Nickel enzymes in microbes

Rational Development of Bacterial Ureases Inhibitors

Urease, an enzyme that catalyzes the hydrolysis of urea, is a virulence factor of various pathogenic bacteria. In particular, Helicobacter pylori, that colonizes the digestive tract and Proteus spp., that can infect the urinary tract, are related to urease activity. Therefore, urease inhibitors are considered as potential therapeutics against these infections. This review describes current knowledge of the structures, activity, and biological importance of bacterial ureases. Moreover, the structure-based design of several classes of bacterial urease inhibitors is presented and discussed. Phosphinic and phosphonic acids were applied as transition-state analogues, while Michael acceptors and ebselen derivatives were applied as covalent binders of cysteine residue. This review incorporates bacterial urease inhibitors from literature published between 2008 and 2021.

Strategy of optimizing anaerobic digestion of cassava distiller wastewater using a novel automatic biological incubation system

Due to the drawbacks of using fossil fuels and the need to mitigate global warming caused by increasing greenhouse gas emissions, agricultural biomass for bioenergy production is gaining great interest around the world. This work presented a study at a biochemical plant in Lianyungang, Jiangsu Province, China to maximize methane production from cassava distiller wastewater. The plant's annual production of cassava distiller wastewater is more than 3 million tons and currently was treated using a series of 5000 m³ Internal Circulation (IC) reactors. Modification was applied at No.19 IC reactor by connecting it to two 1 m³ automatic biological incubators called Information Bio-Booster (IBB). The effluent of the IC reactor was fed into the IBBs and iron, cobalt and nickel were added directly in the IBBs. The function of the IBBs was to regulate the microbial community. Afterwards, the microorganisms in the IBBs were pumped back into the IC reactor to participate in the methane production reaction. Daily net increase of methane content and COD removal reached 8.02% and 33% respectively in No.19 IC reactor comparing to the unadjusted reactors. Preliminary lab experiments found that improvements of biogas production, enhanced COD removal and VS removal was closely related to the enhancement of anaerobic microbial communities' diversity and the promotion of enzyme activity through the addition of the metal salts. Daily economic value could be estimated to be $218 which indicated the application potential of using the proposed system to enhance anaerobic digestion at industrial plants for bioenergy production.

Characteristics and in situ remediation effects of heavy metal immobilizing bacteria on cadmium and nickel co-contaminated soil

Cadmium (Cd) and nickel (Ni) in soil have caused serious environmental problems and increased healthy risks to humans and biota, it is vital important and necessary to develop effective methods to resolve the combined contaminated problems. In this study, strains L5 and L6 with good heavy metal resistant and immobilizing capacities were isolated from Cd and Ni contaminated soil. Bacterial characteristic experiment illustrated that many functional groups (-OH, -NH₂ and -COO et al.) were distributed on the surface of L5 and L6. Under the stress of heavy metals, bacterial appearances were distorted. The pot experiment indicated that the concentrations of HOAc-extractable Cd and Ni in soil reduced 6.26-15.33% and 13.31-19.53% with the inoculation of L5 and L6. In addition, the immobilization rates on Cd and Ni improved 61.27-128.50% and 23.69-39.66% with re-inoculation of strains L5 and L6 at 30 days, respectively. After inoculation of strains L5 and L6 for 60 days, the activities of FDA hydrolysis, acid phosphatase, urease, invertase and dehydrogenase in soil increased obviously. Furthermore, bacterial diversity indexes and community structure of soil were also improved. Thus, given the beneficial remediation effects of the isolated strains, L5 and L6 have great potentials for heavy metals contaminated soil remediation.

Ni(II) Interactions in Boreal Paenibacillus sp., Methylobacterium sp., Paraburkholderia sp., and Pseudomonas sp. Strains Isolated From an Acidic, Ombrotrophic Bog

