Article
Chemistry, Multidisciplinary
Alessandro Alcinesio, Idil Cazimoglu, Gabriella Raye Kimmerly, Vanessa Restrepo Schild, Ravinash Krishna Kumar, Hagan Bayley
Summary: The authors applied modular design to construct modular synthetic tissues, assembling different functional 3D-printed building blocks for storing and releasing reagents, performing logic operations, responding to magnetic fields, and encapsulating living cells. They successfully built synthetic tissues capable of transmitting electrical signals and assembled hybrid tissues composed of both synthetic modules and modules containing living cells. By incorporating mutant protein nanopores within the building blocks, they created modular synthetic tissues with electrical outputs modulated by chemical inputs.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Review
Biochemistry & Molecular Biology
Haibo Wang, Yu He, Meiling Jian, Xingang Fu, Yuheng Cheng, Yujia He, Jun Fang, Lin Li, Dan Zhang
Summary: Natural products, with their diverse structures, play significant roles in clinical cancer therapy as nearly 65% of anticancer drugs are either natural products or derivatives. The development of biosynthetic technologies has led to the discovery of an increasing number of natural products used as candidates for clinical cancer therapy.
Article
Cell Biology
Jingru Zhou, Qiangqiang Ge, Dandan Wang, Qiong Guo, Yuyong Tao
Summary: This study developed a synthetic receptor system with dual control through the incorporation of two transmembrane helices, combined with a sensor-actuator device with minimal background signals and a positive loop circuit. The system can sensitively respond to extracellular protein signals and be readily adapted to different inputs and release customized outputs. It is promising for fundamental research and translational applications in cell engineering.
Article
Biochemical Research Methods
Laszlo Mozsik, Carsten Pohl, Vera Meyer, Roel A. L. Bovenberg, Yvonne Nygard, Arnold J. M. Driessen
Summary: This paper presents a collection of 96 genetic parts that can be used in synthetic biology research in fungi, allowing for the assembly of complex multipartite components. It provides a standardized and modular approach for the rapid assembly of synthetic transcription units.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Yongil Yang, Jun Hyung Lee, Magen R. Poindexter, Yuanhua Shao, Wusheng Liu, Scott C. Lenaghan, Amir H. Ahkami, Eduardo Blumwald, Charles Neal Stewart
Summary: Researchers identified five synthetic promoters in hybrid poplar that showed better inducibility under abiotic stress conditions compared to native promoters, demonstrating the potential of synthetic biology in producing transgenic plants with improved stress resistance traits.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Mirco Plante
Summary: Synthetic biology is an emerging research field that aims to understand, modify, and create new biological entities by adopting a modular and systemic approach. This discipline has generated diverse approaches, bringing together practices and conceptualizations from various disciplines, which can lead to confusion within the field. This manuscript provides an epistemological analysis of synthetic biology to better define its objects of study and specific objectives.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Jacob Beal, Brian Teague, John T. Sexton, Sebastian Castillo-Hair, Nicholas A. DeLateur, Meher Samineni, Jeffrey J. Tabor, Ron Weiss
Summary: Reliable and predictable engineering of cellular behavior is a key goal of synthetic biology. This study provides a quantitative mathematical bound on the relationship between predictability of results, model accuracy, measurement precision, and device characteristics. The findings can guide the measurement precision requirements for engineering genetic regulatory networks and recommend best practices for quality control of flow cytometry data.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jaco Botha, Haley R. Pugsley, Aase Handberg
Summary: This study compared the performance of traditional flow cytometry with high-resolution imaging flow cytometry, finding the latter to have higher sensitivity and repeatability in detecting and quantifying extracellular vesicles. By selecting the appropriate flow cytometry platform, researchers can better conduct EV studies, improving the reliability and reproducibility of research results.
Article
Biochemical Research Methods
Alexander C. Pfotenhauer, Alessandro Occhialini, Mary-Anne Nguyen, Helen Scott, Lezlee T. Dice, Stacee A. Harbison, Li Li, D. Nikki Reuter, Tayler M. Schimel, C. Neal Stewart, Jacob Beal, Scott C. Lenaghan
Summary: While installation of complex genetic circuits in microorganisms is routine, synthetic biology toolbox faces limitations in plants due to lack of combinatorial analysis, long design-build-test cycles, and naming standardization. This study designed, built, and tested 91 transgene cassettes using plant regulatory elements, showing different expression strengths in plant tissues with high correlation between canopies, individual leaves, and protoplasts. The efforts led to characterization of a 37-member plant regulatory element library, providing data for standardized construct design in plant metabolic engineering.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Rong Gong, Le Yu, Yini Qin, Neil P. J. Price, Xinyi He, Zixin Deng, Wenqing Chen
Summary: Antibiotic resistance is a growing threat to global health, prompting the need to accelerate the development of new drugs derived from natural products. Nucleoside antibiotics play significant roles in healthcare and plant protection, and understanding their biosynthesis can enhance production and structural diversification. Recent advancements in synthetic biology strategies are improving the production of nucleoside antibiotics and accessing their chemical diversities.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Surgery
Qiang Fu, Kang Mi Lee, Guoli Huai, Kevin Deng, Divyansh Agarwal, Charles G. Rickert, Noel Feeney, Rudy Matheson, Hongji Yang, Christian LeGuern, Shaoping Deng, James F. Markmann
Summary: Regulatory B cells (Bregs) have been found to have potential as anti-rejection therapy in organ transplantation, particularly Bregs-TLR cells stimulated by TLR ligands that can prevent allograft rejection. These Bregs-TLR cells can suppress B cell proliferation, leading to a decline in antibody responses to antigenically disparate skin grafts. Additionally, the specificity of Breg BCR plays a crucial role in regulation.
