Cell therapy approaches that employ engineered mam-malian cells for on-demand production of therapeutic agents in the patient's body are moving beyond proof-of-concept in translational medicine.The therapeutic cel...Cell therapy approaches that employ engineered mam-malian cells for on-demand production of therapeutic agents in the patient's body are moving beyond proof-of-concept in translational medicine.The therapeutic cells can be customized to sense user-defined signals,pro-cess them,and respond in a programmable and pre-dictable way.In this paper,we introduce the available tools and strategies employed to design therapeutic cells.Then,various approaches to control cell behav-iors,including open-loop and closed-loop systems,are discussed.We also highlight therapeutic applications of engineered cells for early diagnosis and treatment of various diseases in the clinic and in experimental dis-ease models.Finally,we consider emerging technolo-gies such as digital devices and their potential for incorporation into future cell-based therapies.展开更多
Synthetic biology(SynBio)is an emerging field of study with great potential in designing,engineering,and constructing new microbial synthetic cells that do not pre-exist in nature or re-engineering existing cells to a...Synthetic biology(SynBio)is an emerging field of study with great potential in designing,engineering,and constructing new microbial synthetic cells that do not pre-exist in nature or re-engineering existing cells to accomplish industrial purposes.Systems biology seeks to understand biology at multiple dimensions,beginning with the molecular and cellular level and progressing to the tissues and organismal level and characterizes cells as complex information-processing systems.SynBio,on the other hand,toggles further and strives to develop and create its systems from scratch.SynBio is now applied in the development of novel therapeutic drugs for the prevention of human diseases,scale up industrial processes,and accomplish previously unfeasible industrial outcomes.This is made possible through significant breakthroughs in DNA sequencing and synthesis technology,as well as insights gained from synthetic chemistry and systems biology.SynBio technologies have allowed for the introduction of improved and synthetic metabolic functionalities in microorganisms to enable the synthesis of a range of pharmacologically-relevant compounds for pharmaceutical exploration.SynBio applications range from finding new ways to making industrial chemical synthesis processes more sustainable as well as the microbial synthesis of improved therapeutic modalities.Hence,this study underpins several innovations,auspicious potentials,and future directions afforded by SynBio that proposes improved industrial microbial synthesis for pharmaceutical exploration.展开更多
Terpenoids are the largest family of natural products.They are made from the building block isoprene pyrophosphate(IPP),and their bioproduction using engineered cell factories has received a great deal of attention.To...Terpenoids are the largest family of natural products.They are made from the building block isoprene pyrophosphate(IPP),and their bioproduction using engineered cell factories has received a great deal of attention.To date,the insufficient metabolic supply of IPP remains a great challenge for the efficient synthesis of terpenoids.In this work,we discover that the imbalanced metabolic flux distribution between the central metabolism and the IPP supply hinders IPP accumulation in Bacillus subtilis(B.subtilis).Therefore,we remodel the IPP metabolism using a series of genetically encoded two-input-multioutput(TIMO)circuits that are responsive to pyruvate or/and malonyl-CoA,resulting in an IPP pool that is significantly increased by up to four-fold.As a proof-of-concept validation,we design an IPP metabolism remodeling strategy to improve the production of three valuable terpenoids,including menaquinone-7(MK-7,4.1-fold),lycopene(9-fold),andβ-carotene(0.9-fold).In particular,the titer of MK-7 in a 50-L bioreactor reached 1549.6 mg·L^(-1),representing the highest titer reported so far.Thus,we propose a TIMO genetic circuits-assisted IPP metabolism remodeling framework that can be generally used for the synergistic fine-tuning of complicated metabolic modules to achieve the efficient bioproduction of terpenoids.展开更多
Although the principles of synthetic biology were initially established in model bacteria,microbial producers,extremophiles and gut microbes have now emerged as valuable prokaryotic chassis for biological engineering....Although the principles of synthetic biology were initially established in model bacteria,microbial producers,extremophiles and gut microbes have now emerged as valuable prokaryotic chassis for biological engineering.Extending the host range in which designed circuits can function reliably and predictably presents a major challenge for the concept of synthetic biology to materialize.In this work,we systematically characterized the cross-species universality of two transcriptional regulatory modules—the T7 RNA polymerase activator module and the repressors module—in three non-model microbes.We found striking linear relationships in circuit activities among different organisms for both modules.Parametrized model fitting revealed host non-specific parameters defining the universality of both modules.Lastly,a genetic NOT gate and a band-pass filter circuit were constructed from these modules and tested in non-model organisms.Combined models employing host non-specific parameters were successful in quantitatively predicting circuit behaviors,underscoring the potential of universal biological parts and predictive modeling in synthetic bioengineering.展开更多
