Biomolecular scaffolds for enhanced signaling and catalytic efficiency

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Engineering of glycosidases and glycosyltransferases

In recent years, substantial advances have been made in the engineering of glycosidases and glycosyltransferases for the synthesis and degradation of glycan structures. Key developments include improvement of the thermostability of xylanase through comprehensive saturation mutagenesis, creation of the first glycosynthase derived from an inverting glycosidase and the emergence of a new class of modified glycosidases capable of efficiently synthesizing thioglycosidic linkages. Of particular note is the increased use of random mutagenesis and directed evolution tactics for tailoring glycosidase activity. Although the engineering of glycosyltransferases is still in its early stages, recent work on the structure-based alteration of substrate specificity and the manipulation of glycosyltransferase profiles in whole cells to effect complex changes in in vivo glycobiology probably foreshadows a wave of considerable innovation in this area.     

Co-pigmentation and flavonoid glycosyltransferases in blue Veronica persica flowers

Glycosylation is one of the key modification steps for plants to produce a broad spectrum of flavonoids with various structures and colors. A survey of flavonoids in the blue flowers of Veronica persica Poiret (Lamiales, Scrophulariaceae), which is native of Eurasia and now widespread worldwide, led to the identification of highly glycosylated flavonoids, namely delphinidin 3-O-(2-O-(6-O-p-coumaroyl-glucosyl)-6-O-p-coumaroyl-glucoside)-5-O-glucoside (1) and apigenin 7-O-(2-O-glucuronosyl)-glucuronide (2), as two of its main flavonoids. Interestingly, the latter flavone glucuronide (2) caused a bathochromic shift on the anthocyanin (1) toward a blue hue in a dose-dependent manner, showing an intermolecular co-pigment effect. In order to understand the molecular basis for the biosynthesis of this glucuronide, we isolated a cDNA encoding a UDP-dependent glycosyltransferase (UGT88D8), based on the structural similarity to flavonoid 7-O-glucuronosyltransferases (F7GAT) from Lamiales plants. Enzyme assays showed that the recombinant UGT88D8 protein catalyzes the 7-O-glucuronosylation of apigenin and its related flavonoids with preference to UDP-glucuronic acid as a sugar donor. Furthermore, we identified and functionally characterized a cDNA encoding another UGT, UGT94F1, as the anthocyanin 3-O-glucoside-2″-O-glucosyltransferase (A3Glc2″GlcT), according to the structural similarity to sugar-sugar glycosyltransferases classified to the cluster IV of flavonoid UGTs. Preferential expression of UGT88D8 and UGT94F1 genes in the petals supports the idea that these UGTs play an important role in the biosynthesis of key flavonoids responsible for the development of the blue color of V. persica flowers.     

The catalytic efficiency of soybean lipoxygenase-1 is enhanced at low gravity

Several cellular processes are modified when cells are placed under conditions of weightlessness. As yet, there is no coherent explanation for these observations, nor it is known which biomolecules might act as gravity sensors. Lipoxygenases generate leukotrienes and lipoxins from arachidonic acid, being responsible for many pharmacological and immunological effects, some of which are known to be affected by microgravity. In the course of the 28th parabolic flight campaign of the European Space Agency we measured the activity of pure soybean lipoxygenase-1 on linoleic acid, by a fibre optics spectrometer developed on purpose. It was found that microgravity reduced the apparent Michaelis-Menten constant (Km) of the enzymatic reaction to one fourth with respect to the 1 g control, whereas, the catalytic constant (k(cat)) was unaffected. Consequently, the catalytic efficiency of lipoxygenase-1 (k(cat)/Km) was approximately four-fold higher in flight than on ground. This unprecedented finding suggests that lipoxygenase-1 might be a molecular target for gravity.     

