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Rational surface charge engineering of haloalkane dehalogenase for boosting the enzymatic performance in organic solvent solutions

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Chinese Journal of Chemical Engineering 2024年第1期65卷 276-285页

作者： Yin Wu Yan Sun Department of Biochemical Engineering School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology(Ministry of Education)Tianjin UniversityTianjin 300350China

Biocatalysis in organic solvents(OSs)has numerous important applications,but native enzymes in OSs often exhibit limited catalytic performance.Herein,we proposed a computation-aided surface charge engineering strategy to improve the catalytic performance of haloalkane dehalogenase DhaA in OSs based on the energetic analysis of substrate binding to the DhaA surface.Several variants with enhanced OS resistance were obtained by replacing negative charged residues on the surface with positive charged residue(Arg).Particularly,a four-substitution variant E16R/E93R/E121R/E257R exhibited the best catalytic performance(five-fold improvement in OS resistance and seven-fold half-life increase in 40%(vol)dimethylsulfoxide).As a result,the overall catalytic performance of the variant could be at least 26 times higher than the wild-type DhaA.Fluorescence spectroscopy and molecular dynamics simulation studies revealed that the residue substitution mainly enhanced OS resistance from four aspects:(a)improved the overall structural stability,(b)increased the hydrophobicity of the local microenvironment around the catalytic triad,(c)enriched the hydrophobic substrate around the enzyme molecule,and(d)lowered the contact frequency between OS molecules and the catalytic triad.Our findings validate that computationaided surface charge engineering is an effective and ingenious rational strategy for tailoring enzyme performance in OSs.

关键词： Surface charge engineering Organic solvent resistance Molecular dynamics simulation Haloalkane dehalogenase

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Inhibition of Defect-Induced Ice Nucleation, Propagation, and Adhesion by Bioinspired Self-Healing Anti-Icing Coatings

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Research 2024年第1期2023卷 237-246页

作者： Shu Tian Ruiqi Li Xinmeng Liu Jiancheng Wang Junyu Yu Sijia Xu Yunqing Tian Jing Yang Lei Zhang Department of Biochemical Engineering Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(MOE)School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300350China Binzhou Institute of Technology Weiqiao-UCAS Science and Technology ParkBinzhou CityShandong Province 256606China

Anti-icing coatings on outdoor infrastructures inevitably suffer from mechanical injuries in numerous icing scenarios such as hailstorms,sandstorms,impacts of foreign objects,and icing–deicing cycles.Herein,the mechanisms of surface-defect-induced icing are clarified.At the defects,water molecules exhibit stronger adsorption and the heat transfer rate increases,accelerating the condensation of water vapor as well as ice nucleation and propagation.Moreover,the ice–defect interlocking structure increases the ice adhesion strength.Thus,a self-healing(at−20℃)antifreeze-protein(AFP)-inspired anti-icing coating is developed.The coating is based on a design that mimics the ice-binding and non-ice-binding sites in AFPs.It enables the coating to markedly inhibit ice nucleation(nucleation temperature<−29.4℃),prevent ice propagation(propagation rate<0.00048 cm^(2)/s),and reduce ice adhesion on the surface(adhesion strength<38.9 kPa).More importantly,the coating can also autonomously self-heal at−20℃,as a result of multiple dynamic bonds in its structure,to inhibit defect-induced icing processes.The healed coating sustains high anti-icing and deicing performance even under various extreme conditions.This work reveals the in-depth mechanism of defect-induced ice formation as well as adhesion,and proposes a self-healing anti-icing coating for outdoor infrastructures.

关键词： coating defect clarified

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Renewable biosynthesis of isoprene from wastewater through a synthetic biology approach:the role of individual organic compounds

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Frontiers of Environmental science & Engineering 2024年第3期18卷 13-24页

作者： Min Yang Xianghui Li Weixiang Chao Xiang Gao Huan Wang Lu Lu State Key Laboratory of Urban Water Resource and Environment School of Civil and Environmental EngineeringHarbin Institute of TechnologyShenzhen 518055China Center for Materials synthetic biology CAS Key Laboratory of Quantitative Engineering Biology of CASShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academic of ScienceShenzhen 518000China Institute of Urban Ecology and Environmental Technology School of Materials and Environmental EngineeringShenzhen Polytechnic UniversityShenzhen 518055China