The aim of synthetic biology is to design artificial biological systems for novel applications.From an engineering perspective,construction of biological systems of defined functionality in a hierarchical way is funda...The aim of synthetic biology is to design artificial biological systems for novel applications.From an engineering perspective,construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field.Here,we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements,synthetic circuits and their assemblies into devices and modules.Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.展开更多
In thepast 2decades,synthetic biologists have applied systematic engineering principles to genetic circuit design to devise biological systems with bespoke behaviors,such as Boolean logic gates,signal filters,oscillat...In thepast 2decades,synthetic biologists have applied systematic engineering principles to genetic circuit design to devise biological systems with bespoke behaviors,such as Boolean logic gates,signal filters,oscillators,state machines,perceptrons,and genetic controllers[1,2].Following a bottom-up strategy,the genetic circuits are designed by assembling a set of well-characterized biological components,or genetic parts[3],and optimized through the iterative Design-Build-Test-Learn(DBTL)cycles.展开更多
As synthetic biology advances,the necessity for robust biocontainment strategies for genetically engineered organisms(GEOs)grows increasingly critical to mitigate biosafety risks related to their potential environment...As synthetic biology advances,the necessity for robust biocontainment strategies for genetically engineered organisms(GEOs)grows increasingly critical to mitigate biosafety risks related to their potential environmental release.This paper aims to evaluate environment signal-dependent biocontainment systems for engineered organisms,focusing specifically on leveraging triggered responses and combinatorial systems.There are different types of triggers-chemical,light,temperature,and pH-this review illustrates how these systems can be designed to respond to environmental signals,ensuring a higher safety profile.It also focuses on combinatorial biocontainment to avoid consequences of unintended GEO release into an external environment.Case studies are discussed to demonstrate the practical applications of these systems in real-world scenarios.展开更多
Cancer therapy remains a critical medical challenge.Immunotherapy is an emerging approach to regulating the immune system to fight cancer and has shown therapeutic potential.Due to their immunogenicity,bacteria have b...Cancer therapy remains a critical medical challenge.Immunotherapy is an emerging approach to regulating the immune system to fight cancer and has shown therapeutic potential.Due to their immunogenicity,bacteria have been developed as drug-delivery vehicles in cancer immunotherapy.However,ensuring the safety and efficacy of this approach poses a considerable challenge.This paper comprehensively explains the fundamental processes and synthesis principles involved in immunotherapy utilizing engineered bacteria.Initially,we list common engineered strains and discuss that growth control through genetic mutation promises therapeutic safety.By considering the characteristics of the tumor microenvironment and the interaction of specific molecules,the precision targeting of tumors can be improved.Furthermore,we present a foundational paradigm for genetic circuit construction to achieve controlled gene activation and logical expression,directly determining drug synthesis and release.Finally,we review the immunogenicity,the expression of immunomodulatory factors,the delivery of immune checkpoint inhibitors,and the utilization of bacteria as tumor vaccines to stimulate the immune system and facilitate the efficacy of cancer immunotherapy.展开更多
Human breast milk(HBM)is composed of various components that are crucial for providing essential nutrients and enhancing infant immune system.Recently,the synthesis of HBM components through microbial fermen-tation ha...Human breast milk(HBM)is composed of various components that are crucial for providing essential nutrients and enhancing infant immune system.Recently,the synthesis of HBM components through microbial fermen-tation has garnered significant attention due to its potential to reduce production costs,simplify manufacturing processes,and mitigate environmental pollution.However,this approach results in low yield and is difficult to scale up at the industrial level.Therefore,various synthetic biology tools have been used to enhance the effi-ciency of HBM component synthesis.This review first summarizes several synthetic biology tools that may improve HBM component production.Next,we have summarized HBM component production using microbial cell factories.Finally,we have summarized the challenges and opportunities presented by the construction of cell factories for the synthesis of HBM using synthetic biology tools.This article therefore provides a general guide to the construction of microbial cell factories for HBM components.展开更多