A bioconjugate of Pseudomonas cepacia lipase with alginate with enhanced catalytic efficiency

A bioconjugate of Pseudomonas cepacia lipase with alginate was prepared by simple adsorption. Atomic force microscope (AFM) images showed that this bioconjugate resulted from adsorption rather than entrapment of the enzyme as enzyme molecules were visible on the gel surface. The soluble bioconjugate exhibited increased enzyme activity in terms of high effectiveness factor (effectiveness factor was 3 for the immobilized preparation) and greater Vmax/Km value (Vmax/Km increased 25 times upon immobilization). This constitutes one of the less frequently observed instances of lipase activation by lid opening as a result of binding to a predominantly hydrophilic molecule. The bioconjugate was also more stable at 55 degrees C as compared to the free enzyme and could be reused for oil hydrolysis up to 4 cycles without any loss in activity. Fluorescence emission spectroscopy showed that the immobilized enzyme had undergone definite conformational changes.     

Engineering of flavonoid O-methyltransferase for a novel regioselectivity

An O-methyltransferase isolated from poplar, POMT7, was identified as a flavone 7-O-methyltransferase. In order to generate a mutant of POMT-7 having a novel regioselectivity, we conducted an error-prone polymerase chain reaction. More than 100 mutants were screened and one of the mutants (POMT-M1) Asp257Gly, methylated the 3-hydroxyl group of flavonols in addition to 7-hydrdoxyl group. The mutation changed asparagine residue at the position of 257 into glycine. The kinetic parameters showed that the wild type POMT7 was better activity toward kaempferol and quercetin than the POMT7-M1. Using E. coli transformant expressing POMT7-M1, 58 μM of 3, 7-O-dimethylquercetin and 70 μM of 3, 7-O-dimethylkaempferol from 100 μM of corresponding substrate were synthesized successfully.     

Cryoconcentration of flavonoid extract for enhanced biophotovoltaics and pH sensitive thin films

Flavonoids are important value added products for dye sensitized solar cells biosensors, functional foods, medicinal supplements, nanomaterial synthesis, and other applications. Brassica oleracea contains high levels of anthocyanins in leaf sap vacuoles, and there are many viable extraction techniques that vary in terms of simplicity, environmental impact, cost, and extract photochemical/electrochemical properties. The efficiency of value added biotechnologies from flavonoid is a function of anthocyanin activity/concentration and molecule stability (i.e., ability to retain molecular resonance under a wide range of conditions). In this paper, we show that block cryoconcentration and partial thawing of anthocyanin from B. oleracea is a green, facile, and highly efficient technique that does not require any special equipment or protocols for producing enhanced value added products. Cryoconcentration increased anthocyanin activity and total phenol content approximately 10 times compared with common extraction techniques. Cryoconcentrated extract had enhanced electrochemical properties (higher oxidation potential), improved chroma, and higher UV absorbance than extract produced with other methods for a pH range of 2–12, with minimal effect on the diffusion coefficient of the extract. As a proof of concept for energy harvesting and sensor applications, dye sensitized solar cells and pH‐sensitive thin films were prepared and tested. These devices were comparable with other recently published biotechnologies in terms of efficacy, but did not require expensive/environmentally detrimental extraction or concentration methods. This low cost, biorenewable, and simple method can be used for development of a variety of value added products. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:206–217, 2018     

Controlling selectivity and enhancing yield of flavonoid glycosides in recombinant yeast

Flavonoid glycosides are known for their medicinal properties and potential use as natural sweeteners. In this study, Saccharomyces cerevisiae expressing a flavonoid glucosyltransferase from Dianthus caryophyllus was used as a whole-cell biocatalyst. The yeast system’s performance was characterized using the flavanone naringenin as a model substrate for the production of naringenin glycosides. It was found that final naringenin glycoside yields increased in a dose-dependent manner with increasing initial naringenin substrate concentrations. However, naringenin concentrations >0.5 mM did not give further enhancements in glycoside yield. In addition, a method for controlling overall selectivity was discovered where the glucose content in the culture medium could be altered to control the selectivity, making either naringenin-7-O-glucoside (N7O) or naringenin-4′-O-glucoside (N4O) the major products. The highest yields achieved were 87 mg/L of N7O and 82 mg/L of N4O using 40MSGI and 2xMSGI media, respectively. The effects of two intermediates involved in UDP-glucose biosynthesis, uridine 5′-monophosphate (UMP) and orotic acid, on glycoside yields were also determined. Addition of UMP to the culture medium significantly decreased glycoside yield. In contrast, addition of orotic acid to the culture medium significantly enhanced the glycoside yield and shifted the selectivity toward N7O. The highest naringenin glycoside yield achieved using 10 mM orotic acid in the 40MSGI media was 155 mg/L, a 71% conversion of substrate to product.     

