Article
Biochemistry & Molecular Biology
Wenjian Han, Wendi Huang, Tong Wei, Yanwen Ye, Miaowei Mao, Zefeng Wang
Summary: This study reports a new RNA editing system that allows precise gene editing using a single engineered protein, without the need for auxiliary RNA. The system achieves high editing efficiency and low off-target effects, making it applicable for correcting disease-associated gene mutations.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Jiaqi Shen, Lequn Geng, Xingyu Li, Catherine Emery, Kayla Kroning, Gwendolyn Shingles, Kerry Lee, Matthias Heyden, Peng Li, Wenjing Wang
Summary: We have developed a pair of chemically activated protein domains (CAPs) that can control the accessibility of short peptides. CAPs are applicable to a range of short peptides and have a chemical dependence up to 156-fold. Our study demonstrates the potential use of CAPs in cell cultures and multiple organs in living animals.
Article
Biochemistry & Molecular Biology
Rosa Merlo, Rosanna Mattossovich, Marianna Genta, Anna Valenti, Giovanni Di Mauro, Alberto Minassi, Riccardo Miggiano, Giuseppe Perugino
Summary: Self-labelling protein tags (SLPs) are versatile tools for sensor imaging that can be genetically fused with any protein of interest. Through computational and structural approaches, a thermostable CLIP-tag named SsOGT-MC8 was developed, which can covalently react with specific substrates at high temperatures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Jhenifer Yonara de Lima, Emanuella de Castro Andreassa, Isis Venturi Biembengut, Tatiana de Arruda Campos Brasil de Souza
Summary: This study investigates the role of T12, Y25, and T89 in the activities of asparaginase and glutaminase. Through structural analysis and enzymatic assays, the study provides insights into the enzymatic behavior of EcA and paves the way for the design of improved EcA enzymes, which is important in the treatment of ALL.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Alexandra Mack, Max Emperle, Philipp Schnee, Sabrina Adam, Juergen Pleiss, Pavel Bashtrykov, Albert Jeltsch
Summary: Somatic R882H DNMT3A mutations are common in AML, but their pathogenic mechanism is unclear. R882H mutations affect the sequence preferences of DNMT3A and have a dominant effect on its catalytic properties in samples containing WT and R882H subunits.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nehad Noby, Rachel L. Johnson, Jonathan D. Tyzack, Amira M. Embaby, Hesham Saeed, Ahmed Hussein, Sherine N. Khattab, Pierre J. Rizkallah, D. Dafydd Jones
Summary: The study on cold active esterase EstN7 reveals that its substrate range is limited but can be broadened through mutations, providing new insights for enzyme engineering.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Fabian B. H. Rehm, Tristan J. Tyler, Simon J. de Veer, David J. Craik, Thomas Durek
Summary: This study reports an engineered enzyme that accepts various nucleophile substrate mimetics, especially when a method to selectively inhibit the reactivity of byproducts is employed. In addition, C-terminal Leu-ethylenediamine motifs are identified as bona fide mimetics of native N-terminal sequences, enabling transpeptidase-catalyzed C-to-C ligations. This work significantly expands the synthetic scope of enzyme-catalyzed protein transpeptidation reactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Ying Xiao, Guoning Zhang, Yingbo Yang, Jingxian Feng, Shi Qiu, Zhuzhen Han, Jiaran Geng, Wansheng Chen
Summary: Understanding the mechanisms of enzyme specificity is increasingly important. This study reveals the acceptor selectivity of CGTases and provides insights into their catalytic mechanism.
BIOORGANIC CHEMISTRY
(2022)
Article
Physics, Multidisciplinary
Marc Schenkelberger, Christian Trapp, Timo Mai, Varun Giri, Mina Mohammadi-Kambs, Albrecht Ott
Summary: The specificity of molecular recognition is crucial for molecular self-organization, with better matching molecules prevailing over competitors. Fluorescence-based techniques were used to study the recognition of DNA oligonucleotide single strands, revealing reduced affinity for certain strands in the presence of a better matching competitor.