YpsR,a pivotal regulatory protein in the quorum-sensing(QS)of Yersinia pseudotuberculosis(Y.pstb),is essential for molecular signaling,yet its molecular mechanisms remain poorly understood.Herein,this study systemati-...YpsR,a pivotal regulatory protein in the quorum-sensing(QS)of Yersinia pseudotuberculosis(Y.pstb),is essential for molecular signaling,yet its molecular mechanisms remain poorly understood.Herein,this study systemati-cally investigates the interactions between YpsR and acyl-homoserine lactones(AHLs),shedding light on the selective mechanism of YpsR to various AHL molecules.Using molecular docking and surface plasmon resonance(SPR)analysis,we confirmed YpsR’s binding affinities,with the strongest observed for 3OC6-HSL,which notably inhibited Y.pstb growth.Additionally,we engineered a whole-cell biosensor based on YpsR-AHL interaction,which exhibited sensitivity to the signal molecule 3OC6-HSL produced by Y.pstb.Furthermore,key YpsR resi-dues(S32,Y50,W54,D67)involved in AHL binding were identified and validated.Overall,this research elu-cidates the mechanisms of QS signal recognition in Y.pstb,providing valuable insights that support the development of diagnostic tools for detecting Y.pstb infections.展开更多
Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants.Limited by few well-characterized bioparts for plant ch...Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants.Limited by few well-characterized bioparts for plant chassis,the development of plant synthetic biology lags behind that of its microbial counterpart.Here,we constructed a web-based Plant Synthetic BioDatabase(PSBD),which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals.Online bioinformatics tools including local BLAST,chem similarity,phylogenetic analysis,and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta.We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quan-titative regulation in tobacco leaves.More powerful synthetic devices were then assembled to amplify the transcriptional signals,enabling enhanced expression offlavivirus non-structure 1 proteins in plants.The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.展开更多
Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade.However,due to comp...Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade.However,due to complexity of cellular metabolism,the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering.Recently,cell-free protein synthesis system(CFPS)has been emerging as an enabling alternative to address challenges in biomanufacturing.This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits(biosensors)to speed up design-build-test(DBT)cycles of metabolic engineering and synthetic biology.展开更多
Backgrounds:As an increasing number of synthetic switches and circuits have been created for plant systems and of synthetic products produced in plant chassis,plant synthetic biology is taking a strong foothold in agr...Backgrounds:As an increasing number of synthetic switches and circuits have been created for plant systems and of synthetic products produced in plant chassis,plant synthetic biology is taking a strong foothold in agriculture and medicine.The ever-exploding data has also promoted the expansion of toolkits in this field.Genetic parts libraries and quantitative characterization approaches have been developed.However,plant synthetic biology is still in its infancy.The considerations for selecting biological parts to design and construct genetic circuits with predictable functions remain desired.Results:In this article,we review the current biotechnological progresses in field of plant synthetic biology.Assembly standardization and quantitative approaches of genetic parts and genetic circuits are discussed.We also highlight the main challenges in the iterative cycles of design-build-test-learn for introducing novel traits into plants.Conclusion:Plant synthetic biology promises to provide important solutions to many issues in agricultural production,human health care,and environmental sustainability.However,tremendous challenges exist in this field.For example,the quantitative characterization of genetic parts is limited;the orthogonality and the transfer functions of circuits are unpredictable;and also,the mathematical modeling-assisted circuits design still needs to improve predictability and reliability.These challenges are expected to be resolved in the near future as interests in this field are intensifying.展开更多
Neuromorphic computing has the potential to achieve the requirements of the next-generation artificial intelligence(AI)systems,due to its advantages of adaptive learning and parallel computing.Meanwhile,biocomputing h...Neuromorphic computing has the potential to achieve the requirements of the next-generation artificial intelligence(AI)systems,due to its advantages of adaptive learning and parallel computing.Meanwhile,biocomputing has seen ongoing development with the rise of synthetic biology,becoming the driving force for new generation semiconductor synthetic biology(SemiSynBio)technologies.DNA-based biomolecules could potentially perform the functions of Boolean operators as logic gates and be used to construct artificial neural networks(ANNs),providing the possibility of executing neuromorphic computing at the molecular level.Herein,we briefly outline the principles of neuromorphic computing,describe the advances in DNA computing with a focus on synthetic neuromorphic computing,and summarize the major challenges and prospects for synthetic neuromorphic computing.We believe that constructing such synthetic neuromorphic circuits will be an important step toward realizing neuromorphic computing,which would be of widespread use in biocomputing,DNA storage,information security,and national defense.展开更多
