Alkali-tolerant high-activity catalase from a thermophilic bacterium and its overexpression in Escherichia coli

Mining and rational design of psychrophilic catalases using metagenomics and deep learning models

A complete catalase-encoding gene, designated soiCat1, was obtained from soil samples via metagenomic sequencing, assembly, and gene prediction. soiCat1 showed 73% identity to a catalase-encoding gene of Mucilaginibacter rubeus strain P1, and the amino acid sequence of soiCAT1 showed 99% similarity to the catalase of a psychrophilic bacterium, Pedobacter cryoconitis. soiCAT1 was identified as a psychrophilic enzyme due to the low optimum temperature predicted by the deep learning model Preoptem, which was subsequently validated through analysis of enzymatic properties. Experimental results showed that soiCAT1 has a very narrow range of optimum temperature, with maximal specific activity occurring at the lowest test temperature (4 °C) and decreasing with increasing reaction temperature from 4 to 50 °C. To rationally design soiCAT1 with an improved temperature range, soiCAT1 was engineered through site-directed mutagenesis based on molecular evolution data analyzed through position-specific amino acid possibility calculation. Compared with the wild type, one mutant, soiCAT1S205K, exhibited an extended range of optimum temperature ranging from 4 to 20 °C. The strategies used in this study may shed light on the mining of genes of interest and rational design of desirable proteins. KEY POINTS: • Numerous putative catalases were mined from soil samples via metagenomics. • A complete sequence encoding a psychrophilic catalase was obtained. • A mutant psychrophilic catalase with an extended range of optimum temperature was engineered through site-directed mutagenesis.

Efficient Mn(II) removal mechanism by Serratia marcescens QZB-1 at high manganese concentration

Manganese (Mn(II)) pollution has recently increased and requires efficient remediation. In this study, Serratia marcescens QZB-1, isolated from acidic red soil, exhibited high tolerance against Mn(II) (up to 364 mM). Strain QZB-1 removed a total of 98.4% of 18 mM Mn(II), with an adsorption rate of 71.4% and oxidation rate of 28.6% after incubation for 48 h. The strain synthesized more protein (PN) to absorb Mn(II) when stimulated with Mn(II). The pH value of the cultural medium continuously increased during the Mn(II) removal process. The product crystal composition (mainly MnO₂ and MnCO₃), Mn-O functional group, and element-level fluctuations confirmed Mn oxidation. Overall, strain QZB-1 efficiently removed high concentration of Mn(II) mainly via adsorption and showed great potential for manganese wastewater removal.

Looking into a highly thermostable and efficient recombinant manganese-catalase from Geobacillusthermopakistaniensis

Catalases, heme or non-heme, are catalysts that decompose hydrogen peroxide. Among them, non-heme or manganese-catalases have been studied from limited organisms. We report here heterologous production of a manganese-catalase, Cat-II_Gt, previously annotated as a hypothetical protein, from a thermophilic bacterium Geobacillus thermopakistaniensis. Recombinant Cat-II_Gt, produced as inactive inclusion bodies in Escherichia coli, was solubilized and refolded into a soluble and highly active form. Sequence homology, absorption spectra, resistance to sodium azide inhibition and activation by Mn²⁺ indicated that it was a manganese-catalase. Metal analysis revealed the presence of ∼2 Mn²⁺ and ∼2 Ca²⁺ per subunit of Cat-II_Gt. Recombinant Cat-II_Gt exhibited highest activity at pH 10.0 and 70°C. The enzyme was highly active with a specific activity of 40,529 μmol min^-1 mg^-1. The apparent K_m and k_cat values were 75 mM and 1.5 × 10⁴ s^-1 subunit^-1, respectively. Recombinant Cat-II_Gt was highly thermostable with a half-life of 30 min at 100°C. The structural attributes of Cat-II_Gt, including the metal and substrate binding residues, were predicted by homology modeling and molecular docking studies. High activity and thermostability and alkaline nature make Cat-II_Gt a potential candidate for textile and paper processing industries.

