the BP86 and B3LYP functionals with a LANL2DZ basis set for Ru and the 6-31G(d) basis set for all other atoms reveal a direct correlation between the oxygenation level and the Ru-P distance with an increase of 0.031 Å per O-atom.

Use of metallopeptide based mimics demonstrates that the metalloprotein nitrile hydratase requires two oxidized cysteinates for catalytic activity

Nitrile hydratases (NHases) are non-heme Fe(III) or non-corrin Co(III) containing metalloenzymes that possess an N(2)S(3) ligand environment with nitrogen donors derived from amidates and sulfur donors derived from cysteinates. A closely related enzyme is thiocyanate hydrolase (SCNase), which possesses a nearly identical active-site coordination environment as CoNHase. These enzymes are redox inactive and perform hydrolytic reactions; SCNase hydrolyzes thiocyanate anions while NHase converts nitriles into amides. Herein an active CoNHase metallopeptide mimic, [Co(III)NHase-m1] (NHase-m1 = AcNH-CCDLP-CGVYD-PA-COOH), that contains Co(III) in a similar N(2)S(3) coordination environment as CoNHase is reported. [Co(III)NHase-m1] was characterized by electrospray ionization-mass spectrometry (ESI-MS), gel-permeation chromatography (GPC), Co K-edge X-ray absorption spectroscopy (Co-S: 2.21 Å; Co-N: 1.93 Å), vibrational, and optical spectroscopies. We find that [Co(III)NHase-m1] will perform the catalytic conversion of acrylonitrile into acrylamide with up to 58 turnovers observed after 18 h at 25 °C (pH 8.0). FTIR data used in concert with calculated vibrational data (mPWPW91/aug-cc-TZVPP) demonstrates that the active form of [Co(III)NHase-m1] has a ligated SO(2) (ν = 1091 cm(-1)) moiety and a ligated protonated SO(H) (ν = 928 cm(-1)) moiety; when only one oxygenated cysteinate ligand (i.e., a mono-SO(2) coordination motif) or the bis-SO(2) coordination motif are found within [Co(III)NHase-m1] no catalytic activity is observed. Calculations of the thermodynamics of ligand exchange (B3LYP/aug-cc-TZVPP) suggest that the reason for this is that the SO(2)/SO(H) equatorial ligand motif promotes both water dissociation from the Co(III)-center and nitrile coordination to the Co(III)-center. In contrast, the under- or overoxidized motifs will either strongly favor a five coordinate Co(III)-center or strongly favor water binding to the Co(III)-center over nitrile binding.

Archaeal RibL: a new FAD synthetase that is air sensitive

FAD synthetases catalyze the transfer of the AMP portion of ATP to FMN to produce FAD and pyrophosphate (PP(i)). Monofunctional FAD synthetases exist in eukaryotes, while bacteria have bifunctional enzymes that catalyze both the phosphorylation of riboflavin and adenylation of FMN to produce FAD. Analyses of archaeal genomes did not reveal the presence of genes encoding either group, yet the archaea contain FAD. Our recent identification of a CTP-dependent archaeal riboflavin kinase strongly indicated the presence of a monofunctional FAD synthetase. Here we report the identification and characterization of an archaeal FAD synthetase. Methanocaldococcus jannaschii gene MJ1179 encodes a protein that is classified in the nucleotidyl transferase protein family and was previously annotated as glycerol-3-phosphate cytidylyltransferase (GCT). The MJ1179 gene was cloned and its protein product heterologously expressed in Escherichia coli. The resulting enzyme catalyzes the adenylation of FMN with ATP to produce FAD and PP(i). The MJ1179-derived protein has been designated RibL to indicate that it follows the riboflavin kinase (RibK) step in the archaeal FAD biosynthetic pathway. Aerobically isolated RibL is active only under reducing conditions. RibL was found to require divalent metals for activity, the best activity being observed with Co(2+), where the activity was 4 times greater than that with Mg(2+). Alkylation of the two conserved cysteines in the C-terminus of the protein resulted in complete inactivation. RibL was also found to catalyze cytidylation of FMN with CTP, making the modified FAD, flavin cytidine dinucleotide (FCD). Unlike other FAD synthetases, RibL does not catalyze the reverse reaction to produce FMN and ATP from FAD and PP(i). Also in contrast to other FAD synthetases, PP(i) inhibits the activity of RibL.

Structural basis for catalytic activation of thiocyanate hydrolase involving metal-ligated cysteine modification

Thiocyanate hydrolase (SCNase) is a member of a family of nitrile hydratase proteins, each of which contains a unique noncorrin cobalt center with two post-translationally modified cysteine ligands, cysteine-sulfenic acid or -sulfenate (Cys-SO(H)), and cysteine-sulfininate (Cys-SO(2)(-)), respectively. We have found that a partially matured recombinant SCNase was activated during storage. The crystal structures of SCNase before and after storage demonstrated that Cys-SO(2)(-) modification of gammaCys131 proceeded to completion prior to storage, while Cys-SO(H) modification of gammaCys133 occurred during storage. SCNase activity was suppressed when gammaCys133 was further oxidized to Cys-SO(2)(-). The correlation between the catalytic activity and the extent of the gammaCys133 modification indicates that the cysteine sulfenic acid modification of gammaCys133 is of primary importance in determining the activity of SCNase.

Self-subunit swapping chaperone needed for the maturation of multimeric metalloenzyme nitrile hydratase by a subunit exchange mechanism also carries out the oxidation of the metal ligand cysteine residues and insertion of cobalt

The incorporation of cobalt into low molecular mass nitrile hydratase (L-NHase) of Rhodococcus rhodochrous J1 has been found to depend on the alpha-subunit exchange between cobalt-free L-NHase (apo-L-NHase lacking oxidized cysteine residues) and its cobalt-containing mediator (holo-NhlAE containing Cys-SO(2)(-) and Cys-SO(-) metal ligands), this novel mode of post-translational maturation having been named self-subunit swapping, and NhlE having been recognized as a self-subunit swapping chaperone (Zhou, Z., Hashimoto, Y., Shiraki, K., and Kobayashi, M. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 14849-14854). We discovered here that cobalt was inserted into both the cobalt-free NhlAE (apo-NhlAE) and the cobalt-free alpha-subunit (apo-alpha-subunit) in an NhlE-dependent manner in the presence of cobalt and dithiothreitol in vitro. Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy analysis revealed that the non-oxidized cysteine residues in apo-NhlAE were post-translationally oxidized after cobalt insertion. These findings suggested that NhlE has two activities, i.e. cobalt insertion and cysteine oxidation. NhlE not only functions as a self-subunit swapping chaperone but also a metallochaperone that includes a redox function. Cobalt insertion and cysteine oxidation occurred under both aerobic and anaerobic conditions when Co(3+) was used as a cobalt donor, suggesting that the oxygen atoms in the oxidized cysteines were derived from water molecules but not from dissolved oxygen. Additionally, we isolated apo-NhlAE after the self-subunit swapping event and found that it was recycled for cobalt transfer into L-NHase.