The biosynthesis of isoprene offers a more sustainable alternative to fossil fuel-based approaches,yet its success has been largely limited to pure organic compounds and the cost remains a challenge.This study proposes a waste-to-wealth strategy for isoprene biosynthesis utilizing genetically engineered E.coli bacteria to convert organic waste from real food wastewater.The impact of organic compounds present in wastewater on E.coli growth and isoprene production was systematically investigated.The results demonstrated that with filtration pretreatment of wastewater,isoprene yield,and production achieved 115 mg/g COD and 7.1 mg/(L·h),respectively.Moreover,even without pretreatment,isoprene yield only decreased by~24%,indicating promising scalability.Glucose,maltose,glycerol,and lactate are effective substrates for isoprene biosynthesis,whereas starch,protein,and acetate do not support E.coli growth.The optimum C/N ratio for isoprene production was found to be 8:1.Furthermore,augmenting essential nutrients in wastewater elevated the isoprene yield increased to 159 mg/g COD.The wastewater biosynthesis significantly reduced the cost(44%–53%decrease,p-value<0.01)and CO_(2)emission(46%–55%decrease,p-value<0.01)compared with both sugar fermentation and fossil fuel–based refining.This study introduced a more sustainable and economically viable approach to isoprene synthesis,offering an avenue for resource recovery from wastewater.

关键词： Wastewater Resource recovery Genetic engineering Biosynthesis Isoprene

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Enhancing whole yeast genome rearrangements through multiple LoxP sym sequences

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science China Life sciences 2024年

作者： Bing-Zhi Li Ying-Jin Yuan Frontiers science Center for synthetic biology and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Frontiers Research Institute for synthetic biology Tianjin University

Genomic rearrangements play a significant role in disease, evolution, and tumorigenesis(Mani and Chinnaiyan,2010). While single nucleotide polymorphisms(SNPs) and small insertions/deletions contribute substantially to genetic variation, discerning the independent impact of structural variations poses a challenge. Additionally, experimental induction and control of structural variations present difficulties that hinder further investigation and exploitation.

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Blockade of CD300A enhances the ability of human NK cells to lyse hematologic malignancies

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Cancer biology & Medicine 2024年第4期21卷 331-346页

作者： Shuangcheng Li Tianci Wang Xinghui Xiao Xiaodong Zheng Haoyu Sun Rui Sun Hongdi Ma Zhigang Tian Xiaohu Zheng Hefei National Research Center for Physical sciences at Microscale The CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesCenter for Advanced Interdisciplinary Science and Biomedicine of IHMDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China Institute of Immunology University of Science and Technology of ChinaHefei 230027China Hefei TG ImmunoPharma Corporation Limited Hefei 230601China Research Unit of NK Cell Study Chinese Academy of Medical SciencesBeijing 100864China Key Laboratory of Quantitative synthetic biology Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Objective: The human cluster of differentiation(CD)300A, a type-I transmembrane protein with immunoreceptor tyrosine-based inhibitory motifs, was investigated as a potential immune checkpoint for human natural killer(NK) cells targeting hematologic malignancies(HMs).Methods: We implemented a stimulation system involving the CD300A ligand, phosphatidylserine(PS), exposed to the outer surface of malignant cells. Additionally, we utilized CD300A overexpression, a CD300A blocking system, and a xenotransplantation model to evaluate the impact of CD300A on NK cell efficacy against HMs in in vitro and in vivo settings. Furthermore, we explored the association between CD300A and HM progression in patients.Results: Our findings indicated that PS hampers the function of NK cells. Increased CD300A expression inhibited HM lysis by NK cells. CD300A overexpression shortened the survival of HM-xenografted mice by impairing transplanted NK cells. Blocking PS–CD300A signals with antibodies significantly amplified the expression of lysis function-related proteins and effector cytokines in NK cells, thereby augmenting the ability to lyse HMs. Clinically, heightened CD300A expression correlated with shorter survival and an “exhausted” phenotype of intratumoral NK cells in patients with HMs or solid tumors.Conclusions: These results propose CD300A as a potential target for invigorating NK cell-based treatments against HMs.

