In order to improve the thermostability of β- 1,3-1,4-glucanase, evolutionary molecular engineering was used to evolve the β-1,3-1,4-glucanase from Bacillus subtilis ZJF-1A5. The process involves random mutation by ...In order to improve the thermostability of β- 1,3-1,4-glucanase, evolutionary molecular engineering was used to evolve the β-1,3-1,4-glucanase from Bacillus subtilis ZJF-1A5. The process involves random mutation by error-prone PCR and DNA shuffling followed by screening on the filter-based assay. Two mutants, EGsl and EGs2, were found to have four and five amino acid substitutions, respectively. These substitutions resulted in an increase in melting temperature from Tm=62.5℃ for the wild-type enzyme to Tm=65.5℃ for the mutant EGsl and 67.5℃ for the mutant EGs2. However, the two mutated enzymes had opposite approaches to produce reducing sugar from lichenin with either much higher （28%） for the former or much lower （21.6%） for the latter in comparison with their parental enzymes. The results demonstrate that directed evolution is an effective approach to improve the thermostability of a mesophilic enzyme.展开更多
Objective To devellop directly molecular evolution Of nitrite oxido-reductase using DNA-shuffling technique because nitrobacteria grow extremelly slow and are unable to nitrify effectively inorganic nitrogen in wastew...Objective To devellop directly molecular evolution Of nitrite oxido-reductase using DNA-shuffling technique because nitrobacteria grow extremelly slow and are unable to nitrify effectively inorganic nitrogen in wastewater treatmem. Methods The norB gene coding the ntitrite oxido-reductase in nitrobacteria was cloned and sequenced. Then, directed molecular evolution of nitrite oxido-reductase was developed by DNA-shuffling of 15 norB genes from different nitrobacteria. Results After DNA-shuffling with sexual PeR and staggered extension process PCR, the sequence was differem from its parental DNA fragmems and the homology ranged from 98% to 99%. The maximum nitrification rate of the modified bacterium of X16 by DNA-shuffling was up to 42.9 mg/L.d, which was almost 10 times higher than that of its parental bacteria. Furthermore, the modified bacterium had the same characteristics of its parental bacteria of E. coli and could grow rapidly in normal cultures. Conclusion DNA-shuffling was successfully used to engineer E. coli, which had norB gene and could degrade inorganic nitrogen effectively.展开更多
To enhance the relative movement of domains, we inserted a random sequence of fifteen-peptide into the three domains of L-aspartase. By means of directed screening, the three isoforms of monomeric, dimmeric and tetram...To enhance the relative movement of domains, we inserted a random sequence of fifteen-peptide into the three domains of L-aspartase. By means of directed screening, the three isoforms of monomeric, dimmeric and tetrameric enzymes were obtained. Compared to the wild-type tetrameric L-asparease, these mutants remained 19.7%, 42.3%, and 92% of the enzyme activity, respectively. Moreover, the examination of enzyme properties revealed that their k_ cat and K_M changed in varying degrees, and the optimum pH shifted towards acidic pH, while the dependence of the activity of enzyme on Mg 2+ concentration and thermostability increased. Therefore this strategy provides a novel approach to directed evolution of enzymes.展开更多
Cu,Zn SOD is a highly conserved enzyme and the controversy about its evolutionary possibility in the near future has been lively. In order to further our understanding of the future fate of human Cu,Zn SOD, we adopt...Cu,Zn SOD is a highly conserved enzyme and the controversy about its evolutionary possibility in the near future has been lively. In order to further our understanding of the future fate of human Cu,Zn SOD, we adopted a strategy relating to the directed evolution to study how the mutants of human Cu,Zn SOD respond to different oxidative stress. After five rounds of screening, we found a mutant that can survive under harsh pressures and DNA sequencing proves that it shows a mutation responsible for the phenomenon. However, under natural pressure, our screening comes to nothing. Then we may draw the following conclusions: the evolution of biological macromolecules in some respect depends on their surroundings and if they are too familiar with a certain environment, they may embody evolutionary inertia.展开更多
Expression of recombinant protein in Escherichia coli （E.coli） is generally considered as one of the ideal systems to produce proteins for industrial production.However,the majority of proteins usually fail to fold ...Expression of recombinant protein in Escherichia coli （E.coli） is generally considered as one of the ideal systems to produce proteins for industrial production.However,the majority of proteins usually fail to fold into their native state and accumulate as insoluble inclusion bodies with no biological activity in E.coli（Yang et al.,2003）.展开更多
The enzymatic depolymerization of polyethylene terephthalate(PET)offers a sustainable approach for the recycling of PET waste.Great efforts have been devoted to engineering PET depolymerases on the substrate binding c...The enzymatic depolymerization of polyethylene terephthalate(PET)offers a sustainable approach for the recycling of PET waste.Great efforts have been devoted to engineering PET depolymerases on the substrate binding cleft and the surrounding loops/α-helices on the surface.Here,we report the systematic engineering of whole β-sheet regions in the core of IsPETase(a PETase from Ideonella sakaiensis)via a fluorescent high-throughput screening assay.Twenty-one beneficial substitutions were obtained and iteratively recombined.The best variant,DepoPETase β,with an increase in the melting temperatures(T_(m))of 22.9℃,exhibited superior depolymerization performance and enabled complete depolymerization of100.5 g of untreated post-consumer PET(pc-PET;0.26% W_(enzyme)/W_(PET) enzyme loading)in liter-scale bioreactor at 50℃within 4 d.Crystallization and molecular dynamics simulations revealed that the improved activity and thermostability of DepoPETase β were due to enhanced hydrogen bonds and salt bridges in the β-sheet region,a more tightly packed structure of the core sheets and the surrounding helix,and improved binding of PET to the active sites.This study not only demonstrates the importance of engineering strategy in theβ-sheet region of PET hydrolases but also provides a potential PET depolymerase for large-scale PET recycling.展开更多
