Article
Multidisciplinary Sciences
Lukas Moeller, Eric J. Aird, Markus S. Schroeder, Lena Kobel, Lucas Kissling, Lilly van de Venn, Jacob E. Corn
Summary: This study presents a HDR improvement strategy called Recursive Editing, which selectively retargets undesired indel outcomes to create more opportunities for HDR. The authors introduce a software tool called REtarget for the design of Recursive Editing experiments. By using REtarget-designed guide RNAs, Recursive Editing can simultaneously enhance HDR efficiency and reduce undesired indels. This approach proves to be easy to use and has little experimental burden.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Victoria Cochran Xie, Matthew J. Styles, Bryan C. Dickinson
Summary: Noncovalent interactions play a crucial role in cellular processes, and by taking inspiration from natural systems, we can design directed evolution platforms to generate proteins that bind to specific biomolecules. Recent advancements have expanded the range of interactions that can be evolved.
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Daisylyn Senna Tan, Yanpu Chen, Ya Gao, Anastasia Bednarz, Yuanjie Wei, Vikas Malik, Derek Hoi-Hang Ho, Mingxi Weng, Sik Yin Ho, Yogesh Srivastava, Sergiy Velychko, Xiaoxiao Yang, Ligang Fan, Johnny Kim, Johannes Graumann, Gary D. Stormo, Thomas Braun, Jian Yan, Hans R. Schoeler, Ralf Jauch
Summary: Transcription factor-driven cell fate engineering requires efficiency, speed, and maturity for clinical translation. Directed evolution led to the discovery of an artificially evolved POU factor (ePOU) that surpasses Oct4 in reprogramming efficacy. ePOU can induce pluripotency with or without Sox2, has altered DNA binding preferences, and accelerates pluripotency network establishment.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Xinbo Huang, Mingxia Wang, Xia Wu, Yanfen Zou, Jinming Xu, Congcong Cao, Qian Ma, Bo Yu, Yuchen Liu, Yaoting Gui
Summary: In this study, a group of single-stranded DNA aptamers with high affinity and high specificity for the Cas9 protein were obtained. The aptamers were found to effectively regulate dCas9-modulated gene transcription and improve the efficiency of gene homologous recombination repair mediated by CRISPR-Cas9. These findings suggest a potential method to better control precise gene editing and enrich the diversity of modulating tools for the CRISPR-Cas9 system.
Article
Biotechnology & Applied Microbiology
Zohreh N. Pourhassan, Haiyang Cui, Neele Muckhoff, Mehdi D. Davari, Sander H. J. Smits, Ulrich Schwaneberg, Lutz Schmitt
Summary: Protein secretion is advantageous for recombinant protein production. Type 1 secretion systems (T1SS) have a simple architecture and are attractive for biotechnological applications. The hemolysin A type 1 secretion system (HlyA T1SS) from Escherichia coli has been used for secretion of heterologous proteins, but its commercial utility is limited by low secretion titers. To improve this, we engineered the inner membrane complex of the system using KnowVolution strategy, resulting in a novel HlyB variant with improved secretion for two hydrolases.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Zhi-Bo Yan, Jing-Long Liang, Fu-Xing Niu, Yu-Ping Shen, Jian-Zhong Liu
Summary: Directed evolution and host strain engineering were used to improve the production of pterostilbene in Escherichia coli, resulting in higher enzyme activity, increased precursor availability, and a significantly higher pterostilbene titer. This study demonstrates the successful enhancement of pterostilbene production through genetic manipulation.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Isabelle R. Taylor, Laura A. Murray-Nerger, Todd M. Greco, Dawei Liu, Ileana M. Cristea, Bonnie L. Bassler
Summary: This study reveals specific protein interactions involving PqsE and the role of RhlR in these interactions. These findings contribute to the understanding of the pathogenic mechanisms and quorum sensing process in Pseudomonas aeruginosa.
