Tailoring the specificity of the type C feruloyl esterase FoFaeC from Fusarium oxysporum towards methyl sinapate by rational redesign based on small molecule docking simulations

The type C feruloyl esterase FoFaeC from Fusarium oxysporum is a newly discovered enzyme with high potential for use in the hydrolysis of lignocellulosic biomass but it shows low activity towards sinapates. In this work, small molecule docking simulations were employed in order to identify important residues for the binding of the four model methyl esters of hydroxycinnamic acids, methyl ferulate/caffeate/sinapate/p-coumarate, to the predicted structure of FoFaeC. Subsequently rational redesign was applied to the enzyme’ active site in order to improve its specificity towards methyl sinapate. A double mutation (F230H/T202V) was considered to provide hydrophobic environment for stabilization of the methoxy substitution on sinapate and a larger binding pocket. Five mutant clones and the wild type were produced in Pichia pastoris and biochemically characterized. All clones showed improved activity, substrate affinity, catalytic efficiency and turnover rate compared to the wild type against methyl sinapate, with clone P13 showing a 5-fold improvement in catalytic efficiency. Although the affinity of all mutant clones was improved against the four model substrates, the catalytic efficiency and turnover rate decreased for the substrates containing a hydroxyl substitution

Engineering tyrosine-based electron flow pathways in proteins: The case of aplysia myoglobin

Tyrosine residues can act as redox cofactors that provide an electron transfer ("hole-hopping") route that enhances the rate of ferryl heme iron reduction by externally added reductants, for example, ascorbate. Aplysia fasciata myoglobin, having no naturally occurring tyrosines but 15 phenylalanines that can be selectively mutated to tyrosine residues, provides an ideal protein with which to study such through-protein electron transfer pathways and ways to manipulate them. Two surface exposed phenylalanines that are close to the heme have been mutated to tyrosines (F42Y, F98Y). In both of these, the rate of ferryl heme reduction increased by up to 3 orders of magnitude. This result cannot be explained in terms of distance or redox potential change between donor and acceptor but indicates that tyrosines, by virtue of their ability to form radicals, act as redox cofactors in a new pathway. The mechanism is discussed in terms of the Marcus theory and the specific protonation/deprotonation states of the oxoferryl iron and tyrosine. Tyrosine radicals have been observed and quantified by EPR spectroscopy in both mutants, consistent with the proposed mechanism. The location of each radical is unambiguous and allows us to validate theoretical methods that assign radical location on the basis of EPR hyperfine structure. Mutation to tyrosine decreases the lipid peroxidase activity of this myoglobin in the presence of low concentrations of reductant, and the possibility of decreasing the intrinsic toxicity of hemoglobin by introduction of these pathways is discussed. © 2012 American Chemical Society

Identification and Characterization of Alternative Promoters, Transcripts and Protein Isoforms of Zebrafish R2 Gene

Ribonucleotide reductase (RNR) is the rate-limiting enzyme in the de novo synthesis of deoxyribonucleoside triphosphates. Expression of RNR subunits is closely associated with DNA replication and repair. Mammalian RNR M2 subunit (R2) functions exclusively in DNA replication of normal cells due to its S phase-specific expression and late mitotic degradation. Herein, we demonstrate the control of R2 expression through alternative promoters, splicing and polyadenylation sites in zebrafish. Three functional R2 promoters were identified to generate six transcript variants with distinct 5′ termini. The proximal promoter contains a conserved E2F binding site and two CCAAT boxes, which are crucial for the transcription of R2 gene during cell cycle. Activity of the distal promoter can be induced by DNA damage to generate four transcript variants through alternative splicing. In addition, two novel splice variants were found to encode distinct N-truncated R2 isoforms containing residues for enzymatic activity but no KEN box essential for its proteolysis. These two N-truncated R2 isoforms remained in the cytoplasm and were able to interact with RNR M1 subunit (R1). Thus, our results suggest that multilayered mechanisms control the differential expression and function of zebrafish R2 gene during cell cycle and under genotoxic stress

