Article
Microbiology
Fabian Stefan Franz Hartmann, Tamara Weiss, Jing Shen, Dora Smahajcsik, Simonas Savickas, Gerd Michael Seibold
Summary: Through the use of a pH-sensitive biosensor and imaging technology, it is possible to visualize the internal pH of Escherichia coli colonies on agar plates, allowing for the rapid screening and selection of mutants with altered internal pH values. The identification of specific genes associated with pH homeostasis and pH stress adaptation further demonstrates the effectiveness of this approach.
Article
Biotechnology & Applied Microbiology
Shuai Jiang, Ruirui Wang, Dehu Wang, Chunguang Zhao, Qian Ma, Heyun Wu, Xixian Xie
Summary: This study combined multilevel rational metabolic engineering with biosensor-assisted mutagenesis screening to exploit the L-arginine production potential of Escherichia coli. Multiple metabolic pathways were reprogrammed to redirect the metabolic flux into L-arginine synthesis, and a toggle switch was designed to dynamically control gene expression. A biosensor-assisted high-throughput screening platform was used to further explore L-arginine production potential. Through this approach, the engineered strain produced the highest values of L-arginine reported so far. The study demonstrated the effectiveness of rational metabolic reprogramming and biosensor-assisted mutagenesis screening in unleashing cellular potential for value-added metabolite production.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Yu-Ping Shen, Yuyang Pan, Fu-Xing Niu, Yu-Ling Liao, Mingtao Huang, Jian-Zhong Liu
Summary: In this study, a biosensor for 4-hydroxyphenylacetic acid (4HPAA) was used to identify preferred mutants for higher 4HPAA production and tolerance. The mutant strain GS-2-4, obtained through atmospheric and room temperature plasma mutagenesis coupled with adaptive laboratory evolution, produced 25.42 g/L 4HPAA. Through whole genome sequencing, chromosomal mutations of GS-2-4 were identified. Important genes, pathways, and regulations involved in 4HPAA biosynthesis were revealed. The combination of acrD-aroG further increased 4HPAA production of GS-2-4 by 37%.
METABOLIC ENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Jian Wang, Chenyi Li, Tian Jiang, Yajun Yan
Summary: In this study, a biosensor-assisted titratable CRISPRi high-throughput (BATCH) screening approach was developed for screening high-production phenotypes in Escherichia coli. The method combines a titratable mismatch CRISPR interference and a biosensor mediated screening. The results demonstrated that this approach can effectively modulate metabolic fluxes and enhance production.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Rui Zhi, Nan Cheng, Guohui Li, Yu Deng
Summary: Adipic acid is an important industrial chemical. The traditional synthesis method causes serious pollution. Bio-based production using metabolic engineering and synthetic biology has advanced, but genetic heterogeneity decreases product titer. In this study, a reverse adipate degradation pathway was expressed, an adipic acid biosensor was designed and optimized, and a high-throughput screening platform was established. The study successfully screened strains with improved adipic acid titer and achieved high yields through fermentation optimization. These strategies provide an efficient method to reduce genetic heterogeneity and improve industrial screening processes.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Deyu Yang, Ziming Yu, Mengxin Zheng, Wei Yang, Zhangcai Liu, Jianhua Zhou, Lu Huang
Summary: Microfluidic platforms are used for drug screening due to their advantages of lower reagent consumption, higher throughput, and automation. However, screening complex antibiotic combinations in a high-throughput and systematic manner is still challenging. To address this issue, an artificial intelligence-accelerated high-throughput combinatorial drug evaluation system (AI-HTCDES) is proposed. This system allows high-throughput production of antibiotic combinations and automated analysis of bacterial growth. It provides useful guidance for clinical use of antibiotic combination therapy and offers a promising tool for combinatorial screenings of other medicines.