Article
Biochemistry & Molecular Biology
Yi-Li Feng, Si-Cheng Liu, Ruo-Dan Chen, Xiu-Na Sun, Jing-Jing Xiao, Ji-Feng Xiang, An-Yong Xie
Summary: In CRISPR/Cas9 genome editing, dCas9 can be loaded onto a DSB-adjacent site to stimulate HDR and suppress c-NHEJ, providing a control over genome editing. This method can increase HDR-mediated CRISPR genome editing without exacerbating off-target effects.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Ha-Young Choi, Hyun Seung Lim, Kwang-Hyun Park, Junheon Kim, Won-Gon Kim
Summary: In this study, the catalytic activity of the BLC enzyme on avermectin was enhanced through directed evolution. Mutants R57H, V227A, and D252V showed specific glycosylation activity for avermectin with increased efficiency, and the triple mutant R57H/V227A/D252V demonstrated the highest activity. The best mutant had improved catalytic efficiencies toward avermectin and UDP-glucose and lower free energy than the wild-type BLC, correlating with improved activity.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Dusko Lainscek, Vida Forstneric, Veronika Mikolic, Spela Malensek, Peter Pecan, Mojca Bencina, Matjaz Sever, Helena Podgornik, Roman Jerala
Summary: The CRISPR/Cas system, when coupled with Exonuclease III, can enhance gene editing efficiency and lead to significant gene knock-out effects, especially in cell lines, primary cells, and in vivo. This approach has great potential for treating diseases with a genetic etiology.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Guoling Li, Haoqiang Wang, Xianwei Zhang, Zhenfang Wu, Huaqiang Yang
Summary: This study presents a strategy to enhance HDR efficiency in animal cells by spatial and temporal colocalization of the donor and Cas9 through coupling the CRISPR system with the transcription factor THAP11. By appending THAP11-specific DNA binding motifs to the double-stranded donor DNA, the HDR efficiency can be significantly improved. The THAP11-fused CRISPR system achieved a more than twofold increase in HDR-mediated knock-in efficiency, and up to 6-fold increase can be achieved through combinational use with the small-molecule HDR enhancer valnemulin.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Klara Markova, Antonin Kunka, Klaudia Chmelova, Martin Havlasek, Petra Babkova, Sergio M. Marques, Michal Vasina, Joan Planas-Iglesias, Radka Chaloupkova, David Bednar, Zbynek Prokop, Jiri Damborsky, Martin Marek
Summary: Enzyme functionality depends on its unique three-dimensional structure, with computational algorithms being used to stabilize proteins for research and biotech applications. In a unique case, introducing eleven stabilizing mutations affected the protein folding energy landscape and resulted in advantageous catalytic domain-swapped dimers.
Article
Chemistry, Physical
Yuanmiao Sun, Gao Chen, Shibo Xi, Zhichuan J. Xu
Summary: Efficient catalyst development is crucial for advancing electrocatalysis techniques. Intrinsic features and properties from transition metal oxides (TMOs) have an impact on reaction activity and mechanism, offering opportunities for further advances in catalytic design. Understanding and utilizing these inherent features in TMOs can lead to better strategies for designing TMO-based electrocatalysts.
Article
Chemistry, Physical
Hee Jun Kim, Sang Heon Kim, Sun-Woo Kim, Jin-Kyeom Kim, Chentian Cao, Yongchul Kim, Ungsoo Kim, Geunsik Lee, Jae-Young Choi, Hyung-Suk Oh, Hyun-Cheol Song, Won Jun Choi, Hyesung Park, Jeong Min Baik
Summary: This study presents a simple and cost-effective method to achieve the crystallization of LaFeO3 perovskite at low temperatures (300-500 degrees C), resulting in an excellent oxygen evolution reaction (OER) catalyst with inherent catalytic surface. The synthesis involved the formation of a cyanogel-peroxo-complex as a metastable molecular precursor, which was obtained via ligand exchange using potassium cyanide solution. The electrocatalysts based on LaFeO3 nanoparticles exhibited remarkable OER performance, surpassing the commercialized IrOx/C catalysts in terms of overpotential and Tafel slope under alkaline conditions. The catalyst's high stability was confirmed by the insignificant potential change during a 50-hour long-term stability test.
