Enhancement of the thermostability of β-1,3-1,4-glucanase by directed evolution

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.

Directed Molecular Evolution of Nitrite Oxido-reductase by DNA-shuffling

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.

Industrial Green Spatial Pattern Evolution of Yangtze River Economic Belt in China

We use the directional slacks-based measure of efficiency and inverse distance weighting method to analyze the spatial pattern evolution of the industrial green total factor productivity of 108 cities in the Yangtze River Economic Belt in 2003–2013.Results show that both the subprime mortgage crisis and ‘the new normal' had significant negative effects on productivity growth,leading to the different spatial patterns between 2003–2008 and 2009–2013.Before 2008,green poles had gathered around some capital cities and formed a tripartite pattern,which was a typical core-periphery pattern.Due to a combination of the polarization and the diffusion effects,capital cities became the growth poles and ‘core' regions,while surrounding areas became the ‘periphery'.This was mainly caused by the innate advantage of capital cities and ‘the rise of central China' strategy.After 2008,the tripartite pattern changed to a multi-poles pattern where green poles continuously and densely spread in the midstream and downstream areas.This is due to the regional difference in the leading effect of green poles.The leading effect of green poles in midstream and downstream areas has changed from polarization to diffusion,while the polarization effect still leads in the upstream area.

Directed Evolution of L-Aspartase by Mobility of Domains

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.

Directed Evolution of Human Cu,Zn-SOD Under Artificial Oxidant Pressures

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.

Creation of cytochrome P450 catalysis depending on a non-natural cofactor for fatty acid hydroxylation

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.

Engineering of cofactor preference and catalytic activity of methanol dehydrogenase by growth-coupled directed evolution

Methanol,produced from carbon dioxide,natural gas,and biomass,has drawn increasing attention as a promising green carbon feedstock for biomanufacturing due to its sustainable and energy-rich properties.Nicotinamide adenine dinucleotide(NAD^(+))-dependent methanol dehydrogenase(MDH)catalyzes the oxidation of methanol to formaldehyde via NADH generation,providing a highly active C1 intermediate and reducing power for subsequent biosynthesis.However,the unsatisfactory catalytic efficiency and cofactor bias of MDH significantly impede methanol valorization,especially in nicotinamide adenine dinucleotide phosphate(NADP^(+))-dependent biosynthesis.Herein,we employed synthetic NADH and NADPH auxotrophic Escherichia coli strains as growth-coupled selection platforms for the directed evolution of MDH from Bacillus stearothermophilus DSM 2334.NADH or NADPH generated by MDH-catalyzed methanol oxidation enabled the growth of synthetic cofactor auxotrophs,establishing a positive correlation between the cell growth rate and MDH activity.Using this principle,MDH mutants exhibiting a 20-fold improvement in catalytic efficiency(k_(cat)/K_(m))and a 90-fold cofactor specificity switch from NAD^(+)to NADP+without a decrease in specific enzyme activity,were efficiently screened from random and semi-rationally designed libraries.We envision that these mutants will advance methanol valorization and that the synthetic cofactor auxotrophs will serve as versatile selection platforms for the evolution of NAD(P)^(+)-dependent enzymes.

High-throughput Screening of the Enantioselectivity of Hyperthermophilic Mutant Esterases from Archaeon Aeropyrum pernix K1 for Resolution of (R,S)-2-Octanol Acetate

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.

Niche Genetic Algorithm with Accurate Optimization Performance

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.

Topology Optimization of Self-Supporting Structures for Additive Manufacturing with Adaptive Explicit Continuous Constraint

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.

Directed evolution of the fusion enzyme for improving astaxanthin biosynthesis in Saccharomyces cerevisiae

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.

Directed evolution of a neutrophilic and mesophilic methanol dehydrogenase based on high-throughput and accurate measurement of formaldehyde

Methanol is a promising one-carbon feedstock for biomanufacturing,which can be sustainably produced from carbon dioxide and natural gas.However,the efficiency of methanol bioconversion is limited by the poor catalytic properties of nicotinamide adenine dinucleotide(NAD^(+))-dependent methanol dehydrogenase(Mdh)that oxidizes methanol to formaldehyde.Herein,the neutrophilic and mesophilic NAD^(+)-dependent Mdh from Bacillus stearothermophilus DSM 2334(Mdh_(Bs))was subjected to directed evolution for enhancing the catalytic activity.The combination of formaldehyde biosensor and Nash assay allowed high-throughput and accurate measurement of formaldehyde and facilitated efficient selection of desired variants.Mdh_(Bs)variants with up to 6.5-fold higher K_(cat)/K_(M)value for methanol were screened from random mutation libraries.The T153 residue that is spatially proximal to the substrate binding pocket has significant influence on enzyme activity.The beneficial T153P mutation changes the interaction network of this residue and breaks theα-helix important for substrate binding into two shortα-helices.Reconstructing the interaction network of T153 with surrounding residues may represent a promising strategy to further improve Mdh_(Bs),and this study provides an efficient strategy for directed evolution of Mdh.