Cervical cancer is a global public health subject as it affects women in the reproductive ages,and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50%mortality rate.Relativel...Cervical cancer is a global public health subject as it affects women in the reproductive ages,and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50%mortality rate.Relatively scant awareness and limited access to effective diagnosis have led to this enormous disease burden,calling for point-of-care,minimally invasive diagnosis methods.Here,an end-to-end quantitative unified pipeline for diagnosis has been developed,beginning with identification of optimal biomarkers,concurrent design of toehold switch sensors,and finally simulation of the designed diagnostic circuits to assess performance.Using miRNA expression data in the public domain,we identified miR-21-5p and miR-20a-5p as blood-based miRNA biomarkers specific to early-stage cervical cancer employing a multi-tier algorithmic screening.Synthetic riboregulators called toehold switches specific to the biomarker panel were then designed.To predict the dynamic range of toehold switches for use in genetic circuits as biosensors,we used a generic grammar of these switches,and built a neural network model of dynamic range using thermodynamic features derived from mRNA secondary structure and interaction.Second-generation toehold switches were used to overcome the design challenges associated with miRNA biomarkers.The resultant model yielded an adj.R^(2)~0.71,outperforming earlier models of toehold-switch dynamic range.Reaction kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA biomarkers.Simulations showed a linear response between 10 nM and 100 nM before saturation.Our study demonstrates an end-to-end computational workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic/nucleic-acid signatures.The approach has the potential to replace iterative experimental trial and error,and focus time,money,and efforts.All software including the toehold grammar parser,neural network model and reaction kinetics simulation are available as open-source software(https://github.com/SASTRA-iGEM2019)under GNU GPLv3 licence.展开更多
Biomaterials have evolved from inert materials to responsive entities,playing a crucial role in disease diagnosis,treatment,and modeling.However,their advancement is hindered by limitations in chemical and mechanical ...Biomaterials have evolved from inert materials to responsive entities,playing a crucial role in disease diagnosis,treatment,and modeling.However,their advancement is hindered by limitations in chemical and mechanical approaches.Synthetic biology enabling the genetically reprograming of biological systems offers a new paradigm.It has achieved remarkable progresses in cell reprogramming,engineering designer cells for diverse applications.Synthetic biology also encompasses cell-free systems and rational design of biological molecules.This review focuses on the application of synthetic biology in theranostics,which boost rapid development of advanced biomaterials.We introduce key fundamental concepts of synthetic biology and highlight frontier applications thereof,aiming to explore the intersection of synthetic biology and biomaterials.This integration holds tremendous promise for advancing biomaterial engineering with programable complex functions.展开更多
In synthetic biology,microbial chassis including yeast Saccharomyces cerevisiae are iteratively engineered with increasing complexity and scale.Wet-lab genetic engineering tools are developed and optimised to facilita...In synthetic biology,microbial chassis including yeast Saccharomyces cerevisiae are iteratively engineered with increasing complexity and scale.Wet-lab genetic engineering tools are developed and optimised to facilitate strain construction but are often incompatible with each other due to shared regulatory elements,such as the galactose-inducible(GAL)promoter in S.cerevisiae.Here,we prototyped the cyanamide-induced ^(I−)SceI expression,which triggered double-strand DNA breaks(DSBs)for selectable marker removal.We further combined cyanamide-induced ^(I−)SceI-mediated DSB and maltose-induced MazF-mediated negative selection for plasmid-free in situ promoter substitution,which simplified the molecular cloning procedure for promoter characterisation.We then characterised three tetracycline-inducible promoters showing differential strength,a non-leakyβ-estradiol-inducible promoter,cyanamide-inducible DDI2 promoter,bidirectional MAL32/MAL31 promoters,and five pairs of bidirectional GAL1/GAL10 promoters.Overall,alternative regulatory controls for genome engineering tools can be developed to facilitate genomic engineering for synthetic biology and metabolic engineering applications.展开更多
文摘Cell therapy approaches that employ engineered mam-malian cells for on-demand production of therapeutic agents in the patient's body are moving beyond proof-of-concept in translational medicine.The therapeutic cells can be customized to sense user-defined signals,pro-cess them,and respond in a programmable and pre-dictable way.In this paper,we introduce the available tools and strategies employed to design therapeutic cells.Then,various approaches to control cell behav-iors,including open-loop and closed-loop systems,are discussed.We also highlight therapeutic applications of engineered cells for early diagnosis and treatment of various diseases in the clinic and in experimental dis-ease models.Finally,we consider emerging technolo-gies such as digital devices and their potential for incorporation into future cell-based therapies.