Chiral N-substituted amino amides and esters are ubiquitous scaffolds in pesticides and pharmaceutical chemicals,but their asymmetric synthesis remains challenging especially for those with multiple chiral centers.In ...Chiral N-substituted amino amides and esters are ubiquitous scaffolds in pesticides and pharmaceutical chemicals,but their asymmetric synthesis remains challenging especially for those with multiple chiral centers.In this study,IR104 from Streptomyces aureocirculatus was identified from 157 wild-type imine reductases for the synthesis of(S)-2-((R)-2-oxo-4-propylpyrrolidin-1-yl)butanamide(antiepileptic drug Brivaracetam)via dynamic kinetic resolution reductive amination from ethyl 3-formylhexanoate and(S)-2-aminobutylamide with high diastereoselectivity.To further improve the catalytic efficiency of IR104,its mutant D191E/L195I/E253S/M258A(M3)was identified by saturation mutagenesis and iterative combinatorial mutagenesis,which exhibited a 102-fold increase in the catalytic efficiency relative to that of wild-type enzyme and high diastereoselectivity(98:2 d.r.).Crystal structural analysis and molecular dynamics simulations provided some insights into the molecular basis for the improved activity of the mutant enzyme.The imine reductase identified in this study could accept chiral amino amides/esters as amino donors for the dynamic kinetic resolution reductive amination of racemicα-substituted aldehydo-esters,expanding the substrate scope of imine reductases in the dynamic kinetic resolution-reductive amination.Finally,IR104-M3 was successfully used for the preparation of Brivaracetam at gram scale.Using this mutant,various N-substituted amino amides/esters with two chiral centers were also synthesized with up to 99:1 d.r.and 96%yields and subsequently converted intoγ-andδ-lactams,providing an efficient protocol for the synthesis of these important compounds via enzymatic dynamic kinetic resolution-reductive amination from simple building blocks.展开更多
Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolution- ary direction dynamically during evolution. After evolution, the solutions’s precision can be greatly improved by ...Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolution- ary direction dynamically during evolution. After evolution, the solutions’s precision can be greatly improved by means of the local searching along the recorded direction. Simulation shows that this algorithm can not only keep population diversity but also find accurate solutions. Although using this method has to take more time compared with the standard GA, it is really worth applying to some cases that have to meet a demand for high solution precision.展开更多
Polysubstituted chiral γ-butyrolactones are the core structural units of many natural products and high value-added flavors and fragrances used in the food and cosmetic industry. Current enzymatic cascade synthesis o...Polysubstituted chiral γ-butyrolactones are the core structural units of many natural products and high value-added flavors and fragrances used in the food and cosmetic industry. Current enzymatic cascade synthesis of these molecules faces the problems of low enzyme activity and phase separation in batch reaction, resulting in low productivity. Herein, we report a new continuous-flow process to synthesize the optically pure Nicotiana tabacum lactone(3S,4S)-4a and whisky lactone(3R,4S)-4b from α,β-unsaturatedγ-ketoesters. A new ene reductase(ER) from Swingsia samuiensi(Ss ER) and a carbonyl reductase(Ss CR)were engineered by directed evolution to improve their activity and thermostability. The continuous-flow preparative reactions were performed in two 3D microfluidic reactors, generating(3S,4S)-4a(99% ee and87% de) and(3R,4S)-4b(99% ee and 98% de) with space-time yields 3 and 7.4 times higher than those of the batch reactions. The significant enhancement in the productivity of enzyme cascade catalysis brought by cutting-edge continuous microfluidic technology will benefit the general multi-enzyme catalytic systems in the future.展开更多
To identify the desired hypertherrnophilic variants within a mutant esterase library for the resolution of （R, S）-2- octanol acetate, a simple, reliable, and versatile method was developed in this study. We built a ...To identify the desired hypertherrnophilic variants within a mutant esterase library for the resolution of （R, S）-2- octanol acetate, a simple, reliable, and versatile method was developed in this study. We built a screening strategy including two steps, first we selected agar plate with substrate to screen the enzymatic activity; secondly we used a pH indicator to screen the enantioselectivity. This method could rapidly detect favorable mutants with high activity and enantioselectivity. A total of 96. 2% of tedious screening work can be precluded using this screening strategy. It is an effective screening for alkyl ester and can be applied to relative screening researches. The four improved mutants were screened from the mutant esterase library. Their enantioselectivities, activities, and structures were investigated at different temperatures.展开更多
Cytochrome P450 enzymes catalyze diverse oxidative transformations at the expense of reduced nicotinamide adenine dinucleotide phosphate(NADPH),however,their applications remain limited largely because NADPH is cost-p...Cytochrome P450 enzymes catalyze diverse oxidative transformations at the expense of reduced nicotinamide adenine dinucleotide phosphate(NADPH),however,their applications remain limited largely because NADPH is cost-prohibitive for biocatalysis at scale yet tightly regulated in host cells.A highly challenging task for P450 catalysis has been to develop an alternative and biocompatible electrondonating system.Here we engineered P450 BM3 to favor reduced nicotinamide cytosine dinucleotide(NCDH)and created non-natural cofactor-dependent P450 catalysis.Two outstanding mutants were identified with over 640-fold NCDH preference improvement and good catalytic efficiencies of over15,000 M^(-1)s^(-1)for the oxidation of the fatty acid probe 12-(para-nitrophenoxy)-dodecanoate.Molecular docking analysis indicated that these mutants bear a compacted cofactor entrance.Upon fusing with an NCD-dependent formate dehydrogenase,fused proteins functioned as NCDH-specific P450catalysts by using formate as the electron donor.Importantly,these mutants and fusions catalyzed NCDH-dependent hydroxylation of fatty acids with similar chain length preference to those by natural P450 BM3 in the presence of NADPH and also similar regioselectivity for subterminal hydroxylation of lauric acid.As P450 BM3 and its variants are catalytically powerful to take diverse substrates and convey different reaction paths,our results offer an exciting opportunity to devise advanced cell factories that convey oxidative biocatalysis with an orthogonal reducing power supply system.展开更多
