Effect of Propeptide Mutations on the Directed Evolution of Rhizomucor miehei Lipase.

BACKGROUND: A series of mutants of Rhizomucor miehei lipase (RML) screened through four rounds of directed evolution were studied. Mutants' triglyceride hydrolysis activity was assessed, and their genes were sequenced. Results showed that mutations in the propeptide can improve the activity of RML during evolution. Two parts of propeptide (wild-type and mutant) and mature region were connected by molecular simulation technology. METHODS: The spatial structure of the most positive mutants containing the mutations in the propeptide was mainly characterized by the increase in the opening angle of the lid structure in the mature region of RML, the enhancement of the hydrophobicity of the active center, and the triad of the active center shifted outward. RESULTS: The three indexes above explain the mechanism of propeptide mutations on the activity change of the target protein. In addition, statistical analysis of all the mutants screened in directed evolution showed that: (1) most of the mutants with increased activity contained mutations of the propeptide, (2) in the later stage of directed evolution, the number of active mutants decreased gradually, and the mutations of inactivated protein mainly occurred in the mature region, and (3) in the last round of directed evolution, the mutations distributed in the propeptide improved the mutant activity further. The results showed that the propeptide reduced RML's evolutionary pressure and delayed the emergence of the evolutionary platform. CONCLUSION: These findings reveal the role of propeptide in the evolution of RML and provide strategies for the molecular transformation of other lipases.

Improvement of methanol tolerance and catalytic activity of Rhizomucor miehei lipase for one-step synthesis of biodiesel by semi-rational design.

Exploiting highly active and methanol-resistant lipase is of great significance for biodiesel production. A semi-rational directed evolution method combined with N-glycosylation is reported, and all mutants exhibiting higher catalytic activity and methanol tolerance than the wild type (WT). Mutant N267 retained 64% activity after incubation in 50% methanol for 8 h, which was 48% greater than that of WT. The catalytic activity of mutants N267 and N167 was 30- and 71- fold higher than that of WT. Molecular dynamics simulations of N267 showed that the formation of new strong hydrogen bonds between glycan and the protein stabilized the structure of lipase and improved its methanol tolerance. N267 achieved biodiesel yields of 99.33% (colza oil) and 81.70% (waste soybean oil) for 24 h, which was much higher than WT (51.6% for rapeseed oil and 44.73% for wasted soybean oil). The engineered ProRML mutant has high potential for commercial biodiesel production.

Comparative Analysis of Different Isolated Oleaginous Mucoromycota Fungi for Their γ-Linolenic Acid and Carotenoid Production.

γ-Linolenic acid (GLA) and carotenoids have attracted much interest due to their nutraceutical and pharmaceutical importance. Mucoromycota, typical oleaginous filamentous fungi, are known for their production of valuable essential fatty acids and carotenoids. In the present study, 81 fungal strains were isolated from different Egyptian localities, out of which 11 Mucoromycota were selected for further GLA and carotenoid investigation. Comparative analysis of total lipids by GC of selected isolates showed that GLA content was the highest in Rhizomucor pusillus AUMC 11616.A, Mucor circinelloides AUMC 6696.A, and M. hiemalis AUMC 6031 that represented 0.213, 0.211, and 0.20% of CDW, respectively. Carotenoid analysis of selected isolates by spectrophotometer demonstrated that the highest yield of total carotenoids (640 µg/g) was exhibited by M. hiemalis AUMC 6031 and M. hiemalis AUMC 6695, and these isolates were found to have a similar carotenoid profile with, ß-carotene (65%), zeaxanthin (34%), astaxanthin, and canthaxanthin (5%) of total carotenoids. The total fatty acids of all tested isolates showed moderate antimicrobial activity against Staphylococcus aureus and Salmonella Typhi, and Penicillium chrysogenum. To the best of our knowledge, this is the first report on the highest yield of total lipid accumulation (51.74% CDW) by a new oleaginous fungal isolate R. pusillus AUMC 11616.A. A new scope for a further study on this strain will be established to optimize and improve its total lipids with high GLA production. So, R. pusillus AUMC 11616.A might be a potential candidate for industrial application.

Coimmobilization of different lipases: Simple layer by layer enzyme spatial ordering.

