Review
Microbiology
Xuemei Gong, Haolin Zhang, Yue Shen, Xian Fu
Summary: The cotranslational incorporation of pyrrolysine (Pyl), the 22nd proteinogenic amino acid, into proteins in response to the UAG stop codon represents an outstanding example of natural genetic code expansion. The PylRS/tRNA(Pyl)-derived pairs are ideal for genetic code expansion to insert noncanonical amino acids (ncAAs) into proteins of interest. Recent efforts have been made to create efficient and orthogonal PylRS/tRNA(Pyl)-derived pairs for incorporation of diverse ncAAs.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yi-Hui Wang, Mu-Lung Jian, Pei-Jung Chen, Jo-Chu Tsou, Le P. Truong, Yane-Shih Wang
Summary: This study explores the application of expanding genetic codes in developing protein cage-based delivery systems, utilizing evolved Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) and tRNA(Pyl) to recognize para-substituted phenylalanine analogs. The engineered variants successfully incorporate p-azido-l-phenylalanine (AzF) into human heavy chain ferritin (Ftn), demonstrating the potential for site-specific drug loading in protein nanocages.
FRONTIERS IN CHEMISTRY
(2021)
Article
Biochemical Research Methods
Qunfeng Zhang, Wenlong Zheng, Zhongdi Song, Qiang Zhang, Lirong Yang, Jianping Wu, Jianping Lin, Gang Xu, Haoran Yu
Summary: This study developed machine learning models to predict the substrate specificity of PylRS for novel NCAAs. The models showed high accuracy and provided a framework for expanding the substrate scope of PylRS variants and developing machine learning models for other PylRS variants.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Ke Liu, Ling Jiang, Shuang Ma, Zhongdi Song, Lun Wang, Qunfeng Zhang, Renhao Xu, Lirong Yang, Jianping Wu, Haoran Yu
Summary: This study constructed a highly active and substrate promiscuous variant of PylRS, which successfully incorporated multiple noncanonical amino acids into proteins. The study further elucidated the impact of these noncanonical amino acids on the catalytic mechanism of enzymes.
BIORESOURCES AND BIOPROCESSING
(2023)
Article
Biochemical Research Methods
Jessica T. Stieglitz, Priyanka Lahiri, Matthew Stout, James A. Van Deventer
Summary: Archaeal pyrrolysyl-tRNA synthetases (PylRSs) have been used to genetically encode over 200 distinct noncanonical amino acids (ncAAs) in proteins in Escherichia coli and mammalian cells. This study demonstrates the potential of using Methanomethylophilus alvus PylRS (MaPylRS) in yeast to incorporate ncAAs into proteins. The addition of MaPylRS to the toolkit of translation machinery in Saccharomyces cerevisiae opens up possibilities for expanding the range of genetically encodable ncAAs.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Erol C. Vatansever, Kai S. Yang, Zhi Zachary Geng, Yuchen Qiao, Pingwei Li, Shiqing Xu, Wenshe Ray Liu
Summary: Researchers have designed a PylRS mutant, oClFRS, which efficiently catalyzes the genetic incorporation of o-substituted phenylalanines and have elucidated its structure and function. The binding of o-ClF in the active site of oClFRS involves two halogen bonds, which are crucial for its activity.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Nikolaj G. Koch, Tobias Baumann, Nediljko Budisa
Summary: Introducing non-canonical amino acids (ncAAs) through engineered orthogonal pairs of aminoacyl-tRNA synthetases and tRNAs is a useful tool for expanding the genetic code, but often limited by low yields of chemically modified target proteins. The solubility and folding of engineered enzymes can be a bottleneck for the production of ncAA-containing proteins in vivo, with strategies such as solubility tags improving enzyme solubility and translation efficiency. These methods enhance protein production with engineered PylRS variants and even wild-type enzymes, showing significant efficiency improvements.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Li Cao, Jun Liu, Farid Ghelichkhani, Sharon Rozovsky, Lei Wang
Summary: Researchers have developed orthogonal tRNA(Pyl)-MaBzKRS pairs for site-specific modification of proteins, allowing for efficient incorporation of epsilon-N-benzoyllysine (BzK) into proteins in E. coli and mammalian cells. MaBzKRS variants with mutations at different positions in the amino acid binding pocket have been identified for incorporating BzK, which could have broad utility in studying the biological effects of lysine benzoylation.