The integration of topology optimization(TO)and additive manufacturing(AM)technologies can create significant synergy benefits,while the lack of AM-friendly TO algorithms is a serious bottleneck for the application of...The integration of topology optimization(TO)and additive manufacturing(AM)technologies can create significant synergy benefits,while the lack of AM-friendly TO algorithms is a serious bottleneck for the application of TO in AM.In this paper,a TO method is proposed to design self-supporting structures with an explicit continuous self-supporting constraint,which can be adaptively activated and tightened during the optimization procedure.The TO procedure is suitable for various critical overhang angles(COA),which is integrated with build direction assignment to reduce performance loss.Besides,a triangular directional self-supporting constraint sensitivity filter is devised to promote the downward evolution of structures and maintain stability.Two numerical examples are presented;all the test cases have successfully converged and the optimized solutions demonstrate good manufacturability.In the meanwhile,a fully self-supporting design can be obtained with a slight cost in performance through combination with build direction assignment.展开更多
Cytidine triphosphate(CTP),as a substance involved in the metabolism of phospholipids,proteins and nucleic acids,has precise drug effects and is a direct precursor for the synthesis of drugs such as citicoline.In this...Cytidine triphosphate(CTP),as a substance involved in the metabolism of phospholipids,proteins and nucleic acids,has precise drug effects and is a direct precursor for the synthesis of drugs such as citicoline.In this study,we established an in vitro six-enzyme cascade system to generate CTP.To avoid thermodynamic bottlenecks,we employed a circuitous and two-stage reaction strategy.Using cytidine as the key substrate,the final product CTP is obtained via the deamination and uridine phosphorylation pathways,relying on the irreversible reaction of cytidine triphosphate synthase to catalyze the amination of uridine triphosphate.Several extremophilic microbial-derived deaminases were screened and characterized,and a suitable cytidine deaminase was selected to match the first-stage reaction conditions.In addition,directed evolution modification of the rate-limiting enzyme CTP synthetase in the pathway yielded a variant that successfully relieved the product feedback inhibition,along with a 1.7-fold increase in activity over the wild type.After optimizing the reaction conditions,we finally carried out the catalytic reaction at an initial cytidine concentration of 20 mM,and the yield of CTP exceeded 82%within 10.0 h.展开更多
We report here a generic,green synthesis of 17 valuable syn-aryl-(2S,3R)-2–chloro-3–hydroxy esters(syn-(2S,3R)-1)in 73%-99%isolated yields along with 6.1:1–83:1 dr and 31%~>99%ee,through dynamic reductive kineti...We report here a generic,green synthesis of 17 valuable syn-aryl-(2S,3R)-2–chloro-3–hydroxy esters(syn-(2S,3R)-1)in 73%-99%isolated yields along with 6.1:1–83:1 dr and 31%~>99%ee,through dynamic reductive kinetic resolution of racemic arylα–chloroβ-keto esters(2)catalyzed by an engineered ketoreductase which was obtained via ep PCR-based directed evolution.The hectogram scale synthesis of syn-(2S,3R)-1b at a substrate concentration of 120 g/L showcased the application potential of the biocatalytic method developed presently.展开更多
Microbial proteins hold great promise as sustainable alternatives for future protein sources,and oleaginous yeast Yarrowia lipolytica has emerged as a recognized platform for heterologous protein expression and secret...Microbial proteins hold great promise as sustainable alternatives for future protein sources,and oleaginous yeast Yarrowia lipolytica has emerged as a recognized platform for heterologous protein expression and secretion.N-terminal signal peptides(SPs)are crucial for directing proteins to the secretion pathway,which offers advantages in both academic and industrial protein production.Although some of the innate SPs of Y.lipolytica have been reported,there is a growing need to expand the genetic toolkit of SPs to support the increasing use of Y.lipolytica as a cell factory for overproduction of various secretory proteins.In this study,we employed an efficient evolutionary approach to rapidly evolve the innate SP XPR2-pre by leveraging Gibson assembly with two syn-thetic overlapping oligos containing high portion of degenerate nucleotides.Using Nanoluc(Nluc)luciferase as a robust reporter,we characterized the intracellular and extracellular enzymatic activity of 447 SP mutants and identified previously undescribed SPs exhibiting superior performance compared to XPR2-pre in Nluc luciferase secretion,with improvements of up to 2.91-fold of enzymatic activity in the supernatant.The generalizability of the top-performing SPs was evaluated using three additional heterologous enzymes(β-galactosidase,α-amylase,and PET hydrolase).Our results confirmed their versatility across different proteins with protein-specific effi-ciency.Additionally,based on our screening,we also evaluated the performance of different feature engineering strategies and machine learning models in the design and prediction of SP mutants.This study integrated rational design,directed evolution and machine learning to identify novel SPs,expanding the repertoire of signal peptides and benefiting secretory protein overexpression in Y.lipolytica.展开更多