AMERICAN JOURNAL OF TRANSPLANTATION
(2021)
Article
Biochemical Research Methods
Franz Opel, Nina A. Siebert, Sabine Klatt, Adrian Tuellinghoff, Janis G. Hantke, Joerg Toepel, Bruno Buehler, Dennis J. Nuernberg, Stephan Klaehn
Summary: Cyanobacteria have attracted great interest in biotechnology for their potential in sustainable, photosynthesis-driven production of fuels and value-added chemicals. However, compared to heterotrophic microorganisms, cyanobacterial model strains still lag behind in terms of molecular tools for engineering their metabolism. Researchers have developed a new tool called the pSOMA shuttle vector series for comprehensive genetic engineering of cyanobacteria and demonstrated its potential in gene expression and transfer.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Younghoon Kim, Sandip Sengupta, Taebo Sim
Summary: The review discusses the anti-tumor activities and synthetic routes of natural and synthetic lactones, highlighting their potential as anticancer agents and aiming to advance the process of oncology drug discovery based on natural products.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biotechnology & Applied Microbiology
Chun-Qiang Li, Hong-Mei Lei, Qian-Yi Hu, Guo-Hong Li, Pei-Ji Zhao
Summary: The review outlines recent advances in synthetic biology of natural drugs, focusing on optimization and reconstruction of biosynthetic pathways for mass production of certain drugs. The study provides new strategies for large-scale preparation of rare natural plant metabolites and highly bioactive microbial compounds. Additionally, it discusses the potential advantages and disadvantages of using synthetic biology and various expression systems for heterologous expression of natural drugs.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Nadia Taou, Michael Lones
Summary: This study introduces a method using synthetic regulatory networks to control and respond to the dynamics of a cell's native regulatory network, with the structure and parameters of the synthetic network optimized using Boolean networks and an evolutionary algorithm. Results show that controllers are effective in driving the target system to specified steady states, with scalability demonstrated for larger controlled networks through experiments with random Boolean networks.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Yihao Zhang, Yu Wang, Luze Xu, Chunbo Lou, Qi Ouyang, Long Qian
Summary: A novel in vitro DNA detection system, named Paired dCas9 (PC) reporter, has been developed for specific DNA detection. The system utilizes a pair of dCas9 proteins linked to split halves of luciferase, enabling rapid prototyping of pathogen DNA detection kits.
Article
Chemistry, Medicinal
Yaojun Tong, Jingyu Zhang, Luoqiang Wang, Qinqin Wang, Huang Huang, Xiangyin Chen, Qing Zhang, Hantian Li, Nuo Sun, Guang Liu, Buchang Zhang, Fuhang Song, Gil Alterovitz, Huanqin Dai, Lixin Zhang
Summary: The study found that peptide-like compounds can generate a hyper-synergistic antifungal effect with rapamycin in both azole-resistant and sensitive clinical C. albicans isolates, targeting the protein Tor1 and affecting the TOR signaling pathway. This provides a novel strategy for controlling drug resistant C. albicans infection in immunocompromised populations by coadministering nontoxic peptide additives with rapamycin, repurposing rapamycin as an antifungal agent with wide applications.
ACS INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Zhi Sun, Weijia Wei, Mingyue Zhang, Wenjia Shi, Yeqing Zong, Yihua Chen, Xiaojing Yang, Bo Yu, Chao Tang, Chunbo Lou
Summary: Researchers successfully achieved stable performance of genetic circuits in the face of environmental perturbations by designing and synthesizing a new robust adaptation circuit. By systematically changing genetic parameters and environmental conditions, they found that the desired function was achieved under various circumstances. This study demonstrates the guiding significance of the top-down design strategy for engineering robust genetic circuits.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biology
Pei Du, Chunbo Lou, Xuejin Zhao, Qihui Wang, Xiangyu Ji, Weijia Wei
Summary: CRISPR-based enzymes offer unique capabilities for designing genetic switches that can operate on multiple levels of gene expression. These genetic switches can be assembled into more complex circuits to achieve functions like inducible switches, non-linear response, and logical biocomputation. As more CRISPR enzymes are discovered, their use in genetic switches will continue to expand into a wider range of applications.