Article
Biochemistry & Molecular Biology
Natalie Krahn, Jingji Zhang, Sergey Melnikov, Jeffery M. Tharp, Alessandra Villa, Armaan Patel, Rebecca J. Howard, Haben Gabir, Trushar R. Patel, Jorg Stetefeld, Joseph Puglisi, Dieter Soll
Summary: Protein translation is achieved through tRNA aminoacylation and ribosomal elongation. This study explores the tRNA identity elements for a Delta pylSn tRNA(Pyl) and identifies five key elements necessary for MaPylRS activity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
David G. Schwark, Margaret A. Schmitt, John D. Fisk
Summary: Genetic code expansion has focused on reassigning amber stop codons to insert non-canonical amino acids into proteins. Efforts have been made to use evolved aminoacyl tRNA synthetase variants to incorporate multiple non-canonical amino acids in response to sense codons. A new highly efficient variant of an orthogonal tRNA/aaRS pair was evolved to activate and incorporate tyrosine, rivaling the efficiency of the wild-type pair.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Nikolaj G. Koch, Peter Goettig, Juri Rappsilber, Nediljko Budisa
Summary: The engineering of PylRS variants capable of incorporating an entire library of aliphatic small-tag ncAAs has been reported. By mutating a specific PylRS, the shortest non-bulky ncAA was successfully designed and incorporated, expanding the range of translationally active small-tag ncAAs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Jonathan T. Fischer, Dieter Soll, Jeffery M. Tharp
Summary: This study evolved MaPylRS enzyme using PANCE technology to obtain a highly active variant, PylRS(opt), which exhibits high activity and selectivity towards multiple amino acid derivatives and can be used to enhance the activity of other PylRS constructs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Chia-Chuan Cho, Lauren R. Blankenship, Xinyu Ma, Shiqing Xu, Wenshe Liu
Summary: The study investigated the amber suppression-based noncanonical amino acid mutagenesis technique in both basic and applied research, discovering a new cleavage mechanism of MmPylRS and stabilizing MmPylRS by introducing the P188G mutation, enabling enhanced incorporation of BocK and other noncanonical amino acids.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Thomas L. Williams, Debra J. Iskandar, Alexander R. Noedling, Yurong Tan, Louis Y. P. Luk, Yu-Hsuan Tsai
Summary: N-terminal mutations in MmPylRS significantly improved the efficiency of unnatural amino acid incorporation, but this improvement did not transfer to MbPylRS.
Article
Biochemistry & Molecular Biology
Jae Hyun Kim, Kilsoo Jung, Chulho Lee, Doona Song, Kibum Kim, Hee Chan Yoo, Seung Joon Park, Jong Soon Kang, Kyeong-Ryoon Lee, Sunghoon Kim, Jung Min Han, Gyoonhee Han
Summary: The enzyme leucyl-tRNA synthetase (LRS) and leucine play a key role in regulating the mTOR signaling pathway, with leucine-dependent mTORC1 activation being mediated by LRS. Previous research on compound BC-LI-0186 showed that inhibiting the LRS-RagD interaction could interfere with the mTORC1 pathway, but the compound had issues with solubility and metabolism. By analyzing the physicochemical properties and metabolites of BC-LI-0186, new compounds 7b and 8a were identified to have improved properties while still maintaining inhibitory activity against mTORC1, offering a potential strategy for developing novel drug candidates for mTORC1-related diseases.
BIOORGANIC CHEMISTRY
(2021)
Article
Biochemical Research Methods
Avinash Muppidi, Sang Jun Lee, Che-Hsiung Hsu, Huafei Zou, Candy Lee, Elsa Pflimlin, Madhupriya Mahankali, Pengyu Yang, Elizabeth Chao, Insha Ahmad, Andreas Crameri, Danling Wang, Ashley Woods, Weijun Shen
BIOCONJUGATE CHEMISTRY
(2019)
Article
Medicine, Research & Experimental
Qian Zhao, Hongjiao Xu, Sihua Hong, Nazi Song, Junqiu Xie, Zhibin Yan, Rui Wang, Pengyu Yang, Xianxing Jiang
MOLECULAR PHARMACEUTICS
(2019)
Article
Chemistry, Multidisciplinary
Juan Tang, Michael A. Robichaux, Kuan-Lin Wu, Jingqi Pei, Nhung T. Nguyen, Yubin Zhou, Theodore G. Wensel, Han Xiao
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Biochemical Research Methods
Peng-Yu Yang, Huafei Zou, Zaid Amso, Candy Lee, David Huang, Ashley K. Woods, Van T. B. Nguyen-Tran, Peter G. Schultz, Weijun Shen
BIOCONJUGATE CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Yuda Chen, Juan Tang, Lushun Wang, Zeru Tian, Adam Cardenas, Xinlei Fang, Abhishek Chatterjee, Han Xiao
Article
Biochemistry & Molecular Biology
Juan Tang, Chenfei Yu, Axel Loredo, Yuda Chen, Han Xiao
Summary: Photoactivatable fluorophores are limited in their applications due to their size and the need for ultraviolet light activation. Research has focused on more efficient protein labeling technologies, including single-step labeling processes. By using genetic code expansion and replacing oxygen with sulfur within existing fluorescent amino acids, the photoactivatable fluorescent amino acid thioacridonylalanine (SAcd) has been successfully incorporated into proteins in a single step.