文摘Synthetic biology(SynBio)is an emerging field of study with great potential in designing,engineering,and constructing new microbial synthetic cells that do not pre-exist in nature or re-engineering existing cells to accomplish industrial purposes.Systems biology seeks to understand biology at multiple dimensions,beginning with the molecular and cellular level and progressing to the tissues and organismal level and characterizes cells as complex information-processing systems.SynBio,on the other hand,toggles further and strives to develop and create its systems from scratch.SynBio is now applied in the development of novel therapeutic drugs for the prevention of human diseases,scale up industrial processes,and accomplish previously unfeasible industrial outcomes.This is made possible through significant breakthroughs in DNA sequencing and synthesis technology,as well as insights gained from synthetic chemistry and systems biology.SynBio technologies have allowed for the introduction of improved and synthetic metabolic functionalities in microorganisms to enable the synthesis of a range of pharmacologically-relevant compounds for pharmaceutical exploration.SynBio applications range from finding new ways to making industrial chemical synthesis processes more sustainable as well as the microbial synthesis of improved therapeutic modalities.Hence,this study underpins several innovations,auspicious potentials,and future directions afforded by SynBio that proposes improved industrial microbial synthesis for pharmaceutical exploration.
基金financially supported by the National Natural Science Foundation of China(32070085,32200050,31871784,and 32021005)the Natural Science Foundation of Jiangsu Province(BK20221079)+4 种基金National Postdoctoral Program for Innovative Talents(BX20220136)the Jiangsu Funding Program for Excellent Postdoctoral Talent(2022ZB498)the Fundamental Research Funds for the Central Universities(JUSRP52019A,JUSRP121010 and JUSRP221013)National Key Research and Development Program of China(2020YFA0908300)Postgraduate Research&Practice Innovation Program of Jiangsu Provence(KYCX18_1797)。
文摘Terpenoids are the largest family of natural products.They are made from the building block isoprene pyrophosphate(IPP),and their bioproduction using engineered cell factories has received a great deal of attention.To date,the insufficient metabolic supply of IPP remains a great challenge for the efficient synthesis of terpenoids.In this work,we discover that the imbalanced metabolic flux distribution between the central metabolism and the IPP supply hinders IPP accumulation in Bacillus subtilis(B.subtilis).Therefore,we remodel the IPP metabolism using a series of genetically encoded two-input-multioutput(TIMO)circuits that are responsive to pyruvate or/and malonyl-CoA,resulting in an IPP pool that is significantly increased by up to four-fold.As a proof-of-concept validation,we design an IPP metabolism remodeling strategy to improve the production of three valuable terpenoids,including menaquinone-7(MK-7,4.1-fold),lycopene(9-fold),andβ-carotene(0.9-fold).In particular,the titer of MK-7 in a 50-L bioreactor reached 1549.6 mg·L^(-1),representing the highest titer reported so far.Thus,we propose a TIMO genetic circuits-assisted IPP metabolism remodeling framework that can be generally used for the synergistic fine-tuning of complicated metabolic modules to achieve the efficient bioproduction of terpenoids.
基金National Natural Science Foundation of China,Grant/Award Number:12090054National Key Research and Development Programof China,Grant/Award Numbers:2020YFA0906900,2021YFF1200500。
文摘Although the principles of synthetic biology were initially established in model bacteria,microbial producers,extremophiles and gut microbes have now emerged as valuable prokaryotic chassis for biological engineering.Extending the host range in which designed circuits can function reliably and predictably presents a major challenge for the concept of synthetic biology to materialize.In this work,we systematically characterized the cross-species universality of two transcriptional regulatory modules—the T7 RNA polymerase activator module and the repressors module—in three non-model microbes.We found striking linear relationships in circuit activities among different organisms for both modules.Parametrized model fitting revealed host non-specific parameters defining the universality of both modules.Lastly,a genetic NOT gate and a band-pass filter circuit were constructed from these modules and tested in non-model organisms.Combined models employing host non-specific parameters were successful in quantitatively predicting circuit behaviors,underscoring the potential of universal biological parts and predictive modeling in synthetic bioengineering.
基金supported by the National Basic Research Program of China(973 Program)(Nos.2009CB918503 and 2006CB911002)to TJ.
文摘The aim of synthetic biology is to design artificial biological systems for novel applications.From an engineering perspective,construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field.Here,we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements,synthetic circuits and their assemblies into devices and modules.Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.