Targeted in vivo hypermutation mediated by base deaminase-T7 RNA polymerase(T7 RNAP)fusions promotes genetic diversification and accelerates continuous directed evolution.Due to the lack of a T7RNAP expression regulat...Targeted in vivo hypermutation mediated by base deaminase-T7 RNA polymerase(T7 RNAP)fusions promotes genetic diversification and accelerates continuous directed evolution.Due to the lack of a T7RNAP expression regulation system and functionally compatible linker for fusion protein expression,T7RNAP-guided continuous evolution has not been established in Bacillus subtilis,which limited long gene fragment continuous evolution targeted on genome.Here,we developed BS-MutaT7 system,which introduced mutations into specific genomic regions by leveraging chimeric fusions of base deaminases with T7RNAP in B.subtilis.We selected seven different sources of adenosine and cytosine deaminases,14 fusion protein linkers to be fused with T7RNAP,constructing four libraries with the size of 5000,where deaminases were fused at either the N-or C-terminus of T7RNAP.Based on the efficiency of binding to T7 promoter and high mutagenesis activity,two optimal chimeric mutators,BS-MutaT7A(TadA8e-Linker0-T7RNAP)and BS-MutaT7C(PmCDA1-(GGGGS)3-T7RNAP co-expressed with UGI)were identified.The target mutation rates reached 1.2×105 per base per generation(s.p.b.)and 5.8×105 s.p.b.,representing 7000-fold and 37,000-fold increases over the genomic mutation rate,respectively.Both exhibited high processivity,maintaining mutation rates of 5.8×106 s.p.b.and 2.9×105 s.p.b.within a 5 kb DNA region.Notably,BS-MutaT7C exhibited superior mutagenic activity,making it well-suited for applications requiring intensive and sustained genomic diversification.Application of BS-MutaT7 enabled a 16-fold increase in tigecycline resistance and enhancedβ-lactoglobulin(β-Lg)expression by evolving the global transcriptional regulator codY,achieving aβ-Lg titer of 3.92 g/L.These results highlight BS-MutaT7 as a powerful and versatile tool for genome-scale continuous evolution in B.subtilis.展开更多
Recently,a novel protein language model(PLM)was published by Liang Hong group in Science Advances1,introducing PRIME(PRotein language model for Intelligent Masked pretraining and Environment prediction,Fig.1).PRIME is...Recently,a novel protein language model(PLM)was published by Liang Hong group in Science Advances1,introducing PRIME(PRotein language model for Intelligent Masked pretraining and Environment prediction,Fig.1).PRIME is a deep learning model designed to predict and improve protein stability and activity without relying on experimental mutagenesis data.This innovative approach leverages a vast dataset of 96 million protein sequences annotated with their host bacterial optimal growth temperatures(OGTs)to develop a model that effectively guides protein engineering across various applications.展开更多
Protein engineering involves modifying proteins'sequences to achieve desired functions,such as enhanced stability,improved activity,altered specificity,reduced immunogenicity,and improved pharmacokinetics.Rational...Protein engineering involves modifying proteins'sequences to achieve desired functions,such as enhanced stability,improved activity,altered specificity,reduced immunogenicity,and improved pharmacokinetics.Rational design and directed evolution(Arnold,1996)are two major traditional approaches for protein engineering.Rational design uses the knowledge of protein structure-function relationships to intentionally introduce specific mutations,while directed evolution mimics natural selection by generating random mutations and screening for desired protein functions.展开更多
catalyzed byβ-carotene hydroxylase(crtZ)andβ-carotene ketolase(crtW)decreases the content of the astaxanthin.Here,we exploited directed evolution of the fusion of crtZ and crtW for improving astaxanthin biosynthesis...catalyzed byβ-carotene hydroxylase(crtZ)andβ-carotene ketolase(crtW)decreases the content of the astaxanthin.Here,we exploited directed evolution of the fusion of crtZ and crtW for improving astaxanthin biosynthesis in Saccharomyces cerevisiae.The results demonstrated that the fusion enzyme of crtZ-crtW with 2 X GGGGS peptides linker can effectively reduce the accumulation of intermediates and improves the content of astaxanthin.Compared with the control strain,the fusion enzyme of ketase and hydroxylase reduced zeaxanthin and canthaxanthin by 7 and 14 times and increased astaxanthin by 1.6 times,respectively.Moreover,9 variant fusion mutants with improved astaxanthin production were generated through directed evolution.Combining these dominant mutants generated a variant,L95S+I206L,which increased the astaxanthin content of 3.8 times than the control strain.The AlphaFold2 assisted structural analysis indicated that these two mutations alter the interaction between the substrate and the enzymes pocket.Our research provided an efficient idea to reduce the accumulation of the intermediate products in complex biosynthesis pathway.展开更多
If cellulose can be effectively hydrolyzed intoglucose by cellulase,the production costs of hydrogen,ethanol or other chemicals from cellulosic materials will begreatly decreased,and economically viable production ofb...If cellulose can be effectively hydrolyzed intoglucose by cellulase,the production costs of hydrogen,ethanol or other chemicals from cellulosic materials will begreatly decreased,and economically viable production ofbiohydrogen and bioethanol will become feasible.Celluloseis degraded into glucoses by multi-component enzymesystems.Nowadays cellulases are widely used in brewing,food,bioenergy,fodder,textiles,paper,pharmaceuticals,environmental protection and other industries.However,existing cellulases have several problems that limit theirwider applications,including the low turnover number forsolid cellulosic materials,and low stability in adapting tovarious application conditions.For example,high temperature,low pH,and so on.Application of directedevolution technology may be one of the most effectiveways for improving the characteristics of cellulases.Thispaper presents a brief review of the cellulases hydrolysismechanism by cellulase,advances in cellulases(endoglucanaseandβ-glucosidase)improvement by directedevolution for several characteristics(for instance,thermalstability,pH adaptability and enzyme activity),limitationsof directed evolution for cellulases,and the outlook fordirected evolution for cellulase.展开更多