Spectroscopic Studies of the Iron and Manganese Reconstituted Tyrosyl Radical in Bacillus Cereus Ribonucleotide Reductase R2 Protein

Ribonucleotide reductase (RNR) catalyzes the rate limiting step in DNA synthesis where ribonucleotides are reduced to the corresponding deoxyribonucleotides. Class Ib RNRs consist of two homodimeric subunits: R1E, which houses the active site; and R2F, which contains a metallo cofactor and a tyrosyl radical that initiates the ribonucleotide reduction reaction. We studied the R2F subunit of B. cereus reconstituted with iron or alternatively with manganese ions, then subsequently reacted with molecular oxygen to generate two tyrosyl-radicals. The two similar X-band EPR spectra did not change significantly over 4 to 50 K. From the 285 GHz EPR spectrum of the iron form, a g1-value of 2.0090 for the tyrosyl radical was extracted. This g1-value is similar to that observed in class Ia E. coli R2 and class Ib R2Fs with iron-oxygen cluster, suggesting the absence of hydrogen bond to the phenoxyl group. This was confirmed by resonance Raman spectroscopy, where the stretching vibration associated to the radical (C-O, ν7a = 1500 cm−1) was found to be insensitive to deuterium-oxide exchange. Additionally, the 18O-sensitive Fe-O-Fe symmetric stretching (483 cm−1) of the metallo-cofactor was also insensitive to deuterium-oxide exchange indicating no hydrogen bonding to the di-iron-oxygen cluster, and thus, different from mouse R2 with a hydrogen bonded cluster. The HF-EPR spectrum of the manganese reconstituted RNR R2F gave a g1-value of ∼2.0094. The tyrosyl radical microwave power saturation behavior of the iron-oxygen cluster form was as observed in class Ia R2, with diamagnetic di-ferric cluster ground state, while the properties of the manganese reconstituted form indicated a magnetic ground state of the manganese-cluster. The recent activity measurements (Crona et al., (2011) J Biol Chem 286: 33053–33060) indicates that both the manganese and iron reconstituted RNR R2F could be functional. The manganese form might be very important, as it has 8 times higher activity

Chemoenzymatic Fractionation and Characterization of Pretreated Birch Outer Bark

In this study, the application of different chemical and enzymatic treatment methods for the fractionation of the birch outer bark components was evaluated. More specifically, untreated and steam exploded, hydrothermally and organosolv treated bark samples were incubated with enzyme mixtures that consisted of cellulases, hemi-cellulases and esterases, and the effect of enzymes was analyzed with P-31 NMR and {C-13-H-1} HSQC. The biocatalysts performed the cleavage of ester bonds resulting in reduction of methoxy and aliphatic groups in the remaining solid fraction, whereas the aromatic fraction remained intact. Moreover, the suberin and lignin fraction were isolated chemically and their properties were characterized by gas chromatography (GC MS), P-31 NMR, {C-13-H-1} HSQC and gel permeation chromatography (GPC). It was demonstrated that the lignin fraction was enriched in guaiacyl phenolics but still contained some associated aliphatic acids and carbohydrates, whereas the suberin fraction presented a polymodal pattern of structures with different molecular weight distributions. This work will help in getting a deeper fundamental knowledge of the bark structure, the intermolecular connection between lignin and suberin fractions, as well as the potential use of enzymes in order to degrade the recalcitrant bark structure toward its valorization

Enzymatic synthesis of bioactive compounds with high potential for cosmeceutical application.

