Review
Biotechnology & Applied Microbiology
Chao Feng, Jing Chen, Wenxin Ye, Kaisen Liao, Zhanshi Wang, Xiaofei Song, Mingqiang Qiao
Summary: Resveratrol, a bioactive natural product, has attracted much attention in the medicine and health care products fields due to its remarkable biological activities. Recent advances in biosynthesis and strain development have provided a safe and efficient route for large-scale resveratrol production. This review summarizes the physiological functions, market applications, and future prospects of resveratrol.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biochemical Research Methods
Dexun Fan, Huayang Tang, Xiaorong Yang, Fengguang Zhao, Shuangyan Han
Summary: This review provides an overview of the strategies for statin production via microbial cell factories, including traditional fermentation culture and modern synthetic biology manufacture. It discusses the complex fermentation parameters and process control technology for submerged fermentation and solid-state fermentation in detail. The potential use of recoverable agricultural wastes/biomass as a fermentation substrate in solid-state fermentation for statin production is emphasized. Additionally, metabolic engineering strategies for constructing robust engineering strains and directed evolution are also discussed. The review highlights the potential and challenges of using microbial cell factories for statin production and aims to promote greener production modes for statins.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Irene Otero-Muras, Pablo Carbonell
Summary: Metabolic engineering involves optimizing processes from single-cell to fermentation to increase production of valuable chemicals. A systems approach has accelerated scaling from rapid prototyping to industrial production, with automated DNA assembly reducing time from conception to production. The success of metabolic engineering often relies on retrobiosynthetic protocols and dynamic regulation strategies assembled as genetic circuits in host strains.
METABOLIC ENGINEERING
(2021)
Review
Biotechnology & Applied Microbiology
Yu-Lei Jia, Shan-Shan Geng, Fei Du, Ying-Shuang Xu, Ling-Ru Wang, Xiao-Man Sun, Qing-Zhuo Wang, Qi Li
Summary: The review highlights the importance of EPA, an essential omega-3 fatty acid, for human health. It discusses the limitations of current fish oil extraction methods for EPA production and the increasing interest in biotechnological approaches using microorganisms. The review also covers recent research on different microorganisms capable of producing EPA and new engineering strategies to enhance EPA biosynthesis.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Jennifer Cable, Joshua N. Leonard, Timothy K. Lu, Zhen Xie, Matthew Wook Chang, Luis Angel Fernandez, Jose M. Lora, Howard L. Kaufman, Francisco J. Quintana, Roger Geiger, Cammie F. Lesser, Jason P. Lynch, David L. Hava, Virginia W. Cornish, Gary K. Lee, Breanna DiAndreth, Michael Fero, Rajkamal Srivastava, Tim De Coster, Kole T. Roybal, Owen J. L. Rackham, Samira Kiani, Iowis Zhu, Rogelio A. Hernandez-Lopez, Tingxi Guo, William C. W. Chen
Summary: Synthetic biology has the potential to transform cell- and gene-based therapies by engineering cells to selectively respond to disease signals, sparing healthy tissue from potential harm.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Sean F. Sullivan, Anuj Shetty, Tharun Bharadwaj, Naveen Krishna, Vikas D. Trivedi, Venkatesh Endalur Gopinarayanan, Todd C. Chappell, Daniel M. Sellers, R. Pravin Kumar, Nikhil U. Nair
Summary: Engineering the utilization of non-native substrates in industrial microbes provides a way to use renewable sources for bioprocesses. Previous research has shown that activating the GAL regulon in Saccharomyces cerevisiae during growth on the non-native substrate xylose enhances gene expression and growth compared to constitutive overexpression of the same pathway. However, this method was not easily adaptable to other non-native substrates. In this study, a variant of Gal3p called Gal3pMC was constructed, which can activate the GAL regulon with diverse substrates and mimic the dynamics of the native system. Testing this regulon approach with non-native lignocellulosic sugars resulted in higher growth rates and final cell densities compared to constitutive overexpression. The co-utilization of multiple non-native substrates suggests that this regulon approach could be universally beneficial for engineering synthetic heterotrophy.