Article
Cell Biology
Luxing Ge, Jian Kang, Xiangchen Dong, Deji Luan, Guanghua Su, Guangpeng Li, Yong Zhang, Fusheng Quan
Summary: This study successfully utilized CRISPR/Cas9 technology to achieve gene mutation and insertion in the bovine genome, confirming the effectiveness of this gene editing strategy. Mutant myoblasts exhibited higher proliferation, myogenic differentiation, and adipogenic transdifferentiation abilities, providing breeding material and technical strategy for high-quality bovine breeding.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shaoxiong Tian, Ge Yu, Huan He, Yu Zhao, Peilu Liu, Alan G. Marshall, Borries Demeler, Scott M. Stagg, Hong Li
Review
Biochemistry & Molecular Biology
Ge Yu, Yu Zhao, Hong Li
Article
Biochemical Research Methods
Travis H. Hand, Anuska Das, Mitchell O. Roth, Chardasia L. Smith, Uriel L. Jean-Baptiste, Hong Li
ACS SYNTHETIC BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Ge Yu, Yu Zhao, Shaoxiong Tian, Jay Rai, Huan He, John Spear, Duncan Sousa, Jinbo Fan, Hong-Guo Yu, Scott M. Stagg, Hong Li
SCIENTIFIC REPORTS
(2019)
Article
Multidisciplinary Sciences
Anuska Das, Travis H. Hand, Chardasia L. Smith, Ethan Wickline, Michael Zawrotny, Hong Li
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Sagar Sridhara, Hemant N. Goswami, Charlisa Whyms, Jonathan H. Dennis, Hong Li
Summary: CRISPR-Cas-based virus detection assays, particularly those utilizing Type III-A CRISPR-Cas system, offer rapid and sensitive detection of viruses like SARS-CoV-2, making them potentially valuable tools for disease diagnosis.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Anuska Das, Hemant N. Goswami, Charlisa T. Whyms, Sagar Sridhara, Hong Li
Summary: CRISPR-based technology has revolutionized biomedicine through its applications in genome editing, therapeutics, and diagnostics. Recent studies have shown that CRISPR enzymes can also be used for nucleic acid detection by collateral and non-specific cleavage of viral DNA or RNA. The diverse compositions, self-foreign nucleic acid recognition mechanisms, usage of second messengers, and enzymology of CRISPR enzymes provide a wide range of diagnostic tools for further innovations. Structural biology plays a crucial role in understanding the activation mechanisms of these CRISPR enzymes.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Mitchell O. Roth, Hong Li
Summary: In this paper, the authors present a successful structure-guided approach to improve the genome-editing efficiency of CRISPR-CasX in Deltaproteobacteria and Planctomycetes.
Article
Biochemistry & Molecular Biology
Yu Zhao, Jay Rai, Hongguo Yu, Hong Li
Summary: This study characterized the structures and conformations of modified and pseudouridine-free ribosomes using electron cryomicroscopy. It found that pseudouridine stabilizes key functional motifs by establishing water-mediated close contacts with the phosphate backbone, while the absence of pseudouridine leads to abnormal inter-subunit movements.
Article
Biology
Yu Zhao, Jay Rai, Chong Xu, Huan He, Hong Li
Summary: AlphaFold-assisted CryoEM structure determination reveals the structure of the Bfr2-Lcp5 complex in the yeast 90S pre-ribosome. The complex interacts similarly to exosome factors Rrp6-Rrp47 and plays a role in regulating 90S transitions.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Sagar Sridhara, Jay Rai, Charlisa Whyms, Hemant Goswami, Huan He, Walter Woodside, Michael P. Terns, Hong Li
Summary: This study investigates the structure and activity of the Lactococcus lactis Csm complex in different functional states using cryoEM, functional assays, and comparative cross-linking. The results suggest that RNA binding influences the conformation and protein dynamics of the Csm complex.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Hemant N. Goswami, Jay Rai, Anuska Das, Hong Li
Summary: Cas7-11 is a Type III-E CRISPR Cas effector that can perform programmable RNA cleavage and has potential applications in RNA interference. The structure of Cas7-11 reveals its molecular basis for RNA processing and interference activities. This knowledge can be used to engineer a compact and programmable RNA interference tool.
Article
Chemistry, Physical
Anuska Das, Jay Rai, Mitchell O. Roth, Yuerong Shu, Megan L. Medina, Mackenzie R. Barakat, Hong Li
Summary: This study reports the conformational changes of Acidothermus cellulolyticus Cas9 along the reaction path, revealing the synchronized cutting mechanism of its two active sites. Altering the metal-coordination residues can change the metal specificity of Cas9.
Article
Biochemistry & Molecular Biology
Jana Sefcikova, Mitchell Roth, Ge Yu, Hong Li