基金Fundamental Research Funds for the Central Universities,Grant/Award Number:226-2022-00214National Key R&D Program of China,Grant/Award Number:2023YFF1204500+1 种基金“Pioneer”and“Leading Goose”R&D Program of Zhejiang,Grant/Award Number:2024C03011National Natural Science Foundation of China,Grant/AwardNumbers:32271475,32320103001。
文摘In thepast 2decades,synthetic biologists have applied systematic engineering principles to genetic circuit design to devise biological systems with bespoke behaviors,such as Boolean logic gates,signal filters,oscillators,state machines,perceptrons,and genetic controllers[1,2].Following a bottom-up strategy,the genetic circuits are designed by assembling a set of well-characterized biological components,or genetic parts[3],and optimized through the iterative Design-Build-Test-Learn(DBTL)cycles.
基金supported by the Major Student Project,Manipal Institute of Technology,Manipal Academy of Higher Educa-tion,Manipal.
文摘As synthetic biology advances,the necessity for robust biocontainment strategies for genetically engineered organisms(GEOs)grows increasingly critical to mitigate biosafety risks related to their potential environmental release.This paper aims to evaluate environment signal-dependent biocontainment systems for engineered organisms,focusing specifically on leveraging triggered responses and combinatorial systems.There are different types of triggers-chemical,light,temperature,and pH-this review illustrates how these systems can be designed to respond to environmental signals,ensuring a higher safety profile.It also focuses on combinatorial biocontainment to avoid consequences of unintended GEO release into an external environment.Case studies are discussed to demonstrate the practical applications of these systems in real-world scenarios.
基金supported by National Key Research and Development Program of China(2023YFC3402600)National Natural Science Foundation of China(W2411072 and 82402460)Sanming Project of Medicine in Shenzhen(SZSM202111011).
文摘Cancer therapy remains a critical medical challenge.Immunotherapy is an emerging approach to regulating the immune system to fight cancer and has shown therapeutic potential.Due to their immunogenicity,bacteria have been developed as drug-delivery vehicles in cancer immunotherapy.However,ensuring the safety and efficacy of this approach poses a considerable challenge.This paper comprehensively explains the fundamental processes and synthesis principles involved in immunotherapy utilizing engineered bacteria.Initially,we list common engineered strains and discuss that growth control through genetic mutation promises therapeutic safety.By considering the characteristics of the tumor microenvironment and the interaction of specific molecules,the precision targeting of tumors can be improved.Furthermore,we present a foundational paradigm for genetic circuit construction to achieve controlled gene activation and logical expression,directly determining drug synthesis and release.Finally,we review the immunogenicity,the expression of immunomodulatory factors,the delivery of immune checkpoint inhibitors,and the utilization of bacteria as tumor vaccines to stimulate the immune system and facilitate the efficacy of cancer immunotherapy.
基金supported by National Key Research and Development Program of China(2023YFA0914500)National Natural Science Foundation of China(32400054)+1 种基金Key Technological Project of Jiangxi Province(20244AFH82001)Chinese Postdoctoral Science Foundation(2024M761180).
文摘Human breast milk(HBM)is composed of various components that are crucial for providing essential nutrients and enhancing infant immune system.Recently,the synthesis of HBM components through microbial fermen-tation has garnered significant attention due to its potential to reduce production costs,simplify manufacturing processes,and mitigate environmental pollution.However,this approach results in low yield and is difficult to scale up at the industrial level.Therefore,various synthetic biology tools have been used to enhance the effi-ciency of HBM component synthesis.This review first summarizes several synthetic biology tools that may improve HBM component production.Next,we have summarized HBM component production using microbial cell factories.Finally,we have summarized the challenges and opportunities presented by the construction of cell factories for the synthesis of HBM using synthetic biology tools.This article therefore provides a general guide to the construction of microbial cell factories for HBM components.
基金the National Natural Science Foundation of China(32270813)Young Scientists Fund of the National Natural Science Foundation of China(22305173)Beijing Natural Science Foundation(5244033)for supporting this work.
文摘YpsR,a pivotal regulatory protein in the quorum-sensing(QS)of Yersinia pseudotuberculosis(Y.pstb),is essential for molecular signaling,yet its molecular mechanisms remain poorly understood.Herein,this study systemati-cally investigates the interactions between YpsR and acyl-homoserine lactones(AHLs),shedding light on the selective mechanism of YpsR to various AHL molecules.Using molecular docking and surface plasmon resonance(SPR)analysis,we confirmed YpsR’s binding affinities,with the strongest observed for 3OC6-HSL,which notably inhibited Y.pstb growth.Additionally,we engineered a whole-cell biosensor based on YpsR-AHL interaction,which exhibited sensitivity to the signal molecule 3OC6-HSL produced by Y.pstb.Furthermore,key YpsR resi-dues(S32,Y50,W54,D67)involved in AHL binding were identified and validated.Overall,this research elu-cidates the mechanisms of QS signal recognition in Y.pstb,providing valuable insights that support the development of diagnostic tools for detecting Y.pstb infections.