Engineering of pyranose 2-oxidase from Peniophora gigantea towards improved thermostability and catalytic efficiency

To improve the stability and catalytic efficiency of pyranose 2-oxidase (P2Ox) by molecular enzyme evolution, we cloned P2Ox cDNA by RACE-PCR from a cDNA library derived from the basidiomycete Peniophora gigantea. The P2Ox gene was expressed in Escherichia coli BL21(DE3), yielding an intracellular and enzymatically active P2OxB with a volumetric yield of 500 units/l. Site-directed mutagenesis was employed to construct the P2Ox variant E540K (termed P2OxB1), which exhibited increased thermo- and pH-stability compared with the wild type, concomitantly with increased catalytic efficiencies (k_cat/K_m) for d-xylose and l-sorbose. P2OxB1 was provided with a C-terminal His₆-tag (termed P2OxB1H) and subjected to directed evolution using error-prone PCR. Screening based on a chromogenic assay yielded the new P2Ox variant K312E (termed P2OxB2H) that showed significant improvements with respect to k_cat/K_m for d-glucose (5.3-fold), methyl--d-glucoside (2.0-fold), d-galactose (4.8-fold), d-xylose (59.9-fold), and l-sorbose (69.0-fold), compared with wild-type P2Ox. The improved catalytic performance of P2OxB2H was demonstrated by bioconversions of l-sorbose that initially was a poor substrate for wild-type P2Ox. This is the first report on the improvement of a pyranose 2-oxidase by a dual approach of site-directed mutagenesis and directed evolution, and the application of the engineered P2Ox in bioconversions.This revised version was published online in February 2005 with corrections to Table 2.     

Chimeric DNA-RNA hammerhead ribozymes have enhanced in vitro catalytic efficiency and increased stability in vivo.

Subsequent to the discovery that RNA can have site specific cleavage activity, there has been a great deal of interest in the design and testing of trans-acting catalytic RNAs as both surrogate genetic tools and as therapeutic agents. We have been developing catalytic RNAs or ribozymes with target specificity for HIV-1 RNA and have been exploring chemical synthesis as one method for their production. To this end, we have chemically synthesized and experimentally analyzed chimeric catalysts consisting of DNA in the non-enzymatic portions, and RNA in the enzymatic core of hammerhead type ribozymes. Substitutions of DNA for RNA in the various stems of a hammerhead ribozyme have been analyzed in vitro for kinetic efficiency. One of the chimeric ribozymes used in this study, which harbors 24 bases of DNA capable of base-pairing interactions with an HIV-1 gag target, but maintains RNA in the catalytic center and in stem-loop II, has a sixfold greater kcat value than the all RNA counterpart. This increased activity appears to be the direct result of enhanced product dissociation. Interestingly, a chimeric ribozyme in which stem-loop II (which divides the catalytic core) is comprised of DNA, exhibited a marked reduction in cleavage activity, suggesting that DNA in this region of the ribozyme can impart a negative effect on the catalytic function of the ribozyme. DNA-RNA chimeric ribozymes transfected by cationic liposomes into human T-lymphocytes are more stable than their all-RNA counterparts. Enhanced catalytic turnover and stability in the absence of a significant effect on Km make chimeric ribozymes favorable candidates for therapeutic agents.     