关键词： NK cell CD300A phosphatidylserine immune checkpoint hematologic malignancy

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Phosphine-catalyzed acyl-transfer of heteroaryl ketones for the construction of N-fused heterocycles

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Chinese Chemical Letters 2024年第3期35卷 252-256页

作者： Yu Zhang De-Rui Han Dan Ye Hong Lu Hao Wei Key Laboratory of synthetic and Natural Functional Molecule of the Ministry of Education College of Chemistry&Materials ScienceNorthwest UniversityXi'an 710069China

An inexpensive phosphine catalyst was used effectively for a transition-metal-free acyl-transfer of N-containing heteroaryl ketones for the rapid synthesis of N-fused heterocycles.The key pre-aromatic spirocyclic intermediate initialized by the single electron transfer(SET)process of Togni's reagentⅡpromoted by the tertiary phosphine resulted in an intriguing and alternative tactic for the cleavage of C–C bonds.By using inexpensive tertiary phosphine as the catalyst,this skeleton-reorganizing approach of N-containing heteroaryl ketones allows a streamlined assembly of complex N-fused heterocycles with broad functional group tolerance.

关键词： Phosphine catalysis Acyl-transfer N-Fused heterocycles C–C bond activation Aromatization

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Construction of plum-branch-like CoSe2@N-Doped carbon/carbon fiber with dual protective mechanisms for enhanced lithium storage

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Progress in Natural science:Materials International 2024年第3期34卷 495-502页

作者： Ying Wang Ming Zhang Lei Chen Yanjuan Li Qingqing Wang Xiaobin Wu Lingdi Shen Xiao Yan School of Chemistry & Materials science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University

Cobalt selenide（CoSe2） emerges as a highly promising anode material for lithium-ion batteries（LIBs） owing to its high theoretical capacity and cost-effectiveness. Despite these merits, its practical utilization faces challenges stemming from substantial volume fluctuations and limited electronic conductivity. To tackle these issues, a plumbranch-like structure of CoSe2@N-doped carbon that embedded in one-dimensional N-doped carbon fibers（CoSe2@NC/CFs）, is successfully synthesized through an in-situ confinement method. Well-defined CoSe2@NC nanoparticles, featuring diameters between 20～30 nm, are uniformly dispersed on both the inner and outer surfaces of the carbon fibers. The distinctive architecture of CoSe2@NC/CFs ensures an increased number of active sites, elevated electronic conductivity, alleviated volume expansion, and accelerated reaction kinetics.Consequently, the CoSe2@NC/CFs exhibits remarkable cycling performance and exceptional rate capability.Operating at a current density of 1000 mA g-1, the CoSe2@NC/CFs anode sustains a capacity of 664 mA h g-1with no obvious capacity decay over 500 cycles. Even at a high current density of 5000 mA g-1, it maintains a capacity of 445 mA h g-1with a mere 0.02 % capacity decay per cycle. This study introduces a novel approach to anode material design, showcasing significant advancements in lithium-ion battery technology.

关键词： Carbon fiber Electrochemical performances Electrode Lithium-ion battery Metal-selenide

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Hybridization chain reaction-based DNA nanomaterials for biosensing,bioimaging and therapeutics

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Chinese Chemical Letters 2024年第2期35卷 223-231页

作者： Zhaoyue Lv Mengxue Huang Peiran Li Mengdi Xu Chi Yao Dayong Yang Frontiers science Center for synthetic biology Key Laboratory of Systems Bioengineering (MOE)Institute of Biomolecular and Biomedical EngineeringSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin 300350China Zhejiang Institute of Tianjin University Ningbo 315201China

DNA nanomaterials hold great promise in biomedical fields due to its excellent sequence programmability,molecular recognition ability and biocompatibility.Hybridization chain reaction(HCR)is a simple and efficient isothermal enzyme-free amplification strategy of DNA,generating nicked double helices with repeated units.Through the design of HCR hairpins,multiple nanomaterials with desired functions are assembled by DNA,exhibiting great potential in biomedical applications.Herein,the recent progress of HCR-based DNA nanomaterials for biosensing,bioimaging and therapeutics are summarized.Representative works are exemplified to demonstrate how HCR-based DNA nanomaterials are designed and constructed.The challenges and prospects of the development of HCR-based DNA nanomaterials are discussed.We envision that rationally designing HCR-based DNA nanomaterials will facilitate the development of biomedical applications.