METABOLIC ENGINEERING
(2023)
Review
Biochemistry & Molecular Biology
Dipinte Gupta, Gauri Sharma, Pooja Saraswat, Rajiv Ranjan
Summary: The recent expansion of knowledge in various disciplines has led to the emergence of interdisciplinary fields, including Synthetic Biology (SynBio), which integrates concepts from biology, chemistry, electrical engineering, and computer science to rewire natural biological pathways through genetic circuits. This has resulted in innovative applications in molecular medicines, pharmaceuticals, biofuels, and crop improvement, mainly utilizing prokaryotic systems but showing growth potential in eukaryotic systems.
MOLECULAR BIOTECHNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Dongsoo Yang, Hyunmin Eun, Cindy Pricilia Surya Prabowo
Summary: Polyketides, a type of natural products, have versatile applications such as pharmaceuticals, nutraceuticals, and cosmetics. Aromatic polyketides, including type II and III polyketides, are important chemicals for human health, such as antibiotics and anticancer agents. However, they are mainly produced from challenging sources like soil bacteria or plants. To address this issue, metabolic engineering and synthetic biology have been used to efficiently engineer model microorganisms for enhanced production of aromatic polyketides. This review discusses the recent advancements and future prospects of metabolic engineering and synthetic biology strategies in the production of type II and type III polyketides in model microorganisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Food Science & Technology
Seung-Oh Seo, Yong-Su Jin
Summary: The growing human population poses a significant challenge to food security, and sustainable food manufacturing processes and alternative foods are necessary. Metabolic engineering and synthetic biology offer solutions for food security and alternative food production. Utilizing microbial fermentation for bioproduction of food ingredients provides a promising and ecofriendly approach to replace conventional manufacturing methods.
ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Andrew Currin, Steven Parker, Christopher J. Robinson, Eriko Takano, Nigel S. Scrutton, Rainer Breitling
Summary: The ability to engineer biological systems is crucial in biotechnology and synthetic biology. Generating genetic diversity is essential to explore variations in phenotype, and recent advancements in DNA synthesis technology have enhanced our ability to create variant libraries. This review focuses on approaches to create diversity from enzyme level to entire pathways in vitro, emphasizing the creation of combinatorial libraries for significant improvements in function.
BIOTECHNOLOGY ADVANCES
(2021)
Review
Biotechnology & Applied Microbiology
Yiwen Jing, Yanxia Wang, Dawei Zhou, Jingnan Wang, Jiawen Li, Jingxiang Sun, Yifan Feng, Fengxue Xin, Wenming Zhang
Summary: This review paper introduces the properties and biosynthetic metabolism process of carotenoids, as well as the methods and strategies for microbial synthesis of carotenoids. The potential applications of carotenoids in food, medicine, cosmetic, and other fields are also discussed.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Chemistry, Multidisciplinary
Logan Thrasher Collins, David T. Curiel
Summary: Synthetic biology focuses on designing and assembling biological parts to construct artificial biological systems, leading to advances in diverse fields like neuroscience, cell-based therapies, and chemical manufacturing; gene therapy has made significant progress in proof-of-concept studies and clinical applications, with adenovirus showing increasing interest as a viral vector for gene therapy.
Article
Biotechnology & Applied Microbiology
J. Carl Schultz, Shekhar Mishra, Emily Gaither, Andrea Mejia, Hoang Dinh, Costas Maranas, Huimin Zhao
Summary: This study explored metabolic engineering approaches to improve the production of fatty alcohols in the oleaginous yeast Rhodotorula toruloides. Deletion of LRO1 or deletion of DGA1 combined with overexpression of ACC1 and ACL1 significantly increased the fatty alcohol production. The deletion of LRO1 surprisingly increased both lipid and fatty alcohol production.
MICROBIAL CELL FACTORIES
(2022)
Review
Biotechnology & Applied Microbiology
Dongdong Zhao, Xinna Zhu, Hang Zhou, Naxin Sun, Ting Wang, Changhao Bi, Xueli Zhang
Summary: Effective metabolic pathways are crucial for efficient cell factories, and utilizing CRISPR technology in pathway engineering can enhance efficiency, reduce costs, and simplify target customization. This technology has been proven to be robust and effective in various organisms.