Structural and functional analyses of a novel manganese-catalase from Bacillus subtilis R5

Catalases catalyze the decomposition of hydrogen peroxide into water and oxygen. Limited reports are available on characterization of manganese-catalases. We describe here molecular cloning and expression in Escherichia coli of a putative manganese-catalase gene from mesophilic bacterium, Bacillus subtilis R5. The gene product, Cat_Bsu, produced as a soluble protein, was purified to apparent homogeneity and biochemically characterized. The absorption spectra and nonsignificant inhibition by sodium azide indicated that it is a manganese-catalase. The protein was in homohexameric form in solution, with a subunit molecular weight of 30 kDa, containing ~2 Mn²⁺ and ~1 Ca²⁺ per subunit. Cat_Bsu showed highest activity at pH 8.0 and 55 °C. It was found to be highly active with a specific activity of 25,290 μmol min^-1 mg^-1 and apparent K_m and k_cat values of 98 mM and 1.27 × 10⁴ s^-1 subunit^-1, respectively. Although from a mesophilic source, it exhibited a half-life of 2 h at 80 °C. Furthermore, the active site and metal binding residues in Cat_Bsu were predicted by homology modelling and molecular docking. To the best of our knowledge, this is the first characterization of a manganese-catalase from genus Bacillus.

Gazing into the remarkable world of non-heme catalases through the window of the cyanobacterial Mn-catalase 'KatB'

Catalases, enzymes that decompose H₂O₂, are broadly categorized as heme catalases or non-heme catalases. The non-heme catalases are also known as Mn-catalases as they have Mn atoms in their active sites. However, unlike the well characterized heme-catalases, the study of Mn-catalases has gained importance only in the last few years. The filamentous, heterocystous, N₂-fixing cyanobacterium Anabaena PCC 7120, shows the presence of two Mn-catalases, KatA and KatB, but lacks heme catalases. Of the two Mn-catalases, KatB, which is induced by salt/desiccation, plays a major role in overcoming salinity/oxidative stress. In this mini review, we have summarized the recent advances made in the field of Mn-catalases, particularly KatB, and have interpreted these results in the larger context of stress physiology. These aspects bring to the fore the distinctive biochemical/structural properties of Mn-catalases and furthermore highlight the in vivo importance of these enzymes in adapting to oxidative stresses.

Cloning, Expression, and Characterization of a Novel Thermophilic Monofunctional Catalase from Geobacillus sp. CHB1

Catalases are widely used in many scientific areas. A catalase gene (Kat) from Geobacillus sp. CHB1 encoding a monofunctional catalase was cloned and recombinant expressed in Escherichia coli (E. coli), which was the first time to clone and express this type of catalase of genus Geobacillus strains as far as we know. This Kat gene was 1,467 bp in length and encoded a catalase with 488 amino acid residuals, which is only 81% similar to the previously studied Bacillus sp. catalase in terms of amino acid sequence. Recombinant catalase was highly soluble in E. coli and made up 30% of the total E. coli protein. Fermentation broth of the recombinant E. coli showed a high catalase activity level up to 35,831 U/mL which was only lower than recombinant Bacillus sp. WSHDZ-01 among the reported catalase production strains. The purified recombinant catalase had a specific activity of 40,526 U/mg and K m of 51.1 mM. The optimal reaction temperature of this recombinant enzyme was 60°C to 70°C, and it exhibited high activity over a wide range of reaction temperatures, ranging from 10°C to 90°C. The enzyme retained 94.7% of its residual activity after incubation at 60°C for 1 hour. High yield and excellent thermophilic properties are valuable features for this catalase in industrial applications.

KatB, a cyanobacterial Mn-catalase with unique active site configuration: Implications for enzyme function

Manganese catalases (Mn-catalases), a class of H2O2 detoxifying proteins, are structurally and mechanistically distinct from the commonly occurring catalases, which contain heme. Active site of Mn-catalases can serve as template for the synthesis of catalase mimetics for therapeutic intervention in oxidative stress related disorders. However, unlike the heme catalases, structural aspects of Mn-catalases remain inadequately explored. The genome of the ancient cyanobacterium Anabaena PCC7120, shows the presence of two Mn-catalases, KatA and KatB. Here, we report the biochemical and structural characterization of KatB. The KatB protein (with a C-terminal his-tag) was over-expressed in Escherichia coli and purified by affinity chromatography. On the addition of Mn(2+) to the E. coli growth medium, a substantial increase in production of the soluble KatB protein was observed. The purified KatB protein was an efficient catalase, which was relatively insensitive to inhibition by azide. Crystal structure of KatB showed a hexameric assembly with four-helix bundle fold, characteristic of the Ferritin-like superfamily. With canonical Glu4His2 coordination geometry and two terminal water ligands, the KatB active site was distinctly different from that of other Mn-catalases. Interestingly, the KatB active site closely resembled the active sites of ruberythrin/bacterioferritin, bi-iron members of the Ferritin-like superfamily. The KatB crystal structure provided fundamental insights into the evolutionary relationship within the Ferritin-like superfamily and further showed that Mn-catalases can be sub-divided into two groups, each with a distinct active site configuration.