基金Project supported by the National Natural Science Foundation of China (No. 20276064) and Natural Science Foundation of ZhejiangProvince (No. Z304076), China
文摘In order to improve the thermostability of β- 1,3-1,4-glucanase, evolutionary molecular engineering was used to evolve the β-1,3-1,4-glucanase from Bacillus subtilis ZJF-1A5. The process involves random mutation by error-prone PCR and DNA shuffling followed by screening on the filter-based assay. Two mutants, EGsl and EGs2, were found to have four and five amino acid substitutions, respectively. These substitutions resulted in an increase in melting temperature from Tm=62.5℃ for the wild-type enzyme to Tm=65.5℃ for the mutant EGsl and 67.5℃ for the mutant EGs2. However, the two mutated enzymes had opposite approaches to produce reducing sugar from lichenin with either much higher （28%） for the former or much lower （21.6%） for the latter in comparison with their parental enzymes. The results demonstrate that directed evolution is an effective approach to improve the thermostability of a mesophilic enzyme.
基金This study was supported by the National High Technology Research and Development Program of China (863 Program) (No. 2001AA214191).
文摘Objective To devellop directly molecular evolution Of nitrite oxido-reductase using DNA-shuffling technique because nitrobacteria grow extremelly slow and are unable to nitrify effectively inorganic nitrogen in wastewater treatmem. Methods The norB gene coding the ntitrite oxido-reductase in nitrobacteria was cloned and sequenced. Then, directed molecular evolution of nitrite oxido-reductase was developed by DNA-shuffling of 15 norB genes from different nitrobacteria. Results After DNA-shuffling with sexual PeR and staggered extension process PCR, the sequence was differem from its parental DNA fragmems and the homology ranged from 98% to 99%. The maximum nitrification rate of the modified bacterium of X16 by DNA-shuffling was up to 42.9 mg/L.d, which was almost 10 times higher than that of its parental bacteria. Furthermore, the modified bacterium had the same characteristics of its parental bacteria of E. coli and could grow rapidly in normal cultures. Conclusion DNA-shuffling was successfully used to engineer E. coli, which had norB gene and could degrade inorganic nitrogen effectively.
文摘To enhance the relative movement of domains, we inserted a random sequence of fifteen-peptide into the three domains of L-aspartase. By means of directed screening, the three isoforms of monomeric, dimmeric and tetrameric enzymes were obtained. Compared to the wild-type tetrameric L-asparease, these mutants remained 19.7%, 42.3%, and 92% of the enzyme activity, respectively. Moreover, the examination of enzyme properties revealed that their k_ cat and K_M changed in varying degrees, and the optimum pH shifted towards acidic pH, while the dependence of the activity of enzyme on Mg 2+ concentration and thermostability increased. Therefore this strategy provides a novel approach to directed evolution of enzymes.
文摘Cu,Zn SOD is a highly conserved enzyme and the controversy about its evolutionary possibility in the near future has been lively. In order to further our understanding of the future fate of human Cu,Zn SOD, we adopted a strategy relating to the directed evolution to study how the mutants of human Cu,Zn SOD respond to different oxidative stress. After five rounds of screening, we found a mutant that can survive under harsh pressures and DNA sequencing proves that it shows a mutation responsible for the phenomenon. However, under natural pressure, our screening comes to nothing. Then we may draw the following conclusions: the evolution of biological macromolecules in some respect depends on their surroundings and if they are too familiar with a certain environment, they may embody evolutionary inertia.
基金supported by the grants of the National Natural Science Foundation of China(No.31070717)Tianjin International Science and Technology Cooperation Project (No.09ZCGHHZ00500)the 111 Project(No.B08011)
文摘Expression of recombinant protein in Escherichia coli （E.coli） is generally considered as one of the ideal systems to produce proteins for industrial production.However,the majority of proteins usually fail to fold into their native state and accumulate as insoluble inclusion bodies with no biological activity in E.coli（Yang et al.,2003）.
基金funded by the National Key Research and Development Program of China(2023YFC3903300)the Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project(TSBICIPIJCP-003,TSBICIP-KJGG-009-0203,and TSBICIP-BRFI-005)the Innovation Fund of Haihe Laboratory of Synthetic Biology(22HHSWSS00018)。
文摘The enzymatic depolymerization of polyethylene terephthalate(PET)offers a sustainable approach for the recycling of PET waste.Great efforts have been devoted to engineering PET depolymerases on the substrate binding cleft and the surrounding loops/α-helices on the surface.Here,we report the systematic engineering of whole β-sheet regions in the core of IsPETase(a PETase from Ideonella sakaiensis)via a fluorescent high-throughput screening assay.Twenty-one beneficial substitutions were obtained and iteratively recombined.The best variant,DepoPETase β,with an increase in the melting temperatures(T_(m))of 22.9℃,exhibited superior depolymerization performance and enabled complete depolymerization of100.5 g of untreated post-consumer PET(pc-PET;0.26% W_(enzyme)/W_(PET) enzyme loading)in liter-scale bioreactor at 50℃within 4 d.Crystallization and molecular dynamics simulations revealed that the improved activity and thermostability of DepoPETase β were due to enhanced hydrogen bonds and salt bridges in the β-sheet region,a more tightly packed structure of the core sheets and the surrounding helix,and improved binding of PET to the active sites.This study not only demonstrates the importance of engineering strategy in theβ-sheet region of PET hydrolases but also provides a potential PET depolymerase for large-scale PET recycling.