METABOLIC ENGINEERING
(2021)
Review
Biotechnology & Applied Microbiology
Govinda R. Navale, Mahesh S. Dharne, Sandip S. Shinde
Summary: Isoprenoids, also known as terpenoids, are diverse organic compounds found abundantly in nature, with various applications in pharmaceutical, nutraceutical, and chemical industries. Recent advancements in metabolic engineering have enabled the production of isoprenoids in heterologous host systems like Escherichia coli and Saccharomyces cerevisiae. Challenges and strategies for scale-up and engineering of isoprenoids in heterologous host systems have been discussed in detail.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Michael J. Volk, Vinh G. Tran, Shih- Tan, Shekhar Mishra, Zia Fatma, Aashutosh Boob, Hongxiang Li, Pu Xue, Teresa A. Martin, Huimin Zhao
Summary: Metabolic engineering aims to improve the production of economically valuable molecules through genetic manipulation. Advancements in this discipline have led to industrial-level molecule production benefiting various industries. This review provides insights into the steps required for a successful metabolic engineering campaign, highlights major applications, and discusses future challenges.
Article
Biotechnology & Applied Microbiology
Shekhar Mishra, Ziyu Wang, Michael J. Volk, Huimin Zhao
Summary: This article reports the development of a kinetic metabolic model of lipid metabolism in Saccharomyces cerevisiae, which integrates various aspects of lipid biosynthesis and transport. The model was trained on lipidomic data and used to design mutant strains for overproduction of lipids. The model-guided experiments led to the discovery of a futile cycle in the triacylglycerol biosynthesis pathway and provided explanations for successful and unsuccessful mutant designs in metabolic engineering.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Zia Fatma, Shih- Tan, Aashutosh Girish Boob, Huimin Zhao
Summary: The non-conventional yeast Issatchenkia orientalis has robust resistance to acidity and has attracted attention for its ability to produce organic acids from various carbon sources. Researchers have developed a genetic toolbox and a bioinformatics pipeline to facilitate multiplex CRISPR-Cas9-mediated genome editing in I. orientalis. They have also created a landing pad system for efficient integration of multiple genes, which has been successfully demonstrated for the production of 5aminolevulinic acid and succinic acid.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Tianhao Yu, Haiyang Cui, Jianan Canal Li, Yunan Luo, Guangde Jiang, Huimin Zhao
Summary: CLEAN is a machine learning algorithm based on contrastive learning that can accurately predict functional annotations of enzymes, especially for less-studied or uncharacterized proteins with multiple activities. It can confidently annotate understudied enzymes, correct mislabeled enzymes, and identify promiscuous enzymes with multiple EC numbers. This tool is of great significance in predicting the functions of uncharacterized enzymes.
Article
Multidisciplinary Sciences
Hengqian Ren, Shravan R. Dommaraju, Chunshuai Huang, Haiyang Cui, Yuwei Pan, Marko Nesic, Lingyang Zhu, David Sarlah, Douglas A. Mitchell, Huimin Zhao
Summary: The authors used bioinformatics and synthetic biology approaches to discover and characterize a novel class of RiPPs with an unusual amino-modified C-terminus. This study reveals a new post-translational modification class in RiPPs and suggests its potential role in membrane targeting.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Jie Meng, Yue Qiu, Yueping Zhang, Huimin Zhao, Shuobo Shi
Summary: This study presents a CRISPR/Cas9 based multiplexed integration (CMI) system in Saccharomyces cerevisiae, which enables quadruple integration at an individual locus without pre-engineering the host. The use of a fused protein, Cas9-Brex27, attracts Rad51 recombinase to the double-strand breaks induced by the CRISPR/Cas9 system. The efficiency of quadruple integration was significantly improved to 53.9% with 40 bp homology arms and 78% with 100 bp homology arms.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Xiong Xiong, Ipek Tasan, Che Yang, Meng Zhang, Gabriela A. Hernandez Gonzalez, Shuting Liu, Pankaj Chaturvedi, Andrew S. Belmont, Huimin Zhao
Summary: Fluorescence microscopy imaging is crucial for studying genome architecture, and programmable DNA-binding proteins like TAL effectors and CRISPR/dCas9 are commonly used in visualizing specific chromosomal sites. This study compared different live-cell chromosome tagging methods and their effects on subnuclear positioning, gene expression, and DNA replication timing. The results showed that the CRISPR-based imaging method could delay DNA replication and sister chromatid resolution in certain regions. However, the subnuclear localization and gene expression were unaffected by both TetO/TetR and CRISPR-based methods, suggesting that CRISPR-based imaging can be used for applications that do not require DNA replication analysis.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tianhao Yu, Aashutosh Girish Boob, Nilmani Singh, Yufeng Su, Huimin Zhao
Summary: Directed evolution is an effective tool for protein engineering, but it can be time-consuming and costly. The combination of machine learning and laboratory automation allows for more efficient evaluation of variants and data collection for developing ML models. This perspective proposes a closed-loop in vitro continuous protein evolution framework that utilizes both ML and automation and provides an overview of recent developments in the field.