Divergent Protein Engineering of Transaminase for the Synthesis of Chiral Rivastigmine and Apremilast Precursors

Comprehensive Summary The implementation of divergent protein engineering on the natural transaminase Vf-ω-TA led to the development of two effective mutants(M2 and M8),enabling the enzymatic synthesis of chiral amine precursors of Rivastigmine and Apremilast,respectively.The evolution of the enzymes was guided by crystal structures and a focused mutagenesis strategy,allowing them to effectively address the challenging ketone substrates with significant steric hindrance.Under the optimized reaction parameters,transamination proceeded smoothly in good conversions and with perfect stereochemical control(>99%ee).These processes utilize inexpensiveα-methylbenzylamine as an amine donor and avoid the continuous acetone removal and costly LDH/GDH/NADH systems.

Synthetic auxotrophs accelerate cell factory development through growth-coupled models

The engineering of microbial cell factories for the production of high-value chemicals from renewable resources presents several challenges,including the optimization of key enzymes,pathway fluxes and metabolic networks.Addressing these challenges involves the development of synthetic auxotrophs,a strategy that links cell growth with enzyme properties or biosynthetic pathways.This linkage allows for the improvement of enzyme properties by in vivo directed enzyme evolution,the enhancement of metabolic pathway fluxes under growth pressure,and remodeling of metabolic networks through directed strain evolution.The advantage of employing synthetic auxotrophs lies in the power of growth-coupled selection,which is not only high-throughput but also labor-saving,greatly simplifying the development of both strains and enzymes.Synthetic auxotrophs play a pivotal role in advancing microbial cell factories,offering benefits from enzyme optimization to the manipulation of metabolic networks within single microbes.Furthermore,this strategy extends to coculture systems,enabling collaboration within microbial communities.This review highlights the recently developed applications of synthetic auxotrophs as microbial cell factories,and discusses future perspectives,aiming to provide a practical guide for growth-coupled models to produce value-added chemicals as part of a sustainable biorefinery.

Continuous-flow synthesis of polysubstituted γ-butyrolactones via enzymatic cascade catalysis

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.

Biocatalytic stereoselective synthesis of methyl mandelates by engineering a cytochrome P450 hydroxylase

Chiral methyl mandelates are useful synthons in organic transformation and pharmaceutical synthesis.Green synthesis of these valuable compounds by direct C–H activating oxidative hydroxylation has attracted keen interest.Described herein is achieving the stereoselective and efficient bio-hydroxylation of methyl 2-phenylacetates to the chiral methyl mandelates by directed evolution of the cytochrome P450DA hydroxylase.In the present study,a new colorimetric high-throughput screening assay was successfully developed based on a dualenzyme cascade for the engineering of the P450DA's hydroxylation activity.Several beneficial variants with enhanced bio-hydroxylation activity were created by combining random mutagenesis and site-saturated/directed mutagenesis strategies.Whole-cell bio-hydroxylation of various methyl 2-phenylacetates using the best septupletmutant P450DA-11 yielded the corresponding chiral methyl mandelates in up to 92%isolated yields and>99%ee.

Advances in the study of directed evolution for cellulases

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.

Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations

Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched.In this study,an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)technology with two synthetic chromosomes,namely synV and synX.The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries.Our findings showed that complex SVs,including a pericentric inversion and a trans-chromosome translocation between synV and synX,resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin.Also,genetic targets were mapped,which resulted in a higher astaxanthin yield,thus demonstrating the SVs’ability to reorganize genetic information along the chromosomes.The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena.Collectively,this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.

Biochemical characterization of a polyethylene terephthalate hydrolase and design of high-throughput screening for its directed evolution

Polyethylene terephthalate(PET),one of the most widely used plastics in the world,causes serious environmental pollution.Recently,researchers have focused their efforts on enzymatic degradation of PET,which is an attractive way of degrading and recycling PET.In this work,PET hydrolase Sb PETase from Schlegelella brevitalea sp.nov.was biochemically characterized,and rational design was performed based on its sequence similarity with the previ-ously reported Is PETase from Ideonella sakaiensis,resulting in a triple mutant with increased activity.Furthermore,using a sec-dependent signal peptide PeIB and colicin release protein Kil,we set up a high-efficiency secretion system of PETase in Escherichia coli BL21(DE3),enabling higher PETase secretion.Utilizing this secretion system,we established a high-throughput screening method named SecHTS(sec retion-based h igh-throughput s creening)and performed directed evolution of Is PETase and Sb PETase through DNA shuffling.Finally,we generated a mutant Is PETase S139T with increased activity from the mutant library.

Development of MEMS directed evolution strategy for multiplied throughput and convergent evolution of cytochrome P450 enzymes

Directed evolution(DE)inspired by natural evolution(NE)has been achieving tremendous successes in protein/enzyme engineering.However,the conventional"one-protein-for-one-task"DE cannot match the"multi-proteins-for-multi-tasks"NE in terms of screening throughput and efficiency,thus often failing to meet the fast-growing demands for biocatalysts with desired properties.In this study,we design a novel"multi-enzymes-for-multi-substrates"(MEMS)DE model and establish the proof-ofconcept by running a NE-mimicking and higher-throughput screening on the basis of"two-P450 s-against-seven-substrates"(2P×7S)in one pot.With the multiplied throughput and improved hit rate,we witness a series of convergent evolution events of the two archetypal cytochrome P450 enzymes(P450 BM3 and P450 cam)in laboratory.It is anticipated that the new strategy of MEMS DE will find broader application for a larger repertoire of enzymes in the future.Furthermore,structural and substrate docking analysis of the two functionally convergent P450 variants provide important insights into how distinct P450 active-sites can reach a common catalytic goal.