This paper shows the step by step coimmobilization of up to five different enzymes following two different orders in the coimmobilization to alter the effect of substrate diffusion limitations. The enzymes were the lipases A and B from Candida antarctica, the lipases from Rhizomocur miehei and, Themomyces lanuginosus and the phospholipase Lecitase Ultra. The utilized strategy was a layer by layer immobilization, coating the immobilized enzymes with polyethylenimine followed by the crosslinking of the enzyme and PEI with glutaraldehyde to prevent enzyme release, and them adding a new lipase layer. The use of previously inactivated biocatalysts (using diethyl p-nitrophenylphosphate) permitted to visualize the immobilization of each enzyme layer, which was later confirmed by SDS-PAGE. This also confirmed the successful and complete covalent crosslinking of the glutaraldehyde treated enzyme layers. Activity of the combibiocatalysts was followed using diverse substrates. The protocol was successful and permitted to immobilize in an ordered way the 5 different enzymes in a down-up distribution.

Efficient biotechnological synthesis of flavor esters using a low-cost biocatalyst with immobilized Rhizomucor miehei lipase.

In this work, the synthesis of two fruit flavor esters, namely methyl and ethyl butyrate, by lipase from Rhizomucor miehei immobilized onto chitosan in the presence of the surfactant sodium dodecyl sulfate SDS was investigated. In the optimized conditions, maximum esterification yield for ethyl butyrate and methyl butyrate was (92 ± 1%) and (89 ± 1%), respectively. Esterification yields for both reactions were comparable or even superior to the ones achieved when the synthesis was catalyzed by a commercial enzyme, Lipozyme®, at the same reaction conditions. For ethyl butyrate, the developed biocatalyst was used for seven consecutive cycles of reaction with retention of its catalytic activity. For methyl butyrate synthesis the biocatalyst was used for four consecutive cycles without loss of its catalytic activity. The results show that chitosan may be employed in obtaining biocatalysts with high catalytic efficiency and can successfully replace the currently commercial available biocatalysts.

Enhancing the Thermostability of Rhizomucor miehei Lipase with a Limited Screening Library by Rational-Design Point Mutations and Disulfide Bonds.

Rhizomucor miehei lipase (RML), as a kind of eukaryotic protein catalyst, plays an important role in the food, organic chemical, and biofuel industries. However, RML retains its catalytic activity below 50°C, which limits its industrial applications at higher temperatures. Soluble expression of this eukaryotic protein in Escherichia coli not only helps to screen for thermostable mutants quickly but also provides the opportunity to develop rapid and effective ways to enhance the thermal stability of eukaryotic proteins. Therefore, in this study, RML was engineered using multiple computational design methods, followed by filtration via conservation analysis and functional region assessment. We successfully obtained a limited screening library (only 36 candidates) to validate thermostable single point mutants, among which 24 of the candidates showed higher thermostability and 13 point mutations resulted in an apparent melting temperature ([Formula: see text]) of at least 1°C higher. Furthermore, both of the two disulfide bonds predicted from four rational-design algorithms were further introduced and found to stabilize RML. The most stable mutant, with T18K/T22I/E230I/S56C-N63C/V189C-D238C mutations, exhibited a 14.3°C-higher [Formula: see text] and a 12.5-fold increase in half-life at 70°C. The catalytic efficiency of the engineered lipase was 39% higher than that of the wild type. The results demonstrate that rationally designed point mutations and disulfide bonds can effectively reduce the number of screened clones to enhance the thermostability of RML.IMPORTANCER. miehei lipase, whose structure is well established, can be widely applied in diverse chemical processes. Soluble expression of R. miehei lipase in E. coli provides an opportunity to explore efficient methods for enhancing eukaryotic protein thermostability. This study highlights a strategy that combines computational algorithms to predict single point mutations and disulfide bonds in RML without losing catalytic activity. Through this strategy, an RML variant with greatly enhanced thermostability was obtained. This study provides a competitive alternative for wild-type RML in practical applications and further a rapid and effective strategy for thermostability engineering.

High-level expression and biochemical characterization of a novel cold-active lipase from Rhizomucor endophyticus.