Article
Biophysics
Jie Liu, Jian-Zhong Xu, Zhi-Ming Rao, Wei-Guo Zhang
Summary: We have developed an enzymatic colorimetric biosensor that allows direct identification of high-level lysine-producing strains by optimizing the export mechanism of L-lysine and the synthesis pathway of lycopene precursors.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Multidisciplinary Sciences
Jae Sung Cho, Dongsoo Yang, Cindy Pricilia Surya Prabowo, Mohammad Rifqi Ghiffary, Taehee Han, Kyeong Rok Choi, Cheon Woo Moon, Hengrui Zhou, Jae Yong Ryu, Hyun Uk Kim, Sang Yup Lee
Summary: Researchers have developed a synthetic sRNA platform that can be used in a wide range of bacteria, allowing knockdown of target genes and reducing virulence-associated phenotypes in pathogens. It can also be used for metabolic engineering to produce specific chemicals. The platform has been successfully tested in 16 bacterial species.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Xinyu Yu, Shuang Li, Huibao Feng, Xihao Liao, Xin-Hui Xing, Zhonghu Bai, Xiuxia Liu, Chong Zhang
Summary: This study developed a CRISPRi-microfluidics screening platform to identify crucial gene targets for enhancing r-protein secretion in Corynebacterium glutamicum. By screening 46,549 single-guide RNAs, unknown targets related to transmembrane transport, amino-acid metabolism, and redox regulation were discovered. These findings were used to construct a hyperproducer for multiple proteins through combinatorial engineering of redox-response transcription factors. The CRISPRi technology and FlAsH-based screening platform used in this study have broad applications for other microbial species and recombinant proteins.
METABOLIC ENGINEERING
(2023)
Article
Agricultural Engineering
Xue Sun, Zetao Peng, Chang Li, Yanling Zheng, Ya'nan Cheng, Jianfei Zong, Fuping Lu, Yu Li, Qinggang Li
Summary: In this study, E. coli MG1655 was engineered to achieve high production of 2'-FL. The expression of 2'-FL synthesis pathway genes was finely regulated and branch pathway genes were deleted. The resulting strain produced 46.06 g/L of 2'-FL in a 5-L fermenter. Through adaptive laboratory evolution, a mutation in the rpoC gene was obtained, leading to improved cell tolerance and 2'-FL production of up to 61.06 g/L. This work provides a strategy for improving 2'-FL accumulation and has important implications for constructing high-level 2'-FL producers in the future.
BIORESOURCE TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
J. Cameron Twitty, Yun Hong, Bria Garcia, Stephanie Tsang, Jennie Liao, Danielle M. Schultz, Jennifer Hanisak, Susan L. Zultanski, Amelie Dion, Dipannita Kalyani, Mary P. Watson
Summary: A deaminative reductive coupling method was developed for the efficient synthesis of noncanonical amino acids and diversification of peptides. The method allows the transformation of natural and commercially available amino acids to aryl alanines and derivatives with varying chain lengths. It has attractive features such as scalability, tolerance of pharma-relevant aryls and biorthogonal functional groups, and applicability to short and macrocyclic peptide substrates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Engineering, Environmental
Toktam Ghadam Soltani, Mansour Mashreghi, Mohammad Reza Housaindokht, Mohamad Hosein Mahmudy Gharaie
Summary: Current arsenic analysis methods in groundwater samples are expensive and complex, leading to delays in detecting arsenic harm. This study optimized a bioluminescent biosensor to detect and measure arsenic in water, showing promising results in a certain concentration range but with toxic effects at higher levels. The use of a modified Gompertz model successfully predicted biosensor growth and highlighted the importance of this environmentally friendly tool with high sensitivity.
PROCESS SAFETY AND ENVIRONMENTAL PROTECTION
(2021)
Review
Biotechnology & Applied Microbiology
Zi-Xu Liu, Si-Ling Huang, Jin Hou, Xue-Ping Guo, Feng-Shan Wang, Ju-Zheng Sheng
Summary: Valuable polysaccharides are typically produced through fermentation using wild-type or metabolically-engineered microbial strains, with high-throughput screening techniques being used to identify cells with high levels of polysaccharide synthesis. Strategies such as fluorescence labeling, fluorescence quenching, and biosensors are effective for cell sorting in industrial strains and pathway optimization for polysaccharide synthesis. Additionally, high-throughput screening using individual whole cells is critical in the discovery and evolution of enzymes involved in polysaccharide biosynthesis, with these enzymes and their mutants being valuable catalysts for saccharide synthesis.