Article
Biology
Xuejin Zhao, Yeqing Zong, Weijia Wei, Chunbo Lou
Summary: This study presents a method for recombining the thaxtomin A gene cluster and improving its yield by obtaining high-yielding Streptomyces hosts. Additionally, an efficient gene editing method based on CRISPR/Cas9 digestion and yeast homologous recombination was developed. Results showed that by replacing promoters and optimizing gene cluster structure, the yield of thaxtomin A was significantly improved.
Review
Biotechnology & Applied Microbiology
Mostafa Basiony, Liming Ouyang, Danni Wang, Jiaming Yu, Liming Zhou, Mohan Zhu, Xuyuan Wang, Jie Feng, Jing Dai, Yijie Shen, Chengguo Zhang, Qiang Hua, Xiuliang Yang, Lixin Zhang
Summary: The demand for natural astaxanthin in the global market is increasing rapidly, and producing it through native producers is facing challenges of limited yield and high cost. Using nonnative microbial cell factories is a promising strategy to overcome these limitations.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Zhenghong Li, Chengyu Zhang, Zhengduo Wang, Hao Yan, Chuan Li, Zhiheng Yang, Zilong Li, Lixin Zhang, Weishan Wang
Summary: With the development of synthetic biology, mathematical information can provide accurate understanding of cell metabolism and growth, and guide precision metabolic engineering. Enzyme kinetic parameters are important for describing enzyme activity and quantitatively understanding biological systems.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Ying Guan, Xinmao Chen, Bin Shao, Xiangyu Ji, Yanhui Xiang, Guoqiang Jiang, Lina Xu, Zhanglin Lin, Qi Ouyang, Chunbo Lou
Summary: This study focuses on mitigating unintended interferences between circuits and host cells and proposes a design scheme to control concentration through feedback modules. By adjusting promoter architectures and cooperativity, several switches were successfully synthesized, improving the product titers and host growth. Furthermore, the functions of a dysregulated multilayer NOR gate were restored through the integration of autorepression modules.
ACS SYNTHETIC BIOLOGY
(2022)
Editorial Material
Biology
Yusuke Kato, Chunbo Lou
Article
Biology
Peng-Lin Wei, Jie Fan, Jingwen Yu, Zihui Ma, Xian Guo, Nancy P. Keller, Erwei Li, Chunbo Lou, Wen-Bing Yin
Summary: This study established a quantitative method for assessing filamentous fungal promoters and obtained a library of 93 native promoter elements from Aspergillus nidulans. The strongest promoters, P-zipA and P-sltA, were identified and successfully used to activate the Afpes1 gene, resulting in the production of new cyclic tetrapeptide derivatives.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Xuejin Zhao, Weijia Wei, Yeqing Zong, Chaoxian Bai, Xian Guo, Hua Zhu, Chunbo Lou
Summary: In this study, an orthogonal transcription system was developed to increase the production of thaxtomin A. By using this system, the yield of thaxtomin A was significantly improved in two different Streptomyces strains.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Xinmao Chen, Ziming Liu, Chunbo Lou, Ying Guan, Qi Ouyang, Yanhui Xiang
Summary: In this study, a cooperative transcription factor was developed by fusing oligomerization domain in mammalian cells, which is critical for the applications of synthetic biology in mammalian cells.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2023)
Letter
Chemistry, Multidisciplinary
Lixin Zhang, Xueting Liu, Xinye Wang, Guoliang Zhu, Heng Song, Ronghai Cheng, Nathchar Naowarojna, Catherine E. E. Costello, Pinghua Liu
Summary: In their recent publication, Cen, Wang, Zhou et al. reported the crystal structure of a ternary complex of the non-heme iron endoperoxidase FtmOx1 and concluded that it supports the CarC-like mechanistic model for catalysis. However, they failed to accurately describe the CarC-like and COX-like models and address their differences, and their data is consistent with the COX-like model after careful analysis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Ronghai Cheng, Andrew C. Weitz, Jared Paris, Yijie Tang, Jingyu Zhang, Heng Song, Nathchar Naowarojna, Kelin Li, Lu Qiao, Juan Lopez, Mark W. Grinstaff, Lixin Zhang, Yisong Guo, Sean Elliott, Pinghua Liu
Summary: This work reports the dual activities of a non-heme iron enzyme OvoA(Mtht) in Methyloversatilis thermotolerans, acting as a thiol oxygenase and a sulfoxide synthase. The control of the enzyme's dual activities by the substrates and the active site iron's secondary coordination shell residues is demonstrated. This finding provides an excellent system for future mechanistic investigation on the modulation of iron-centers' electronic properties for different reactivities.
Article
Ecology
Qian Du, Biao Ren, Jinzhi He, Xian Peng, Qiang Guo, Liwei Zheng, Jiyao Li, Huanqin Dai, Vivian Chen, Lixin Zhang, Xuedong Zhou, Xin Xu
Summary: This study revealed a significant increase in colonization of Candida albicans in root carious lesions, which altered the microbial ecology of oral biofilm, leading to enhanced tooth demineralization and carious lesion severity. The cariogenicity-promoting activity of C. albicans was shown to be dependent on the PHR2 gene.