OBJECTIVES: To identify novel cold-active lipases from fungal sources and improve their production by heterologous expression in Pichia pastoris. RESULTS: A novel cold-active lipase gene (ReLipB) from Rhizomucor endophyticus was cloned. ReLipB was expressed at a high level in Pichia pastoris using high cell-density fermentation in a 5-l fermentor with the highest lipase activity of 1395 U/ml. The recombinant lipase (RelipB) was purified and biochemically characterized. ReLipB was most active at pH 7.5 and 25 °C. It was stable from pH 4.5-9.0. It exhibited broad substrate specificity towards p-nitrophenyl (pNP) esters (C2-C16) and triacylglycerols (C2-C12), showing the highest specific activities towards pNP laurate (231 U/mg) and tricaprylin (1840 U/mg), respectively. In addition, the enzyme displayed excellent stability with high concentrations of organic solvents including cyclohexane, n-hexane, n-heptane, isooctane and petroleum ester and surfactants. CONCLUSIONS: A novel cold-active lipase from Rhizomucor endophyticus was identified, expressed at a high level and biochemically characterized. The high yield and unique enzymatic properties make this lipase of some potential for industrial applications.

Biotransformation of oleanolic and maslinic methyl esters by Rhizomucor miehei CECT 2749.

The pentacyclic triterpenoids methyl oleanolate, methyl maslinate, methyl 3ß-hydroxyolean-9(11),12-dien-28-oate, and methyl 2α,3ß-dihydroxy-12ß,13ß-epoxyolean-28-oate were biotransformed by Rhizomucor miehei CECT 2749. Microbial transformation of methyl oleanolate produced only a 7ß,30-dihydroxylated metabolite with a conjugated 9(11),12-diene system in the C ring. Biotransformation of the substrate with this 9(11),12-diene system gave the same 7ß,30-dihydroxylated compound together with a 7ß,15α,30-trihydroxyl derivative. The action of this fungus (R. miehei) on methyl maslinate was more varied, isolating metabolites with a 30-hydroxyl group, a 9(11),12-diene system, an 11-oxo group, or an 12-oxo group. Microbial transformation of the substrate with a 12ß,13ß-epoxy function resulted in the isolation of two metabolites with 12-oxo and 28,13ß-olide groups, hydroxylated or not at C-7ß, together with a 30-hydroxy-12-oxo derivative. The structures of these derivatives were deduced by extensive and rigorous spectroscopic studies.

The first crystal structure of a glycoside hydrolase family 17 ß-1,3-glucanosyltransferase displays a unique catalytic cleft.

ß-1,3-Glucanosyltransferase (EC 2.4.1.-) plays an important role in the formation of branched glucans, as well as in cell-wall assembly and rearrangement in fungi and yeasts. The crystal structures of a novel glycoside hydrolase (GH) family 17 ß-1,3-glucanosyltransferase from Rhizomucor miehei (RmBgt17A) and the complexes of its active-site mutant (E189A) with two substrates were solved at resolutions of 1.30, 2.30 and 2.27 Å, respectively. The overall structure of RmBgt17A had the characteristic (ß/α)8 TIM-barrel fold. The structures of RmBgt17A and other GH family 17 members were compared: it was found that a conserved subdomain located in the region near helix α6 and part of the catalytic cleft in other GH family 17 members was absent in RmBgt17A. Instead, four amino-acid residues exposed to the surface of the enzyme (Tyr135, Tyr136, Glu158 and His172) were found in the reducing terminus of subsite +2 of RmBgt17A, hindering access to the catalytic cleft. This distinct region of RmBgt17A makes its catalytic cleft shorter than those of other reported GH family 17 enzymes. The complex structures also illustrated that RmBgt17A can only provide subsites -3 to +2. This structural evidence provides a clear explanation of the catalytic mode of RmBgt17A, in which laminaribiose is released from the reducing end of linear ß-1,3-glucan and the remaining glucan is transferred to the end of another ß-1,3-glucan acceptor. The first crystal structure of a GH family 17 ß-1,3-glucanosyltransferase may be useful in studies of the catalytic mechanism of GH family 17 proteins, and provides a basis for further enzymatic engineering or antifungal drug screening.

Fungal isolates from a Pu-erh type tea fermentation and their ability to convert tea polyphenols to theabrownins.