MICROBIAL CELL FACTORIES
(2021)
Article
Biophysics
Guoyun Sun, Yaokang Wu, Ziyang Huang, Yanfeng Liu, Jianghua Li, Guocheng Du, Xueqin Lv, Long Liu
Summary: This study developed a high-throughput sorting system based on glucosamine measurement for the directed evolution of an enzyme involved in glucosamine production. By designing a novel bacteria-based biosensor, the system enabled high-throughput detection and sorting of glucosamine in droplets. The results demonstrated increased enzyme activity and the potential application of this sorting technology in industrial production.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Matthew A. Davis, Vivian Yaci Yu, Beverly Fu, Miao Wen, Edward J. Koleski, Joshua Silverman, Charles A. Berdan, Daniel K. Nomura, Michelle C. Y. Chang
Summary: Living organisms can synthesize a wide range of chemical compounds for growth and maintenance, and genetic engineering can manipulate these processes. However, altering the fundamental chemical behavior remains challenging. By harnessing the power of evolution, researchers have achieved high yields in the synthesis of three chemicals and identified metabolic control points.
Article
Engineering, Civil
Gang Zheng, Xingyuan Gu, Tianqi Zhang, Jibin Sun, Weihong Zheng, Qi Fan, Jingbo Tong, Yu Diao
Summary: In this study, a novel artificial intelligence method, random forest, was used to predict the vertical displacement of bridge piers above EPBM tunnels, and Naive Bayes theory was introduced for statistical analysis. The in situ observations showed successful control of EPBM variables to ensure safe passage.
EUROPEAN JOURNAL OF ENVIRONMENTAL AND CIVIL ENGINEERING
(2022)
Review
Biotechnology & Applied Microbiology
Yu Wang, Ye Liu, Ping Zheng, Jibin Sun, Meng Wang
Summary: Genome engineering is crucial for understanding microorganisms and their practical applications, with new technologies such as base editing allowing for nucleotide transitions without inducing lethal mutations or dependence on inefficient processes like homologous recombination. This opens up new avenues for engineering industrially and clinically relevant microorganisms.
TRENDS IN BIOTECHNOLOGY
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Zhihui Zhang, Yu Wang, Ping Zheng, Jibin Sun
Summary: Methanol and formaldehyde, toxic C1 compounds generated during lignin bioconversion, can be detoxified and assimilated by methylotrophs to produce useful metabolites and cell biomass. Constructing integrated biosystems shows promise for utilizing toxic C1 byproducts and promoting lignin valorization.
TRENDS IN BIOTECHNOLOGY
(2021)
Article
Biophysics
Xue Sun, Qinggang Li, Yu Wang, Wenjuan Zhou, Yanmei Guo, Jiuzhou Chen, Ping Zheng, Jibin Sun, Yanhe Ma
Summary: In this study, a new strategy for constructing whole-cell biosensors based on aminoacyl-tRNA synthetases (aaRSs) was proposed. By engineering aaRSs, the biosensors showed specificity and potential for developing sensors for various amino acids.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Multidisciplinary Sciences
Yu Wang, Haijiao Cheng, Yang Liu, Ye Liu, Xiao Wen, Kun Zhang, Xiaomeng Ni, Ning Gao, Liwen Fan, Zhihui Zhang, Jiao Liu, Jiuzhou Chen, Lixian Wang, Yanmei Guo, Ping Zheng, Meng Wang, Jibin Sun, Yanhe Ma
Summary: Reprogramming complex cellular metabolism requires simultaneous regulation of multigene expression. This study introduces a new method called BETTER, which utilizes CRISPR-guided base editors to generate a large number of genetic combinations in situ, simultaneously altering the expression of multiple genes. Application of this method in industrially important and model microorganisms demonstrates its potential for large-scale fine-tuning of multigene expression in various microorganisms.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Jingwen Huang, Jiuzhou Chen, Yu Wang, Tuo Shi, Xiaomeng Ni, Wei Pu, Jiao Liu, Yingyu Zhou, Ningyun Cai, Shuangyan Han, Ping Zheng, Jibin Sun
Summary: By developing a hyperosmotic stress inducible gene expression system, successful gene auto-regulation was achieved in C. glutamicum, significantly increasing lysine production.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Liwen Fan, Yu Wang, Jin Qian, Ning Gao, Zhihui Zhang, Xiaomeng Ni, Letian Sun, Qianqian Yuan, Ping Zheng, Jibin Sun
Summary: This study identifies limiting factors of methanol metabolism and provides engineering targets for developing superior synthetic methylotrophs.