Structure-function relationships for Schizophyllum commune trehalose phosphorylase and their implications for the catalytic mechanism of family GT-4 glycosyltransferases

The cDNA encoding trehalose phosphorylase, a family GT-4 glycosyltransferase from the fungus Schizophyllum commune, was isolated and expressed in Escherichia coli to yield functional recombinant protein in its full length of 737 amino acids. Unlike the natural phosphorylase that was previously obtained as a truncated 61 kDa monomer containing one tightly bound Mg2+, the intact enzyme produced in E. coli is a dimer and not associated with metal ions [Eis, Watkins, Prohaska and Nidetzky (2001) Biochem. J. 356, 757-767]. MS analysis of the slow spontaneous conversion of the full-length enzyme into a 61 kDa fragment that is fully active revealed that critical elements of catalysis and specificity of trehalose phosphorylase reside entirely in the C-terminal protein part. Intact and truncated phosphorylases thus show identical inhibition constants for the transition state analogue orthovanadate and alpha,alpha-trehalose (K(i) approximately 1 microM). Structure-based sequence comparison with retaining glycosyltransferases of fold family GT-B reveals a putative active centre of trehalose phosphorylase, and results of site-directed mutagenesis confirm the predicted crucial role of Asp379, His403, Arg507 and Lys512 in catalysis and also delineate a function of these residues in determining the large preference of the wild-type enzyme for the phosphorolysis compared with hydrolysis of alpha,alpha-trehalose. The pseudo-disaccharide validoxylamine A was identified as a strong inhibitor of trehalose phosphorylase (K(i)=1.7+/-0.2 microM) that displays 350-fold tighter binding to the enzyme-phosphate complex than the non-phosphorolysable substrate analogue alpha,alpha-thio-trehalose. Structural and electronic features of the inhibitor that may be responsible for high-affinity binding and their complementarity to an anticipated glucosyl oxocarbenium ion-like transition state are discussed.     

Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli

The identification of optimal genotypes that result in improved production of recombinant metabolites remains an engineering conundrum. In the present work, various strategies to reengineer central metabolism in Escherichia coli were explored for robust synthesis of flavanones, the common precursors of plant flavonoid secondary metabolites. Augmentation of the intracellular malonyl coenzyme A (malonyl-CoA) pool through the coordinated overexpression of four acetyl-CoA carboxylase (ACC) subunits from Photorhabdus luminescens (PlACC) under a constitutive promoter resulted in an increase in flavanone production up to 576%. Exploration of macromolecule complexes to optimize metabolic efficiency demonstrated that auxiliary expression of PlACC with biotin ligase from the same species (BirAPl) further elevated flavanone synthesis up to 1,166%. However, the coexpression of PlACC with Escherichia coli BirA (BirAEc) caused a marked decrease in flavanone production. Activity improvement was reconstituted with the coexpression of PlACC with a chimeric BirA consisting of the N terminus of BirAEc and the C terminus of BirAPl. In another approach, high levels of flavanone synthesis were achieved through the amplification of acetate assimilation pathways combined with the overexpression of ACC. Overall, the metabolic engineering of central metabolic pathways described in the present work increased the production of pinocembrin, naringenin, and eriodictyol in 36 h up to 1,379%, 183%, and 373%, respectively, over production with the strains expressing only the flavonoid pathway, which corresponded to 429 mg/liter, 119 mg/liter, and 52 mg/liter, respectively.     

Engineering enhanced protein disaggregases for neurodegenerative disease

Abstract

Protein misfolding and aggregation underpin several fatal neurodegenerative diseases, including Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). There are no treatments that directly antagonize the protein-misfolding events that cause these disorders. Agents that reverse protein misfolding and restore proteins to native form and function could simultaneously eliminate any deleterious loss-of-function or toxic gain-of-function caused by misfolded conformers. Moreover, a disruptive technology of this nature would eliminate self-templating conformers that spread pathology and catalyze formation of toxic, soluble oligomers. Here, we highlight our efforts to engineer Hsp104, a protein disaggregase from yeast, to more effectively disaggregate misfolded proteins connected with PD, ALS, and FTD. Remarkably subtle modifications of Hsp104 primary sequence yielded large gains in protective activity against deleterious α-synuclein, TDP-43, FUS, and TAF15 misfolding. Unusually, in many cases loss of amino acid identity at select positions in Hsp104 rather than specific mutation conferred a robust therapeutic gain-of-function. Nevertheless, the misfolding and toxicity of EWSR1, an RNA-binding protein with a prion-like domain linked to ALS and FTD, could not be buffered by potentiated Hsp104 variants, indicating that further amelioration of disaggregase activity or sharpening of substrate specificity is warranted. We suggest that neuroprotection is achievable for diverse neurodegenerative conditions via surprisingly subtle structural modifications of existing chaperones.     