The natural microbiota involved in the fermentation influence the quality and taste of fully postfermented teas such as China's Pu-erh tea. Ten microbial isolates representing 6 species were recovered from a solid-state fermentation of a Pu-erh type tea. The isolates were Aspergillus tubingensis, Aspergillus marvanovae, Rhizomucor pusillus, Rhizomucor tauricus, Aspergillus fumigatus, and Candida mogii. With the exception of A. marvanovae and C. mogii, all these microorganisms have been previously reported in solid-state fermentations of native Pu-erh tea. The ability of the isolates for converting the tea polyphenols to bioactive theabrownins in infusions of sun-dried green tea leaves in a submerged fermentation process was subsequently investigated. All isolates except C. mogii TISTR 5938 effectively produced theabrownins in a 4-d fermentation in shake flasks at 40 °C, 250 rpm. A. tubingensis TISTR 3646, A. tubingensis TISTR 3647, A. marvanovae TISTR 3648, and A. fumigatus TISTR 3654 produced theabrownins at particularly high levels of 6.5, 12.4, 11.1, and 8.4 g/L, respectively.

Identification and characterization of D-xylose reductase involved in pentose catabolism of the zygomycetous fungus Rhizomucor pusillus.

Rhizomucor pusillus NBRC 4578 efficiently produces ethanol from lignocellulosic biomass because of its ability to ferment not only d-glucose, but also d-xylose. When the strain was cultivated on d-xylose, ethanol was gradually formed in the culture medium with a decrease in d-xylose and the simultaneous accumulation of xylitol, which suggested that the strain catabolized d-xylose with d-xylose reductase (XR) and xylitol dehydrogenase (XDH). XR (RpXR) was purified to homogeneity from the crude extract prepared from the mycelia of the strain grown on d-xylose. The purified enzyme was found to be NADPH-dependent and prefer pentoses such as d-xylose, d-ribose, and l-arabinose as substrates. Isolation of the genomic DNA and cDNA of the xyl1 gene encoding RpXR revealed that the gene was interrupted by two introns and the exon of the gene encoded a protein composed of 322 amino acids with a Mr of 36,724. Phylogenetic analysis showed that RpXR is more related to 4-dihydromethyltrisporate dehydrogenases from Mucoraseae fungi rather than the previously reported fungal XRs. Quantitative real-time PCR indicated that transcription of the xyl1 gene was marked in the presence of d-xylose and l-arabinose, but was week in the presence of d-glucose. These biochemical and expression analyses suggest that RpXR is involved in the catabolism of l-arabinose as well as d-xylose. This is the first report of the purification, characterization, and gene cloning of XR from zygomycetous fungi.

Using cassava distiller's dried grains as carbon and microbe sources to enhance denitrification of nitrate-contaminated groundwater.

Nitrate removal from synthetic and real groundwater was investigated by using cassava distiller's dried grains (CDDG), which served as sole carbon source as well as the only microbe seed. It was found that remarkably higher total nitrogen removal efficiency (96.8 ± 0.6 %) could be reached; the accumulation of nitrite and the releases of organic compounds, meanwhile, were insignificant in the denitrification process. Scanning electron microscope (SEM) analysis showed that CDDG were degraded during the denitrification process. Further investigation showed that CDDG were anaerobically hydrolyzed and acidified to butyric acid, acetic acid, and carbohydrate, which could be utilized directly as the reducing equivalent providers for denitrification by the microorganisms separated from CDDG. Microbial community analysis revealed that the fungi and bacteria present in the original CDDG functioned as the denitrifiers, which mainly consisted of Aspergillus (69.8 %) and Rhizomucor (15.9 %) in the fungi community and Burkholderia (20.6 %) and Rhizobium (15.9 %) in the bacteria community, respectively. Finally, the use of CDDG as both carbon and microbial sources for real groundwater denitrification was testified to be feasible and safe with a total nitrogen removal efficiency of around 100 %.

The structure of a glycoside hydrolase family 81 endo-ß-1,3-glucanase.