MICROBIAL BIOTECHNOLOGY
(2021)
Review
Microbiology
Timothy C. Cairns, Xiaomei Zheng, Ping Zheng, Jibin Sun, Vera Meyer
Summary: Filamentous fungi are successful in various habitats due to their ability to secrete a diverse range of molecules. Understanding fungal secretion mechanisms has led to the development of novel technologies in different sectors, including biosensors for fungal diseases and bioremediation strategies.
Article
Agriculture, Multidisciplinary
Zhihua Nie, Pi Liu, Yu Wang, Xuan Guo, Zijian Tan, Jie Shen, Zijing Tang, Jianping Lin, Jibin Sun, Ping Zheng, Leilei Zhu
Summary: This study focused on protein engineering of the mechanosensitive glutamate exporter MscCG2 to improve glutamate excretion efficiency, using directed evolution and computer-assisted design. The engineered variants showed increased levels of glutamate excretion and enhanced efflux of 4-fluoroglutamate, with structural analysis revealing changes in the size of MscCG2 portals and inner channel. These findings demonstrate the potential of protein engineering in enhancing bioproduction through improved secretion efficiency of exporters.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Jiuzhou Chen, Yu Wang, Ping Zheng, Jibin Sun
Summary: Selecting desired variants from protein libraries is a challenging task in directed evolution. Engineering synthetic auxotrophs, which establish a connection between cell growth and protein properties, enables growth-coupled selection experiments that are high throughput and compatible with continuous evolution. In silico simulation-guided metabolic reprogramming can assist in the design of customized synthetic auxotrophs.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Jiao Liu, Moshi Liu, Tuo Shi, Guannan Sun, Ning Gao, Xiaojia Zhao, Xuan Guo, Xiaomeng Ni, Qianqian Yuan, Jinhui Feng, Zhemin Liu, Yanmei Guo, Jiuzhou Chen, Yu Wang, Ping Zheng, Jibin Sun
Summary: In this study, the authors use CRISPR technology and CRISPRi screening to convert a wild-type Corynebacterium glutamicum to a hyperproducer of L-proline, an amino acid with various applications. By optimizing the biosynthetic enzyme and regulating the carbon flux, they achieved efficient production of L-proline.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Timothy C. Cairns, Xiaomei Zheng, Claudia Feurstein, Ping Zheng, Jibin Sun, Vera Meyer
Summary: Submerged fermentation using filamentous fungal cell factories is important for producing useful molecules, and macromorphologies formed during fermentation have a critical impact on product titres and bioreactor performance. To address this, a library of conditional expression mutants in Aspergillus niger was developed, providing strains with distinct and tunable macromorphologies. The study also revealed the connection between pellet formation, strain fitness, and filamentous growth, and demonstrated how conditional expression of the kinase gene pkh2 can decouple various parameters. Further analysis of this gene and related pathways may enable more precise engineering of A. niger macromorphology.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tongtong Zhang, Jiuzhou Chen, Ping Zheng, Weimin Gong, Jibin Sun, Haiping Liu
Summary: Rp-HemA from Rhodopseudomonas palustris was found to have high activity as an ALAS enzyme. The crystal structure of Rp-HemA revealed open, half close, and close conformations. The newly observed half close conformation may also be conserved in the ALAS family. The pre-existing close and half close conformations in Rp-HemA may play a crucial role in its high activity.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Xiaomei Zheng, Timothy C. Cairns, Xiaomei Ni, Lihui Zhang, Huanhuan Zhai, Vera Meyer, Ping Zheng, Jibin Sun
Summary: This study investigates the role of the pkaC gene in regulating hyphal growth and citric acid production in Aspergillus niger during fermentation. The overexpression of pkaC improves hyphal growth and increases citric acid titres. Metabolomic and transcriptomic analysis provides insights into the molecular mechanisms underlying hyperproductivity and pellet growth.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Timothy C. Cairns, Tom de Kanter, Xiaomei Z. Zheng, Ping Zheng, Jibin Sun, Vera Meyer
Summary: In this study, the researchers predicted six morphology and productivity associated 'morphogenes' that impact total secreted protein in A. niger using gene coexpression network data. They found that radial growth rate and heat stress tolerance were positively correlated with protein titres, while submerged pellet diameter and cell wall integrity were negatively associated with productivity. This study identified potential genetic targets for maximizing protein titres and provided chassis strains with controllable macromorphologies for pilot fermentation studies.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2023)