Engineering a catalytic metal binding site into a calcium-independent phosphatidylinositol-specific phospholipase C leads to enhanced stereoselectivity

Eukaryotic phosphatidylinositol-specific phospholipase Cs (PI-PLCs) utilize calcium as a cofactor during catalysis, whereas prokaryotic PI-PLCs use a spatially conserved guanidinium group from Arg69. In this study, we aimed to construct a metal-dependent mutant of a bacterial PI-PLC and characterize the catalytic role of the metal ion, seeking an enhanced understanding of the functional differences between these two positively charged moieties. The following results indicate that a bona fide catalytic metal binding site was created by the single arginine-to-aspartate mutation at position 69: (1) The R69D mutant was activated by Ca(2+), and the activation was specific for R69D, not for other mutants at this position. (2) Titration of R69D with Ca(2+), monitored by (15)N-(1)H HSQC (heteronuclear single quantum coherence) NMR, showed that addition of Ca(2+) to R69D restores the environment of the catalytic site analogous to that attained by the WT enzyme. (3) Upon Ca(2+) activation, the thio effect of the S(P)-isomer of the phosphorothioate analogue (k(O)/k(Sp) = 4.4 x 10(5)) approached a value similar to that of the WT enzyme, suggesting a structural and functional similarity between the two positively charged moieties (Arg69 and Asp69-Ca(2+)). The R(P)-thio effect (k(O)/k(Rp) = 9.4) is smaller than that of the WT enzyme by a factor of 5. Consequently, R69D-Ca(2+) displays higher stereoselectivity (k(Rp)/k(Sp) = 47,000) than WT (k(Rp)/k(Sp) = 7600). (4) Results from additional mutagenesis analyses suggest that the Ca(2+) binding site is comprised of side chains from Asp33, Asp67, Asp69, and Glu117. Our studies provide new insight into the mechanism of metal-dependent and metal-independent PI-PLCs.     

Cloning,expression, and directed evolution of carbonyl reductase from Leifsonia xyli HS0904 with enhanced catalytic efficiency

(R)-[3,5-bis(trifluoromethyl)phenyl] ethanol ((R)-BTPE) is a valuable chiral intermediate for the synthesis of antiemetic drug Aprepitant and Fosaprepitant. A Leifsonia xyli HS0904-derived carbonyl reductase (LXCAR), an effective biocatalyst for the asymmetric reduction of 3,5-bis(trifluoromethyl) acetophenone (BTAP) to (R)-BTPE, was overexpressed in Escherichia coli BL21 (DE3). Bioinformatics analysis indicated that the amino acid sequence of recombinant LXCAR showed 89 % similarity to short-chain dehydrogenase/reductase. E. coli recombinant carbonyl reductase crude extract showed a specific activity of 1.54 U/mg, which was 62 times higher than that of L. xyli HS0904 crude extract. By using error-prone polymerase chain reaction and site-directed mutagenesis, the engineered LXCAR demonstrated superior catalytic activity toward BTAP, and the obtained mutant LXCAR-S154Y exhibited nearly 13-fold, 5.4-fold, and 2.3-fold increase in k _cat/K _m value, k _cat value, and specific activity toward BTAP, respectively, compared to the recombinant LXCAR. Additionally, the reduction of BTAP by whole cells of mutant LXCAR-S154Y afforded a best yield of 99.6 % for (R)-BTPE within 2 h at 200 mM BTAP, which was shortened by 28 and 2 h compared to those catalyzed by L. xyli HS0904 cells and recombinant E. coli cells expressing LXCAR, respectively. Moreover, a yield of 82.5 % for (R)-BTPE was achieved within 12 h at an increased BTAP concentration of up to 1,000 mM (256 g/l), representing a 1.9-fold increase over the recombinant LXCAR. Homology modeling and docking analysis revealed the molecular basis for the high catalytic activity of mutant LXCAR-S154Y toward BTAP. The results present here provide a promising alternative for economical and efficient production of chiral alcohols by engineered LXCAR.