关键词： DNA nanotechnology Hybridization chain reaction DNA nanomaterials Biosensing Bioimaging Therapeutics

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6-Phosphogluconate dehydrogenase 2 bridges the OPP and shikimate pathways to enhance aromatic amino acid production in plants

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science China Life sciences 2024年

作者： Qian Tang Yuxin Huang Zhuanglin Shen Linhui Sun Yang Gu Huiqing He Yanhong Chen Jiahai Zhou Limin Zhang Cuihuan Zhao Shisong Ma Yunhai Li Jie Wu Qiao Zhao Shenzhen Key Laboratory of synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic Genomics Key Laboratory of Quantitative Synthetic Biology Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced Technology Chinese Academy of Sciences University of Chinese Academy of sciences CAS Key Laboratory for Quantitative Engineering biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Key Laboratory of Quantitative synthetic biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Key Laboratory of Agricultural Microbiology of Heilongjiang Province Northeast Agricultural University Center for Plant biology School of Life Sciences Tsinghua University State Key Laboratory of Plant Cell and Chromosome Engineering CAS Centre for Excellence in Molecular Plant Biology Institute of Genetics and Developmental Biology The Innovative Academy of Seed Design Chinese Academy of Sciences MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics School of Life Sciences University of Science and Technology of China Innovation Academy for Seed Design Chinese Academy of Sciences

The oxidative pentose phosphate(OPP) pathway provides metabolic intermediates for the shikimate pathway and directs carbon flow to the biosynthesis of aromatic amino acids(AAAs), which serve as basic protein building blocks and precursors of numerous metabolites essential for plant growth. However, genetic evidence linking the two pathways is largely unclear. In this study, we identified 6-phosphogluconate dehydrogenase 2(PGD2), the rate-limiting enzyme of the cytosolic OPP pathway, through suppressor screening of arogenate dehydrogenase 2(adh2) in Arabidopsis. Our data indicated that a single amino acid substitution at position 63(glutamic acid to lysine) of PGD2 enhanced its enzyme activity by facilitating the dissociation of products from the active site of PGD2, thus increasing the accumulation of AAAs and partially restoring the defective phenotype of adh2. Phylogenetic analysis indicated that the point mutation occurred in a well-conserved amino acid residue. Plants with different amino acids at this conserved site of PGDs confer diverse catalytic activities, thus exhibiting distinct AAAs producing capability. These findings uncover the genetic link between the OPP pathway and AAAs biosynthesis through PGD2. The gain-of-function point mutation of PGD2 identified here could be considered as a potential engineering target to alter the metabolic flux for the production of AAAs and downstream compounds.

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Recent progress in MOFs-based nanozymes for biosensing

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Nano Research 2024年第1期17卷 39-64页

作者： Imamdin Chandio Yongjian Ai Lei Wu Qionglin Liang MOE Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical biology Department of ChemistryLaboratory of Flexible Electronics TechnologyCenter for Synthetic and Systems BiologyTsinghua University-Peking University Joint Centre for Life SciencesTsinghua UniversityBeijing 100084China

Nanozymes are nanomaterials with enzyme-mimicking catalytic activity.Compared to natural enzymes,nanozymes show various properties such as easy to manufacture,stable,adjustable,and inexpensive.Nanozymes play key roles in biosensing,biocatalysis,and disease treatment.As an important kind of nanozymes,metal-organic framework(MOF)-based nanozymes are receiving a lot of attention due to their structural properties and composition.Rationally developing MOF with enzymes-like catalytic properties has opened new perspectives in biosensing.This review summarizes the up-to-date developments in synthesizing two-dimensional and three-dimensional MOF-based nanozymes and their applications in biosensing.Firstly,classification of nanozymes obtained by MOFs is categorized,and different properties of MOF-based nanozymes are described.Then,the distinctive applications of MOF-based nanozymes in identifying various analytes are thoroughly summarized.Finally,the recent challenges and progressive directions in this area are highlighted.

关键词： metal-organic frameworks nanozymes metal-organic framework (MOF)-based nanozymes biosensing analytes

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