The uptake of nickel [Ni(II)] by Paenibacillus sp., Methylobacterium sp., Paraburkholderia sp., and Pseudomonas sp. strains isolated from a boreal bog was studied using batch experiments. All strains removed Ni(II) from the solution and the uptake efficiency was affected by the nutrient source, incubation temperature, time, and pH. As highest Ni uptake (with a maximum Kd of 1890 L/kg DW) was recorded for the Pseudomonas sp. strains, these bacteria were used in the following protein expression (SDS-PAGE and MALDI-TOFF), transmission electron microscopy (TEM) and EDS experiments. In addition, Freundlich and Langmuir sorption isotherms were determined. In the Ni(II) treated cells, dense crystalline intra-cellular accumulations were observed in TEM examinations, which were identified as Ni accumulations using EDS. SDS-PAGE and MALDI-TOFF spectra of Ni(II) treated cells showed several changes in the protein profiles, which can indicate active accumulation of Ni in these bacteria. Concurrently, we observed Ni(II) uptake to follow Freundlich and Langmuir isotherms, suggesting straight cellular biosorption in addition to the intra-cellular accumulation. The role of cellular (cell membrane and cell wall) functional groups involved in Ni(II) binding were therefore studied using Fourier transformation infrared spectroscopy. These analyses supported the potential role of the alcoholic hydroxyl, carboxyl and amine groups in Ni(II) binding in these bacteria, therefore suggesting two different Ni(II) uptake mechanisms; (i) intra-cellular accumulation [possibly connected to detoxification of Ni(II)], and (ii) straight biosorption on cell membrane/wall functional groups.

Coordination behavior and bio-potent aspects of Ni(II) with 2-aminobenzamide and some amino acid mixed ligands--Part II: Synthesis, spectral, morphological, pharmacological and DNA interaction studies

A series of novel bioactive mixed ligand Ni(II) complexes (1a-1d) have been synthesised by using 2-aminobenzamide (2AB) and some bio-relevant amino acid ligands. The synthesised Ni(II) complexes were structurally characterized by various physico-chemical and spectral studies. Elemental analysis and molar conductance values suggest that 1:1:1 stoichiometry with non-electrolytic nature. Based on the spectral studies, both the ligands act as bidentate and they chelate with Ni(II) ion via amino-NH2 and amido-O and deprotonated carboxylato-O and amino-NH2 atoms respectively to form a stable six, five membered chelate rings with mononuclear octahedral geometry. Thermal studies show the presence of coordinated water and acetate molecules in the coordination. The powder X-ray diffractogram and SEM pictograph imply that all the complexes have fine crystalline peaks with homogeneous surface morphology. In vitro antimicrobial and antioxidant studies indicate the complexes are more active than free 2-aminobenzamide ligand. The Ni(II)-2AB-gly/phe complexes (1a and 1d) show significant oxidative cleavage and DNA binding activities. Moreover, the 3D molecular modeling, analysis of the complexes has also been studied.

The intrinsic dynamics and function of nickel-binding regulatory protein: insights from elastic network analysis

Nickel-responsive protein NikR regulates the nickel uptake in nickel-dependent bacteria by interacting with the operator of nikABCDE and subsequently repressing the transcription of NikABCDE, an ABC-type nickel transporter system. The function of NikR and its affinity for the operator DNA is highly conformation-dependent, which has been confirmed by three independent crystallographic studies on NikR proteins from different bacteria. Depending on the intracellular nickel concentration, NikR is able to adopt either the open form or one of the two closed forms (cis and trans) that differ in the domain-domain arrangement. Only the closed cis form is optimal for DNA binding. We examined the low-resolution vibrational spectrum of NikR in each conformational form using the elastic network model and observed large-scale domain-domain vibrations that are closely related to the conformational transitions required for function, particularly the symmetric bending mode and the asymmetric twisting mode. This analysis on the intrinsic dynamics coded in the three-dimensional molecular construct allows us to examine the proposed mechanisms of NikR regulation from the standpoint of protein collective motions. Our findings further support the three-state equilibrium hypothesis proposed by others, and imply that an isolated closed cis form may be dynamically unstable but can be stabilized by DNA binding. However, we also found that the simple C(alpha)-model used in the current analysis is insufficient to capture the impact of nickel binding on the protein dynamics, for which an all-atom model with detailed atom typing is more appropriate.