文摘Chiral N-substituted amino amides and esters are ubiquitous scaffolds in pesticides and pharmaceutical chemicals,but their asymmetric synthesis remains challenging especially for those with multiple chiral centers.In this study,IR104 from Streptomyces aureocirculatus was identified from 157 wild-type imine reductases for the synthesis of(S)-2-((R)-2-oxo-4-propylpyrrolidin-1-yl)butanamide(antiepileptic drug Brivaracetam)via dynamic kinetic resolution reductive amination from ethyl 3-formylhexanoate and(S)-2-aminobutylamide with high diastereoselectivity.To further improve the catalytic efficiency of IR104,its mutant D191E/L195I/E253S/M258A(M3)was identified by saturation mutagenesis and iterative combinatorial mutagenesis,which exhibited a 102-fold increase in the catalytic efficiency relative to that of wild-type enzyme and high diastereoselectivity(98:2 d.r.).Crystal structural analysis and molecular dynamics simulations provided some insights into the molecular basis for the improved activity of the mutant enzyme.The imine reductase identified in this study could accept chiral amino amides/esters as amino donors for the dynamic kinetic resolution reductive amination of racemicα-substituted aldehydo-esters,expanding the substrate scope of imine reductases in the dynamic kinetic resolution-reductive amination.Finally,IR104-M3 was successfully used for the preparation of Brivaracetam at gram scale.Using this mutant,various N-substituted amino amides/esters with two chiral centers were also synthesized with up to 99:1 d.r.and 96%yields and subsequently converted intoγ-andδ-lactams,providing an efficient protocol for the synthesis of these important compounds via enzymatic dynamic kinetic resolution-reductive amination from simple building blocks.
文摘Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolution- ary direction dynamically during evolution. After evolution, the solutions’s precision can be greatly improved by means of the local searching along the recorded direction. Simulation shows that this algorithm can not only keep population diversity but also find accurate solutions. Although using this method has to take more time compared with the standard GA, it is really worth applying to some cases that have to meet a demand for high solution precision.
基金financially sponsored by the National Key Research and Development Program of China (No.2021YFC2102804)the National Natural Science Foundation of China(No.22078096)。
文摘Polysubstituted chiral γ-butyrolactones are the core structural units of many natural products and high value-added flavors and fragrances used in the food and cosmetic industry. Current enzymatic cascade synthesis of these molecules faces the problems of low enzyme activity and phase separation in batch reaction, resulting in low productivity. Herein, we report a new continuous-flow process to synthesize the optically pure Nicotiana tabacum lactone(3S,4S)-4a and whisky lactone(3R,4S)-4b from α,β-unsaturatedγ-ketoesters. A new ene reductase(ER) from Swingsia samuiensi(Ss ER) and a carbonyl reductase(Ss CR)were engineered by directed evolution to improve their activity and thermostability. The continuous-flow preparative reactions were performed in two 3D microfluidic reactors, generating(3S,4S)-4a(99% ee and87% de) and(3R,4S)-4b(99% ee and 98% de) with space-time yields 3 and 7.4 times higher than those of the batch reactions. The significant enhancement in the productivity of enzyme cascade catalysis brought by cutting-edge continuous microfluidic technology will benefit the general multi-enzyme catalytic systems in the future.
基金Supported by the National Natural Science Foundation of China(Nos30400081, 30570405 and 20672045)the Key Tech-nology Research and Development Program of China(No2004BA713D03-04)
文摘To identify the desired hypertherrnophilic variants within a mutant esterase library for the resolution of （R, S）-2- octanol acetate, a simple, reliable, and versatile method was developed in this study. We built a screening strategy including two steps, first we selected agar plate with substrate to screen the enzymatic activity; secondly we used a pH indicator to screen the enantioselectivity. This method could rapidly detect favorable mutants with high activity and enantioselectivity. A total of 96. 2% of tedious screening work can be precluded using this screening strategy. It is an effective screening for alkyl ester and can be applied to relative screening researches. The four improved mutants were screened from the mutant esterase library. Their enantioselectivities, activities, and structures were investigated at different temperatures.
基金supported by the National Key R&D Program of China(2019YFA0904900)the National Natural Science Foundation of China(21877112,21837002,21721004)。
文摘Cytochrome P450 enzymes catalyze diverse oxidative transformations at the expense of reduced nicotinamide adenine dinucleotide phosphate(NADPH),however,their applications remain limited largely because NADPH is cost-prohibitive for biocatalysis at scale yet tightly regulated in host cells.A highly challenging task for P450 catalysis has been to develop an alternative and biocompatible electrondonating system.Here we engineered P450 BM3 to favor reduced nicotinamide cytosine dinucleotide(NCDH)and created non-natural cofactor-dependent P450 catalysis.Two outstanding mutants were identified with over 640-fold NCDH preference improvement and good catalytic efficiencies of over15,000 M^(-1)s^(-1)for the oxidation of the fatty acid probe 12-(para-nitrophenoxy)-dodecanoate.Molecular docking analysis indicated that these mutants bear a compacted cofactor entrance.Upon fusing with an NCD-dependent formate dehydrogenase,fused proteins functioned as NCDH-specific P450catalysts by using formate as the electron donor.Importantly,these mutants and fusions catalyzed NCDH-dependent hydroxylation of fatty acids with similar chain length preference to those by natural P450 BM3 in the presence of NADPH and also similar regioselectivity for subterminal hydroxylation of lauric acid.As P450 BM3 and its variants are catalytically powerful to take diverse substrates and convey different reaction paths,our results offer an exciting opportunity to devise advanced cell factories that convey oxidative biocatalysis with an orthogonal reducing power supply system.