Endo-ß-1,3-glucanases catalyze the hydrolysis of ß-1,3-glycosidic linkages in glucans. They are also responsible for rather diverse physiological functions such as carbon utilization, cell-wall organization and pathogen defence. Glycoside hydrolase (GH) family 81 mainly consists of ß-1,3-glucanases from fungi, higher plants and bacteria. A novel GH family 81 ß-1,3-glucanase gene (RmLam81A) from Rhizomucor miehei was expressed in Escherichia coli. Purified RmLam81A was crystallized and the structure was determined in two crystal forms (form I-free and form II-Se) at 2.3 and 2.0 Šresolution, respectively. Here, the crystal structure of a member of GH family 81 is reported for the first time. The structure of RmLam81A is greatly different from all endo-ß-1,3-glucanase structures available in the Protein Data Bank. The overall structure of the RmLam81A monomer consists of an N-terminal ß-sandwich domain, a C-terminal (α/α)6 domain and an additional domain between them. Glu553 and Glu557 are proposed to serve as the proton donor and basic catalyst, respectively, in a single-displacement mechanism. In addition, Tyr386, Tyr482 and Ser554 possibly contribute to both the position or the ionization state of the basic catalyst Glu557. The first crystal structure of a GH family 81 member will be helpful in the study of the GH family 81 proteins and endo-ß-1,3-glucanases.

Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids.

To improve the performance of yeast surface-displayed Rhizomucor miehei lipase (RML) in the production of human milk fat substitute (HMFS), we mutated amino acids in the lipase substrate-binding pocket based on protein hydrophobicity, to improve esterification activity. Five mutants: Asn87Ile, Asn87Ile/Asp91Val, His108Leu/Lys109Ile, Asp256Ile/His257Leu, and His108Leu/Lys109Ile/Asp256Ile/His257Leu were obtained and their hydrolytic and esterification activities were assayed. Using Discovery Studio 3.1 to build models and calculate the binding energy between lipase and substrates, compared to wild-type, the mutant Asp256Ile/His257Leu was found to have significantly lower energy when oleic acid (3.97 KJ/mol decrease) and tripalmitin (7.55 KJ/mol decrease) were substrates. This result was in accordance with the esterification activity of Asp256Ile/His257Leu (2.37-fold of wild-type). The four mutants were also evaluated for the production of HMFS in organic solvent and in a solvent-free system. Asp256Ile/His257Leu had an oleic acid incorporation of 28.27% for catalyzing tripalmitin and oleic acid, and 53.18% for the reaction of palm oil with oleic acid. The efficiency of Asp256Ile/His257Leu was 1.82-fold and 1.65-fold that of the wild-type enzyme for the two reactions. The oleic acid incorporation of Asp256Ile/His257Leu was similar to commercial Lipozyme RM IM for palm oil acidolysis with oleic acid. Yeast surface-displayed RML mutant Asp256Ile/His257Leu is a potential, economically feasible catalyst for the production of structured lipids.

Biotransformation of oleanolic and maslinic acids by Rhizomucor miehei.

Microbial transformation of oleanolic acid by Rhizomucor miehei produced three metabolites. A known compound, a 30-hydroxyl derivative (queretaroic acid), and two 7ß,30- and 1ß,30-dihydroxylated metabolites, respectively. The action of the same fungus (R. miehei) on maslinic acid produced an olean-11-en-28,13ß-olide derivative, a metabolite hydroxylated at C-30, an 11-oxo derivative, and two metabolites with an 11α,12α-epoxy group, hydroxylated or not at C-30. Their structures were elucidated by extensive analyses of their spectroscopic data, and also by chemical correlations.

Biotransformation and improved enzymatic extraction of chlorogenic acid from coffee pulp by filamentous fungi.

The highest enzymatic extraction of covalent linked chlorogenic (36.1%) and caffeic (CA) (33%) acids from coffee pulp (CP) was achieved by solid-state fermentation with a mixture of three enzymatic extracts produced by Aspergillus tamarii, Rhizomucor pusillus, and Trametes sp. Enzyme extracts were produced in a practical inexpensive way. Synergistic effects on the extraction yield were observed when more than one enzyme extract was used. In addition, biotransformation of chlorogenic acid (ChA) by Aspergillus niger C23308 was studied. Equimolar transformation of ChA into CA and quinic acids (QA) was observed during the first 36 h in submerged culture. Subsequently, after 36 h, equimolar transformation of CA into protocatechuic acid was observed; this pathway is being reported for the first time for A. niger. QA was used as a carbon source by A. niger C23308. This study presents the potential of using CP to produce enzymes and compounds such as ChA with biological activities.