Article
Biochemistry & Molecular Biology
Melissa A. Gray, Michal A. Stanczak, Natalia R. Mantuano, Han Xiao, Johan F. A. Pijnenborg, Stacy A. Malaker, Caitlyn L. Miller, Payton A. Weidenbacher, Julia T. Tanzo, Green Ahn, Elliot C. Woods, Heinz Laeubli, Carolyn R. Bertozzi
NATURE CHEMICAL BIOLOGY
(2020)
Article
Chemistry, Applied
Axel Loredo, Lushun Wang, Shichao Wang, Han Xiao
Summary: A simple and general strategy has been developed to prepare colorimetric and fluorogenic probes for the selective detection of mercury ions in water environments by performing a single-atom replacement within common fluorophores. These probes exhibit pronounced signal changes in the presence of mercury ions, with high selectivity, excellent sensitivity, and rapid responses, making them suitable for visualizing mercury in both aqueous and intracellular environments.
Article
Biochemistry & Molecular Biology
Sophia Z. Shalhout, Peng-Yu Yang, Edyta M. Grzelak, Kayla Nutsch, Sida Shao, Claudio Zambaldo, Jonathan Iaconelli, Lara Ibrahim, Caroline Stanton, Stormi R. Chadwick, Emily Chen, Michael DeRan, Sijia Li, Mitchell Hull, Xu Wu, Arnab K. Chatterjee, Weijun Shen, Fernando D. Camargo, Peter G. Schultz, Michael J. Bollong
Summary: The study identified a small molecule, PY-60, that activates YAP and promotes expansion of epidermal keratinocytes. PY-60's target, ANXA2, is released from the cell membrane to promote YAP's transcriptional activity. This work reveals ANXA2 as a druggable component of the Hippo pathway for promoting regenerative repair in disease.
NATURE CHEMICAL BIOLOGY
(2021)
Review
Biochemical Research Methods
Kuan-Lin Wu, Chenfei Yu, Catherine Lee, Chao Zuo, Zachary T. Ball, Han Xiao
Summary: Antibodies, particularly IgG, are widely used biomolecules in research, diagnostics, and therapy. To enhance their specificity, bioorthogonal handles have been introduced, showing advantages over traditional labeling methods. However, additional chemical treatment or protein engineering is still necessary for these site-specific modifications.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Shudan Yang, Lushun Wang, Axel Loredo, Shichao Wang, Nischal Ada, Han Xiao
Summary: The use of light to activate prodrugs shows promise in precise drug release control, reducing side effects, and enhancing therapeutic effectiveness. A novel prodrug system has been developed using a heavy-atom-free photosensitizer to generate singlet oxygen, triggering the conversion of the prodrug into its active form. Photo-unclick prodrugs of paclitaxel (PTX), combretastatin A-4 (CA-4), and 10-hydroxy-7-ethylcamptothecin (SN-38) have been successfully created, demonstrating decreased toxicity without light and increased toxicity under red light exposure.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Lushun Wang, Chia-Heng Hsiung, Xiaojing Liu, Shichao Wang, Axel Loredo, Xin Zhang, Han Xiao
Summary: This study demonstrates the design and synthesis of a series of solvent-sensitive fluorophores that respond solely to polarity. These fluorophores can be used to detect protein aggregation in live cells and reveal polarity differences among different types of aggregates.
Article
Chemistry, Multidisciplinary
Lushun Wang, Shichao Wang, Juan Tang, Vanessa B. Espinoza, Axel Loredo, Zeru Tian, R. Bruce Weisman, Han Xiao
Summary: In this study, a series of photoactivatable probes were prepared using the oxime moiety as a new class of photolabile caging group. The oxime-caged fluorophores can be oxidized to their carbonyl derivatives upon light irradiation, restoring strong fluorophore fluorescence. Oximes represent a new class of visible-light photocages that can be widely used for cellular imaging, sensing, and photo-controlled molecular release.
Article
Chemistry, Multidisciplinary
Juan Tang, Lushun Wang, Axel Loredo, Carson Cole, Han Xiao
Article
Chemistry, Multidisciplinary
Axel Loredo, Juan Tang, Lushun Wang, Kuan-Lin Wu, Zane Peng, Han Xiao