基金supported by the National Key Research and Development Program of China (2018YFA0900600)the National Natural Science Foundation of China (32070328 and 22077129)+6 种基金the Strategic Priority Research Program"Molecular Mechanism of Plant Growth and Development"of CAS (XDB27020202)the Natural Science Foundation of Shanghai Municipal Science and Technology Committee (21ZR1470900)the Program of Shanghai Academic Research Leader (20XD1404400)supported by the Construction of the Registry and Database of Bioparts for Synthetic Biology of the Chinese Academy of Science (ZSYS-016)the International Partnership Program of Chinese Academy of Science (153D31KYSB20170121)the Derivative Bank of Chinese Biological Resources (KFJ-BRP-009-002)the National Key Laboratory of Plant Molecular Genetics,SIPPE,CAS.Y.S.is supported by the Foundation of Youth Innovation Promotion Association of the Chinese Academy of Sciences.
文摘Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants.Limited by few well-characterized bioparts for plant chassis,the development of plant synthetic biology lags behind that of its microbial counterpart.Here,we constructed a web-based Plant Synthetic BioDatabase(PSBD),which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals.Online bioinformatics tools including local BLAST,chem similarity,phylogenetic analysis,and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta.We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quan-titative regulation in tobacco leaves.More powerful synthetic devices were then assembled to amplify the transcriptional signals,enabling enhanced expression offlavivirus non-structure 1 proteins in plants.The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.
基金This work was financially supported by the National Natural Science Foundation of China(Grant No.21606205,21576232&21506185)the Fundamental Research Funds for the Central Universities,and the Startup Fund from Zhejiang University.
文摘Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade.However,due to complexity of cellular metabolism,the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering.Recently,cell-free protein synthesis system(CFPS)has been emerging as an enabling alternative to address challenges in biomanufacturing.This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits(biosensors)to speed up design-build-test(DBT)cycles of metabolic engineering and synthetic biology.
基金supported by the National Key Research and Development Program of China(No.2018YFA0900600)the Strategic Priority Research Program“Molecular mechanism of Plant Growth and Development”of Chinese Academy of Science(No.XDB27020202)+6 种基金the National Natural Science Foundation of China(Nos.22077129,32070328 and 41876084)the Natural Science Foundation of Shanghai Municipal Science and Technology Committee(No.21ZR1470900)the Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project(No.TSBICIP-KJGG-002-15)the Program of Shanghai Academic Research Leader(No.20XD1404400)financially supported by the Construction of the Registry and Database of Bioparts for Synthetic Biology of the Chinese Academy of Science(No.ZSYS-016)the International Partnership Program of Chinese Academy of Science(No.153D31KYSB20170121)the National Key Laboratory of Plant Molecular Genetics,SIPPE,Chinese Academy of Science.
文摘Backgrounds:As an increasing number of synthetic switches and circuits have been created for plant systems and of synthetic products produced in plant chassis,plant synthetic biology is taking a strong foothold in agriculture and medicine.The ever-exploding data has also promoted the expansion of toolkits in this field.Genetic parts libraries and quantitative characterization approaches have been developed.However,plant synthetic biology is still in its infancy.The considerations for selecting biological parts to design and construct genetic circuits with predictable functions remain desired.Results:In this article,we review the current biotechnological progresses in field of plant synthetic biology.Assembly standardization and quantitative approaches of genetic parts and genetic circuits are discussed.We also highlight the main challenges in the iterative cycles of design-build-test-learn for introducing novel traits into plants.Conclusion:Plant synthetic biology promises to provide important solutions to many issues in agricultural production,human health care,and environmental sustainability.However,tremendous challenges exist in this field.For example,the quantitative characterization of genetic parts is limited;the orthogonality and the transfer functions of circuits are unpredictable;and also,the mathematical modeling-assisted circuits design still needs to improve predictability and reliability.These challenges are expected to be resolved in the near future as interests in this field are intensifying.