Cosmeceuticals are cosmetic products containing biologically active ingredients purporting to offer a pharmaceutical therapeutic benefit. The active ingredients can be extracted and purified from natural sources (botanicals, herbal extracts, or animals) but can also be obtained biotechnologically by fermentation and cell cultures or by enzymatic synthesis and modification of natural compounds. A cosmeceutical ingredient should possess an attractive property such as anti-oxidant, anti-inflammatory, skin whitening, anti-aging, anti-wrinkling, or photoprotective activity, among others. During the past years, there has been an increased interest on the enzymatic synthesis of bioactive esters and glycosides based on (trans)esterification, (trans)glycosylation, or oxidation reactions. Natural bioactive compounds with exceptional theurapeutic properties and low toxicity may offer a new insight into the design and development of potent and beneficial cosmetics. This review gives an overview of the enzymatic modifications which are performed currently for the synthesis of products with attractive properties for the cosmeceutical industry

Spruce bark‐extracted lignin and tannin‐based bioresin‐adhesives : Effect of curing temperatures on the thermal properties of the resins

In this study, formaldehyde‐free bioresin adhesives were synthesised from lignin and tannin, which were obtained from softwood bark. The extraction was done via organosolv treatment and hot water extraction, respectively. A non‐volatile, non‐toxic aldehyde, glyoxal, was used as a substitute for formaldehyde in order to modify the chemical structure of both the lignin and tannin. The glyoxal modification reaction was confirmed by ATR–FTIR spectroscopy. Three different resin formulations were prepared using modified lignin along with the modified tannin. The thermal properties of the modified lignin, tannin, and the bioresins were assessed by DSC and TGA. When the bioresins were cured at a high temperature (200 ℃) by compression moulding, they exhibited higher thermal stability as well as an enhanced degree of cross‐linking compared to the low temperature‐cured bioresins. The thermal properties of the resins were strongly affected by the compositions of the resins as well as the curing temperatures.

Isolation and Characterization of Organosolv and Alkaline Lignins from Hardwood and Softwood Biomass

Isolation of lignins from hardwood and softwood biomass samples, containing 26.1\% and 28.1\% lignin, respectively, has been performed with the use of alkaline and organosolv pretreatment methods. The effect of catalyst loading, ethanol content, particle size, and pretreatment time on the yields and properties of the isolated lignins were investigated. Alkaline lignins had higher carbohydrate content-up to 30\%- and exhibited higher molecular weights in the range of 3000 Da, with a maximum phenolic hydroxyl content of 1 mmol g(-1) for birch and 2 mmol g(-1) for spruce. Organosolv lignins, on the other hand, showed high purity-93\% or higher-despite the more extensive biomass dissolution into the pretreatment medium; they also exhibited a lower range of molecular weights between 600 and 1600 Da depending on the source and pretreatment conditions. Due to the lower molecular weight, phenolic hydroxyl content was also increased, reaching as high as 4 mmol g(-1) with a simultaneous decrease in aliphatic hydroxyl content as low as 0.6 mmol g(-1). Efficient lignin dissolution of 62\% for spruce and 69\% for birch, achieved at optimal pretreatment conditions, was combined with extensive hemicellulose removal

Integrating biometallurgical recovery of metals with biogenic synthesis of nanoparticles

Industrial activities, such as mining, electroplating, cement production, and metallurgical operations, as well as manufacturing of plastics, fertilizers, pesticides, batteries, dyes or anticorrosive agents, can cause metal contamination in the surrounding environment. This is an acute problem due to the non-biodegradable nature of metal pollutants, their transformation into toxic and carcinogenic compounds, and bioaccumulation through the food chain. At the same time, platinum group metals and rare earth elements are of strong economic interest and their recovery is incentivized. Microbial interaction with metals or metals-bearing minerals can facilitate metals recovery in the form of nanoparticles. Metal nanoparticles are gaining increasing attention due to their unique characteristics and application as antimicrobial and antibiofilm agents, biocatalysts, in targeted drug delivery, for wastewater treatment, and in water electrolysis. Ideally, metal nanoparticles should be homogenous in shape and size, and not toxic to humans or the environment. Microbial synthesis of nanoparticles represents a safe, and environmentally friendly alternative to chemical and physical methods. In this review article, we mainly focus on metal and metal salts nanoparticles synthesized by various microorganisms, such as bacteria, fungi, microalgae, and yeasts, as well as their advantages in biomedical, health, and environmental applications. © 2020 The Author(s