CbiX-homologous protein (CbiXhp), a metal-binding protein, fromStreptomyces seoulensisis involved in expression of nickel-containing superoxide dismutase

To find the accessory proteins participating in expression and maturation of nickel-containing superoxide dismutase (NiSOD), a metal-binding protein (CbiXhp) homologous to cobaltochelatase (CbiX) of Bacillus megaterium was isolated by nickel-nitrilotriacetic acid resin from Streptomyces seoulensis. The deduced amino acid sequence of cbiXhp showed 87% and 39% identity to CbiX of Streptomyces coelicolor and that of B. megaterium, respectively. Overexpression of CbiXhp increased the activity and the expression of NiSOD in the presence and absence of nickel, but to a lesser extent in its absence. This result indicates that CbiXhp is involved in the expression of NiSOD.

Requirement of nickel metabolism proteins HypA and HypB for full activity of both hydrogenase and urease in Helicobacter pylori

The nickel-containing enzymes hydrogenase and urease require accessory proteins in order to incorporate properly the nickel atom(s) into the active sites. The Helicobacter pylori genome contains the full complement of both urease and hydrogenase accessory proteins. Two of these, the hydrogenase accessory proteins HypA (encoded by hypA) and HypB (encoded by hypB), are required for the full activity of both the hydrogenase and the urease enzymes in H. pylori. Under normal growth conditions, hydrogenase activity is abolished in strains in which either hypA (HypA:kan) or hypB (HypB:kan) have been interrupted by a kanamycin resistance cassette. Urease activity in these strains is 40 (HypA:kan)- and 200 (HypB:kan)-fold lower than for the wild-type (wt) strain 43504. Nickel supplementation in the growth media restored urease activity to almost wt levels. Hydrogenase activity was restored to a lesser extent, as has been observed for hyp mutants in other (H(2)-oxidizing) bacteria. Expression levels of UreB (the urease large subunit) were not affected by inactivation of either hypA or hypB, as determined by immunoblotting. Urease activity was not affected by lesions in the genes for either the hydrogenase accessory proteins HypD or HypF or the hydrogenase large subunit structural gene, indicating that the urease deficiency was not caused by lack of hydrogenase activity. When crude extracts of wt, HypA:kan and HypB:kan were separated by anion exchange chromatography, the urease-containing fractions of the mutant strains contained about four (HypA:kan)- and five (HypB:kan)-fold less nickel than did the urease from wt, indicating that the lack of urease activity in these strains results from a nickel deficiency in the urease enzyme.

Synthesis and characterization of square planar nickel(II)-arylthiolate complexes with the biphenyl-2,2'-dithiolate ligand

Two new NiIIS4 complexes with the biphenyl-2,2'-dithiolate ligand (L) are reported. The dinuclear complex 1, [Ni2L3]2-, was formed in the reaction of 2-3 equiv of Na2L and [NiCl4]2- and the mononuclear complex [NiL2]2- (2) by using 4-10 equiv of Na2L. Complexes 1 and 2 have been crystallographically characterized. (Et4N)2[1].0.5S2Ph2, CH3CN: C60H71N3Ni2S7, triclinic, P1, a = 13.806(2) A, b = 14.267(2) A, c = 16.873(2) A, alpha = 69.263(10) degrees, beta = 69.267(8) degrees, gamma = 83.117(10) degrees, Z = 2, R1 = 0.0752 (wR2 = 0.2011). (Et4N)(Na.CH3CN)[2]: C34H39N2NaNiS4, triclinic, P1, a = 9.9570(10) A, b = 13.2670(10) A, c = 13.9560(10) A, alpha = 108.489(7) degrees, beta = 90.396(6) degrees, gamma = 103.570(4) degrees, Z = 2, R1 = 0.0390 (wR2 = 0.0995). Both complexes are square planar about the nickel ion in the solid state as well as in solution. Most Ni(II)-thiolate complexes are square planar except the tetrahedral mononuclear complexes with monodentate arylthiolate ligands that cannot force a square planar geometry. The ligand (L) has some flexibility to change its bite angle via the phenyl-phenyl bond and should not force a planar geometry on its complexes either. Therefore, it is interesting that 2 has adopted a square planar structure. Complex 2 readily converts to 1 in solution when not in the presence of excess L in a process that is presumably similar to that known for other mononuclear, bidentate ligated Ni(II) complexes. Both complexes, at least in the solid state, appear to have an inclination to bind another metal ion on one face of the complex (Ni2+ in 1, Na+ in 2). We hope to take advantage of this in future work to synthesize relevant model complexes for the active sites of the nickel-iron hydrogenases after suitable modifications are made to L.