文摘Neuromorphic computing has the potential to achieve the requirements of the next-generation artificial intelligence(AI)systems,due to its advantages of adaptive learning and parallel computing.Meanwhile,biocomputing has seen ongoing development with the rise of synthetic biology,becoming the driving force for new generation semiconductor synthetic biology(SemiSynBio)technologies.DNA-based biomolecules could potentially perform the functions of Boolean operators as logic gates and be used to construct artificial neural networks(ANNs),providing the possibility of executing neuromorphic computing at the molecular level.Herein,we briefly outline the principles of neuromorphic computing,describe the advances in DNA computing with a focus on synthetic neuromorphic computing,and summarize the major challenges and prospects for synthetic neuromorphic computing.We believe that constructing such synthetic neuromorphic circuits will be an important step toward realizing neuromorphic computing,which would be of widespread use in biocomputing,DNA storage,information security,and national defense.
文摘Cervical cancer is a global public health subject as it affects women in the reproductive ages,and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50%mortality rate.Relatively scant awareness and limited access to effective diagnosis have led to this enormous disease burden,calling for point-of-care,minimally invasive diagnosis methods.Here,an end-to-end quantitative unified pipeline for diagnosis has been developed,beginning with identification of optimal biomarkers,concurrent design of toehold switch sensors,and finally simulation of the designed diagnostic circuits to assess performance.Using miRNA expression data in the public domain,we identified miR-21-5p and miR-20a-5p as blood-based miRNA biomarkers specific to early-stage cervical cancer employing a multi-tier algorithmic screening.Synthetic riboregulators called toehold switches specific to the biomarker panel were then designed.To predict the dynamic range of toehold switches for use in genetic circuits as biosensors,we used a generic grammar of these switches,and built a neural network model of dynamic range using thermodynamic features derived from mRNA secondary structure and interaction.Second-generation toehold switches were used to overcome the design challenges associated with miRNA biomarkers.The resultant model yielded an adj.R^(2)~0.71,outperforming earlier models of toehold-switch dynamic range.Reaction kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA biomarkers.Simulations showed a linear response between 10 nM and 100 nM before saturation.Our study demonstrates an end-to-end computational workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic/nucleic-acid signatures.The approach has the potential to replace iterative experimental trial and error,and focus time,money,and efforts.All software including the toehold grammar parser,neural network model and reaction kinetics simulation are available as open-source software(https://github.com/SASTRA-iGEM2019)under GNU GPLv3 licence.
基金supported by grants from the National Natural Science Foundation of China(82372403,32322003)Shenzhen Institute of Synthetic Biology Scientific Research Program(DWKF20190010,JCHZ20200005)+3 种基金Fundamental Research Funds for the Central Universities of South China University of Technology(2023ZYGXZR095)National Natural Science Foundation of Guangdong Province(2020A1515111079)Guangzhou Science and technology planning project(202201010695)Zhuhai Industry-University-Research Cooperation Project(2220004002580).
文摘Biomaterials have evolved from inert materials to responsive entities,playing a crucial role in disease diagnosis,treatment,and modeling.However,their advancement is hindered by limitations in chemical and mechanical approaches.Synthetic biology enabling the genetically reprograming of biological systems offers a new paradigm.It has achieved remarkable progresses in cell reprogramming,engineering designer cells for diverse applications.Synthetic biology also encompasses cell-free systems and rational design of biological molecules.This review focuses on the application of synthetic biology in theranostics,which boost rapid development of advanced biomaterials.We introduce key fundamental concepts of synthetic biology and highlight frontier applications thereof,aiming to explore the intersection of synthetic biology and biomaterials.This integration holds tremendous promise for advancing biomaterial engineering with programable complex functions.
基金supported by the Australian Government through the Australian Research Council Centres of Excellence funding scheme(project CE200100029).
文摘In synthetic biology,microbial chassis including yeast Saccharomyces cerevisiae are iteratively engineered with increasing complexity and scale.Wet-lab genetic engineering tools are developed and optimised to facilitate strain construction but are often incompatible with each other due to shared regulatory elements,such as the galactose-inducible(GAL)promoter in S.cerevisiae.Here,we prototyped the cyanamide-induced ^(I−)SceI expression,which triggered double-strand DNA breaks(DSBs)for selectable marker removal.We further combined cyanamide-induced ^(I−)SceI-mediated DSB and maltose-induced MazF-mediated negative selection for plasmid-free in situ promoter substitution,which simplified the molecular cloning procedure for promoter characterisation.We then characterised three tetracycline-inducible promoters showing differential strength,a non-leakyβ-estradiol-inducible promoter,cyanamide-inducible DDI2 promoter,bidirectional MAL32/MAL31 promoters,and five pairs of bidirectional GAL1/GAL10 promoters.Overall,alternative regulatory controls for genome engineering tools can be developed to facilitate genomic engineering for synthetic biology and metabolic engineering applications.