Biotransformation of progesterone by Absidia griseolla var. igachii and Rhizomucor pusillus.

Biotransformation of progesterone using Absidia griseolla var. igachii and Rhizomucor pusillus strains as biocatalysts were investigated. Microbial hydroxylation of progesterone by A. griseolla produced two hydroxylated pregnane-like steroids. The metabolites identified as 6ß,14α-dihydroxyprogesterone and 7α,14α-dihydroxyprogesterone. R. pusillus produced 6ß,11α-dihydroxyprogesterone with excellent yield (65.5%) and 7α,14α-dihydroxyprogesterone. These metabolites were purified by TLC followed by their identification through (1)H, (13)C NMR and other spectroscopic data.

High-throughput screening of B factor saturation mutated Rhizomucor miehei lipase thermostability based on synthetic reaction.

Conventional lipase screening methods are mostly based on hydrolytic activity, which may not always be the best method to assess the enzyme activity, especially for evaluating synthetic activity. Here we developed a high throughput and visual method to screen clones with high synthetic activity and used it to assess lipases thermostability. All mutants' lipase synthetic activity were identified through esterification of caprylic acid and ethanol with methyl red as the pH indicator adding in the substrates on according to the color change halo around the colony on culture plates since synthetic reaction was often accompanied with a rise in pH. After two rounds operation with the pH indicator screening method, we obtained a double mutant Asn120Lys/Lys131Phe from the Rhizomucor miehei lipase saturation mutated library based on amino acid residue B factors. The mutant's initial synthetic activity was a little higher than wild type and its thermostability in synthetic reaction was enhanced, which remained 63.1% residual activity after being heated at 70°C for 5h comparing to 51.0% of wild type. The double mutant with the two residue replacements balanced well between stability and activity. Yeast surface display technology and the pH indicator method, combined with colony screening were shown to facilitate high-throughput screening for lipase synthetic activity.

Potential of thermophilic fungus Rhizomucor pusillus NRRL 28626 in biotransformation of antihelmintic drug albendazole.

In the present investigation, thermophilic fungus Rhizomucor pusillus was used to study biotransformation of antihelmintic drug albendazole to produce its active metabolite, albendazole sulfoxide and novel metabolites of commercial interest. A two-stage fermentation procedure was followed for biotransformation of albendazole. The transformation was identified and structures were confirmed by high-performance liquid chromatography and liquid chromatography-tandem mass spectrometry analysis. Four metabolites albendazole sulfoxide, the active metabolite, albendazole sulfone, N-methyl metabolite of albendazole sulfoxide, and a novel metabolite were produced. The study demonstrates the biotransformation ability of thermophilic fungus R. pusillus NRRL28626 in the production of, the active metabolite of albendazole which has industrial and economic importance, other metabolites and a novel metabolite in an ecofriendly way.

Synthesis and properties of a novel biosuperabsorbent from alkali soluble Rhizomucor pusillus proteins.

A novel biosuperabsorbent protein hydrogel was prepared from protein-rich alcoholic-alkali soluble parts of zygomycete Rhizomucor pusillus biomass. The fungal protein content was 46.8%, and the lipid content was 13.1%. Extraction of protein from this microorganism through the method applied prevents protein decomposition, resulting in maximum yield. After alcoholic-alkaline extraction, the proteins from the biomass were acylated using ethylenediaminetetraacetic dianhydride and subsequently treated with glutaraldehyde as a crosslinker for further experiments. Thermal consistency was investigated by means of two different methods: thermal denaturation via differential scanning calorimetry and thermal decomposition study via thermogravimetric analysis. The swelling behaviour of the crosslinked hydrogel was measured in deionised water, 0.9% NaCl solution and synthetic urine, which were 87.6, 43 and 38.6 g/g water after 24 h, respectively. Moreover, the isoelectric point (pI) of the hydrogel was determined as pH = 8 by studying swelling behaviour at different pHs. In addition, the dependencies of the swelling behaviour with regard to the chemical modification, the ionic strength, the degree of crosslinking, as well as water absorbency with or without load were studied.