Purification, cloning, expression, and biochemical characterization of a monofunctional catalase, KatP, from Pigmentiphaga sp. DL-8

Catalases are essential components of the cellular equipment used to cope with oxidative stress. The monofunctional catalase KatP was purified from Pigmentiphaga sp. using ammonium sulfate precipitation (ASP), diethylaminoethyl ion exchange chromatography (IEC), and hydrophobic interaction chromatography (HIC). The purified catalase formed polymer with an estimated monomer molecular mass of 54kDa, which were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and zymogram analysis. KatP exhibited a specific catalytic activity of 73,000U/mg, which was higher than that of catalase-1 of Comamonas terrigena N3H (55,900U/mg). Seven short tryptic fragments of this catalase were obtained by electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF MS/MS), and the gene, katP, was cloned by PCR amplification and overexpressed in Escherichia coli BL21 (DE3). Based on the complete amino acid sequence, KatP was identified as a clade 3 monofunctional catalase. The specific activities of recombinant KatP for hydrogen peroxide (690,000U/mg) increased 9-fold over that of the parent strain. The Km and Vmax of recombinant KatP were 9.48mM and 81.2mol/minmg, respectively. The optimal pH and temperature for KatP were 7.0 and 37°C, respectively, and the enzyme displayed abroad pH-stable range of 4.0-11.0. The enzyme was inhibited by Zn(2+), Cu(2+), Cr(2+), and Mn(2+), whereas Fe(3+) and Mg(2+) stimulated KatP enzymatic activity. Interestingly, the catalase activity of recombinant KatP displayed high stability under different temperature and pH conditions, suggesting that KatP is a potential candidate for the production of catalase.

In vitro and in vivo inhibitory effects of some fungicides on catalase produced and purified from white-rot fungus Phanerochaete chrysosporium

In this study, in vitro and in vivo effects of some commonly used fungicides, antibiotics, and various chemicals on isolated and purified catalase from Phanerochaete chrysosporium were investigated. The catalase was purified 129.10-fold by using 60% ammonium sulfate and 60% ethanol precipitations, DEAE-cellulose anion exchange and Sephacryl-S-200 gel filtration chromatographies from P. chrysosporium growth in carbon- and nitrogen-limited medium for 12 days. The molecular weight of native purified catalase from P. chrysosporium was found to be 290 ± 10 kDa, and sodium dodecyl sulfate (SDS)-PAGE results indicated that enzyme consisted of four apparently identical subunits, with a molecular weight of 72.5 ± 2.5 kDa. Kinetic characterization studies showed that optimum pH and temperature, Km and Vmax values of the purified catalase which were stable in basic region and at comparatively high temperatures were 7.5, 30°C, 289.86 mM, and 250,000 U/mg, respectively. The activity of purified catalase from P. chrysosporium was significantly inhibited by dithiothreitol (DTT), 2-mercaptoethanol, iodoacetamide, EDTA, and sodium dodecyl sulfate (SDS). It was found that while antibiotics had no inhibitory effects, 45 ppm benomyl, 144 ppm captan, and 47.5 ppm chlorothalonil caused 14.52, 10.82, and 38.86% inhibition of purified catalase, respectively. The inhibition types of these three fungicides were found to be non-competitive inhibition with the Ki values of 1.158, 0.638, and 0.145 mM and IC50 values of 0.573, 0.158, 0.010 mM, respectively. The results of in vivo experiments also showed that benomyl, captan and chlorothalonil caused 15.25, 1.96, and 36.70% activity decreases after 24-h treatments compared to that of the control.

Isolation and in vivo hepatoprotective activity of Melothria heterophylla (Lour.) Cogn. against chemically induced liver injuries in rats

OBJECTIVE

To investigate hepatoprotective activity of ethanol extract of Melothria heterophylla Lour Cogn. (EEMH) against CCl(4)-induced hepatic damage in rats.

METHODS

β-sitosterol was isolated by column chromatography and characterized spectroscopically. Two different doses (200 and 400 mg/kg bw) of EEMH were administered orally in alternate days. The hepatoprotective activity was studied in liver by measuring biochemical parameters such as serum aspartate amino transferase (AST), alanine amino transferase (ALT), alkaline phosphatase (ALP), total protein and total bilirubin. Lipid peroxidation product and different antioxidant enzyme activities were assessed in liver homogenate.

RESULTS

EEMH reduced all biochemical parameters and lipid peroxidation, as well as it increased the antioxidant enzyme activities in comparison with silymarin. The protective effect of the extract on CCl(4) induced damage was confirmed by histopathological examination of the liver.

CONCLUSIONS

This result strongly supports the protective effect of EEMH against acute liver injury, and may be attributed to its antioxidative activity.