基金supported by the National Key Research and Development Program of China(2018YFB1106303)Scientific Research Foundation of CAUC(2017QD10S).
文摘The integration of topology optimization(TO)and additive manufacturing(AM)technologies can create significant synergy benefits,while the lack of AM-friendly TO algorithms is a serious bottleneck for the application of TO in AM.In this paper,a TO method is proposed to design self-supporting structures with an explicit continuous self-supporting constraint,which can be adaptively activated and tightened during the optimization procedure.The TO procedure is suitable for various critical overhang angles(COA),which is integrated with build direction assignment to reduce performance loss.Besides,a triangular directional self-supporting constraint sensitivity filter is devised to promote the downward evolution of structures and maintain stability.Two numerical examples are presented;all the test cases have successfully converged and the optimized solutions demonstrate good manufacturability.In the meanwhile,a fully self-supporting design can be obtained with a slight cost in performance through combination with build direction assignment.
基金supported by the National Key Research and Development Program of China(2022YFC3401700)the National Natural Science Foundation of China(Grant No.32171478)the Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project(Grant No.TSBICIP-KJGG-009).
文摘Cytidine triphosphate(CTP),as a substance involved in the metabolism of phospholipids,proteins and nucleic acids,has precise drug effects and is a direct precursor for the synthesis of drugs such as citicoline.In this study,we established an in vitro six-enzyme cascade system to generate CTP.To avoid thermodynamic bottlenecks,we employed a circuitous and two-stage reaction strategy.Using cytidine as the key substrate,the final product CTP is obtained via the deamination and uridine phosphorylation pathways,relying on the irreversible reaction of cytidine triphosphate synthase to catalyze the amination of uridine triphosphate.Several extremophilic microbial-derived deaminases were screened and characterized,and a suitable cytidine deaminase was selected to match the first-stage reaction conditions.In addition,directed evolution modification of the rate-limiting enzyme CTP synthetase in the pathway yielded a variant that successfully relieved the product feedback inhibition,along with a 1.7-fold increase in activity over the wild type.After optimizing the reaction conditions,we finally carried out the catalytic reaction at an initial cytidine concentration of 20 mM,and the yield of CTP exceeded 82%within 10.0 h.
基金The National Key Research and Development Program of China(Nos.2021YFA0911400 and 2021YFF0600704)the National Natural Science Foundation of China(Nos.22071033 and 21801047)are acknowledged for the financial supports。
文摘We report here a generic,green synthesis of 17 valuable syn-aryl-(2S,3R)-2–chloro-3–hydroxy esters(syn-(2S,3R)-1)in 73%-99%isolated yields along with 6.1:1–83:1 dr and 31%~>99%ee,through dynamic reductive kinetic resolution of racemic arylα–chloroβ-keto esters(2)catalyzed by an engineered ketoreductase which was obtained via ep PCR-based directed evolution.The hectogram scale synthesis of syn-(2S,3R)-1b at a substrate concentration of 120 g/L showcased the application potential of the biocatalytic method developed presently.
基金supported by the National Natural Science Foundation of China(no.22378083)Mengniu group with project number EN2400037.
文摘Microbial proteins hold great promise as sustainable alternatives for future protein sources,and oleaginous yeast Yarrowia lipolytica has emerged as a recognized platform for heterologous protein expression and secretion.N-terminal signal peptides(SPs)are crucial for directing proteins to the secretion pathway,which offers advantages in both academic and industrial protein production.Although some of the innate SPs of Y.lipolytica have been reported,there is a growing need to expand the genetic toolkit of SPs to support the increasing use of Y.lipolytica as a cell factory for overproduction of various secretory proteins.In this study,we employed an efficient evolutionary approach to rapidly evolve the innate SP XPR2-pre by leveraging Gibson assembly with two syn-thetic overlapping oligos containing high portion of degenerate nucleotides.Using Nanoluc(Nluc)luciferase as a robust reporter,we characterized the intracellular and extracellular enzymatic activity of 447 SP mutants and identified previously undescribed SPs exhibiting superior performance compared to XPR2-pre in Nluc luciferase secretion,with improvements of up to 2.91-fold of enzymatic activity in the supernatant.The generalizability of the top-performing SPs was evaluated using three additional heterologous enzymes(β-galactosidase,α-amylase,and PET hydrolase).Our results confirmed their versatility across different proteins with protein-specific effi-ciency.Additionally,based on our screening,we also evaluated the performance of different feature engineering strategies and machine learning models in the design and prediction of SP mutants.This study integrated rational design,directed evolution and machine learning to identify novel SPs,expanding the repertoire of signal peptides and benefiting secretory protein overexpression in Y.lipolytica.