Review
Chemistry, Physical
Tianhao Yu, Aashutosh Girish Boob, Michael J. Volk, Xuan Liu, Haiyang Cui, Huimin Zhao
Summary: Retrobiosynthesis is an effective and sustainable approach for producing functional molecules. Machine learning has recently been integrated into the retrobiosynthesis design toolbox and has shown promising results in various stages of synthesis design workflow. The ability of machine learning to learn from existing knowledge, recognize complex patterns, and generalize to unknowns makes it a potential solution for biological problems. This review summarizes the recent progress in machine learning models for molecular synthesis, highlighting their advantages and discussing the challenges and future prospects.
Article
Multidisciplinary Sciences
Meng Zhang, Mary Elisabeth Ehmann, Srija Matukumalli, Aashutosh Girish Boob, David M. Gilbert, Huimin Zhao
Summary: Chromatin boundary elements are difficult to define and characterize. Here the authors report Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains (SHIELD) for high-throughput screening of barrier-type DNA elements in human cells.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Yujie Yuan, Chengyou Shi, Huimin Zhao
Summary: Natural products (NPs) produced by microorganisms and plants are important sources of drugs, herbicides, and fungicides. Recent advances in DNA sequencing, bioinformatics, and genome mining have generated a vast amount of data on NP biosynthesis, which has been used to develop machine learning (ML) tools for NP discovery and prediction of bioactivities. This review summarizes the latest developments and challenges in the application of ML tools in NP research.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
GuangRong Peh, Gregory A. Gunawan, Terence Tay, Elaine Tiong, Lee Ling Tan, Shimin Jiang, Yi Ling Goh, Suming Ye, Joel Wong, Christopher J. Brown, Huimin Zhao, Ee Lui Ang, Fong Tian Wong, Yee Hwee Lim
Summary: In this study, we expanded the specificity of RadH and found that it effectively halogenates hydroxyquinoline and hydroxybenzothiophene. Assay optimization revealed the importance of balancing cofactor concentrations and utilizing a GDHi cofactor recycling system to improve conversion and efficiency. We also obtained the crystal structure of RadH and conducted docking studies to identify binding and catalytic sites for substrates.
Review
Engineering, Biomedical
Meng Zhang, Zhixin Zhu, Guanhua Xun, Huimin Zhao
Summary: Since the original repurposing of CRISPR/Cas9 system, there have been significant improvements in efficiently manipulating the mammalian genome. However, challenges remain in translating CRISPR-based gene editing technologies into safe and effective therapeutics, including limited target scope and off-target activity. This review focuses on recent advances in addressing these challenges, such as engineering novel CRISPR/Cas systems and developing DSB-free genome editors.
CURRENT OPINION IN BIOMEDICAL ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Maolin Li, Wesley Harrison, Zhengyi Zhang, Yujie Yuan, Huimin Zhao
Summary: Strategies for achieving remote stereocontrol in asymmetric catalysis with azaarenes have been limited by the inherent rigidity of the azaarene ring structure. However, a photoenzymatic process using an ene-reductase system can modulate the enantioselectivity of remote carbon-centred radicals on azaarenes by chiral hydrogen atom transfer. This allows for the production of a wide range of azaarenes with remote gamma-stereocentres, showcasing the potential of biocatalysts for remote site stereoselectivity.
Article
Chemistry, Multidisciplinary
Abdelilah Asserghine, Aravind Baby, Seth T. Putnam, Peisen Qian, Elizabeth Gao, Huimin Zhao, Joaquin Rodriguez-Lopez
Summary: This study investigates the impact of the oxygen reduction reaction (ORR) on the sulfation of LAB anodes, and finds that the presence of oxygen significantly enhances the sulfation reaction and leads to the formation of reactive oxygen species (ROS). The findings have important implications for the cycle life of LABs and the generation of CO and CO2 during related chemical reactions.