基金supported by the National Key Research and Development Program(2024YFF1106800)National Natural Sci-ence Foundation of China(32172349)+2 种基金the Foundation for Innovative Research Groups of the National Natural Science Foundation of China(32021005)the Jiangsu Basic Research Center for Synthetic Biology(BK20233003)the Natural Science Foundation of Jiangsu Province(BK20202002).
文摘Targeted in vivo hypermutation mediated by base deaminase-T7 RNA polymerase(T7 RNAP)fusions promotes genetic diversification and accelerates continuous directed evolution.Due to the lack of a T7RNAP expression regulation system and functionally compatible linker for fusion protein expression,T7RNAP-guided continuous evolution has not been established in Bacillus subtilis,which limited long gene fragment continuous evolution targeted on genome.Here,we developed BS-MutaT7 system,which introduced mutations into specific genomic regions by leveraging chimeric fusions of base deaminases with T7RNAP in B.subtilis.We selected seven different sources of adenosine and cytosine deaminases,14 fusion protein linkers to be fused with T7RNAP,constructing four libraries with the size of 5000,where deaminases were fused at either the N-or C-terminus of T7RNAP.Based on the efficiency of binding to T7 promoter and high mutagenesis activity,two optimal chimeric mutators,BS-MutaT7A(TadA8e-Linker0-T7RNAP)and BS-MutaT7C(PmCDA1-(GGGGS)3-T7RNAP co-expressed with UGI)were identified.The target mutation rates reached 1.2×105 per base per generation(s.p.b.)and 5.8×105 s.p.b.,representing 7000-fold and 37,000-fold increases over the genomic mutation rate,respectively.Both exhibited high processivity,maintaining mutation rates of 5.8×106 s.p.b.and 2.9×105 s.p.b.within a 5 kb DNA region.Notably,BS-MutaT7C exhibited superior mutagenic activity,making it well-suited for applications requiring intensive and sustained genomic diversification.Application of BS-MutaT7 enabled a 16-fold increase in tigecycline resistance and enhancedβ-lactoglobulin(β-Lg)expression by evolving the global transcriptional regulator codY,achieving aβ-Lg titer of 3.92 g/L.These results highlight BS-MutaT7 as a powerful and versatile tool for genome-scale continuous evolution in B.subtilis.
文摘Recently,a novel protein language model(PLM)was published by Liang Hong group in Science Advances1,introducing PRIME(PRotein language model for Intelligent Masked pretraining and Environment prediction,Fig.1).PRIME is a deep learning model designed to predict and improve protein stability and activity without relying on experimental mutagenesis data.This innovative approach leverages a vast dataset of 96 million protein sequences annotated with their host bacterial optimal growth temperatures(OGTs)to develop a model that effectively guides protein engineering across various applications.
文摘Protein engineering involves modifying proteins'sequences to achieve desired functions,such as enhanced stability,improved activity,altered specificity,reduced immunogenicity,and improved pharmacokinetics.Rational design and directed evolution(Arnold,1996)are two major traditional approaches for protein engineering.Rational design uses the knowledge of protein structure-function relationships to intentionally introduce specific mutations,while directed evolution mimics natural selection by generating random mutations and screening for desired protein functions.
基金funded by the Ministry of Science and Technology,the National Key Research and Development Program of China (2021YFC2100800)the National Natural Science Foundation of China (31800719,and 21621004).
文摘catalyzed byβ-carotene hydroxylase(crtZ)andβ-carotene ketolase(crtW)decreases the content of the astaxanthin.Here,we exploited directed evolution of the fusion of crtZ and crtW for improving astaxanthin biosynthesis in Saccharomyces cerevisiae.The results demonstrated that the fusion enzyme of crtZ-crtW with 2 X GGGGS peptides linker can effectively reduce the accumulation of intermediates and improves the content of astaxanthin.Compared with the control strain,the fusion enzyme of ketase and hydroxylase reduced zeaxanthin and canthaxanthin by 7 and 14 times and increased astaxanthin by 1.6 times,respectively.Moreover,9 variant fusion mutants with improved astaxanthin production were generated through directed evolution.Combining these dominant mutants generated a variant,L95S+I206L,which increased the astaxanthin content of 3.8 times than the control strain.The AlphaFold2 assisted structural analysis indicated that these two mutations alter the interaction between the substrate and the enzymes pocket.Our research provided an efficient idea to reduce the accumulation of the intermediate products in complex biosynthesis pathway.
基金This research was supported by the National Natural Science Foundation of China(Grant No.30870037)Research Fund for the Doctoral Program of Higher Education of China(No.20102329120002)China Postdoctoral Science Foundation(No.20090450983).
文摘If cellulose can be effectively hydrolyzed intoglucose by cellulase,the production costs of hydrogen,ethanol or other chemicals from cellulosic materials will begreatly decreased,and economically viable production ofbiohydrogen and bioethanol will become feasible.Celluloseis degraded into glucoses by multi-component enzymesystems.Nowadays cellulases are widely used in brewing,food,bioenergy,fodder,textiles,paper,pharmaceuticals,environmental protection and other industries.However,existing cellulases have several problems that limit theirwider applications,including the low turnover number forsolid cellulosic materials,and low stability in adapting tovarious application conditions.For example,high temperature,low pH,and so on.Application of directedevolution technology may be one of the most effectiveways for improving the characteristics of cellulases.Thispaper presents a brief review of the cellulases hydrolysismechanism by cellulase,advances in cellulases(endoglucanaseandβ-glucosidase)improvement by directedevolution for several characteristics(for instance,thermalstability,pH adaptability and enzyme activity),limitationsof directed evolution for cellulases,and the outlook fordirected evolution for cellulase.