NEW JOURNAL OF PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Francesco Rinaldi, Fabrizio Schipani, Beatrice Balboni, Federico Catalano, Roberto Marotta, Samuel H. Myers, Viola Previtali, Marina Veronesi, Luigi Scietti, Valentina Cecatiello, Sebastiano Pasqualato, Jose Antonio Ortega, Stefania Girotto, Andrea Cavalli
Summary: This study successfully developed a monomeric recombinant form of human RAD51 and identified the most suitable conditions to stabilize the monomer using different buffers. The monomer of human RAD51 provides a crucial biological tool for investigating RAD51-mediated homologous recombination and paves the way for more reliable studies on structure, mechanism, and drug discovery.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Isabel Cea-Rama, Cristina Coscolin, Panagiotis Katsonis, Rafael Bargiela, Peter N. Golyshin, Olivier Lichtarge, Manuel Ferrer, Julia Sanz-Aparicio
Summary: This study investigated the mutation of a serine ester hydrolase EH3 to explore the switching of substrate ambiguity and chiral specificity. The results showed that specific amino acid substitutions at key positions can lead to both substrate-ambiguous and chiral-specific enzyme properties, supporting the idea that enzymes can evolve sequence positions to control substrate scope and stereospecificity.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Fabian B. H. Rehm, Tristan J. Tyler, Kuok Yap, Thomas Durek, David J. Craik
Summary: The use of enzymes, specifically asparaginyl endopeptidases (AEPs), for site-specific modification of proteins/peptides has become a popular method in studying protein/peptide functions or generating therapeutic conjugates. A novel approach using metal-complexation-based strategy has been developed to shift the AEP-catalyzed transpeptidation equilibrium towards product formation, allowing efficient peptide/protein labeling and enhancing protein-protein ligation. This method shows promise in facilitating the formation of transpeptidation products that are typically challenging to attain.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Karina Yui Eto, Stephen M. Kwong, Patrick T. LaBreck, Jade E. Crow, Daouda A. K. Traore, Nipuna Parahitiyawa, Heather M. Fairhurst, D. Scott Merrell, Neville Firth, Charles S. Bond, Joshua P. Ramsay
Summary: The study investigates the horizontal transfer mechanism of plasmids in Staphylococcus aureus, finding that plasmids related to pWBG749 are mobilizable due to the presence of oriT sequences. The research shows that SmpO proteins in pWBG749 predominantly form tetramers and bind specific sites within oriT sequences, with a substitution in pWBG749 being able to switch oriT-binding specificity. In vivo experiments demonstrate that the substitution broadens the mobilized oriT subtypes, suggesting a potential evolutionary intermediate that could facilitate a switch between oriT specificities.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Michael Burger, Seraina Kaelin, Jean-Christophe Leroux
Summary: Non-viral gene delivery agents mainly rely on charge-based and hydrophobic interactions, while the human protein TFAM utilizes specific protein-protein and protein-DNA interactions to form nanoparticles with DNA. In this study, TFAM's properties are repurposed to create a DNA transfection agent through protein engineering. The TFAM/DNA complexes are stabilized by introducing cysteine point mutations and covalently fusing with other proteins to enable endosomal escape and DNA protection. This TFAM-based DNA scaffold shows promising activity in transfecting cells.
Article
Multidisciplinary Sciences
Antony D. St-Jacques, Joshua M. Rodriguez, Matthew G. Eason, Scott M. Foster, Safwat T. Khan, Adam M. Damry, Natalie K. Goto, Michael C. Thompson, Roberto A. Chica
Summary: This study presents a computational method to tune the conformational landscape of enzymes for enhanced catalytic efficiency with non-native substrates. By redesigning the conformational states and equilibria of an aminotransferase, the authors achieved customized biocatalysts with increased activity and altered substrate selectivity.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Morgan E. Carter, Matthew Helm, Antony V. E. Chapman, Emily Wan, Ana Maria Restrepo Sierra, Roger W. Innes, Adam J. Bogdanove, Roger P. Wise
MOLECULAR PLANT-MICROBE INTERACTIONS
(2019)
Article
Biochemistry & Molecular Biology
Betty W. Shen, Lindsey Doyle, Phil Bradley, Daniel F. Heiter, Keith D. Lunnen, Geoffrey G. Wilson, Barry L. Stoddard
NUCLEIC ACIDS RESEARCH
(2019)
Article
Evolutionary Biology
Sara C. D. Carpenter, Lawan Kladsuwan, Sang-Wook Han, Sutruedee Prathuangwong, Adam J. Bogdanove
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Plant Sciences
David J. Studholme, Emmanuel Wicker, Sadik Muzemil Abrare, Andrew Aspin, Adam Bogdanove, Kirk Broders, Zoe Dubrow, Murray Grant, Jeffrey B. Jones, Georgina Karamura, Jillian Lang, Jan Leach, George Mahuku, Gloria Valentine Nakato, Teresa Coutinho, Julian Smith, Carolee T. Bull
Article
Genetics & Heredity
Andrew C. Read, Matthew J. Moscou, Aleksey V. Zimin, Geo Pertea, Rachel S. Meyer, Michael D. Purugganan, Jan E. Leach, Lindsay R. Triplett, Steven L. Salzberg, Adam J. Bogdanove
Article
Biochemistry & Molecular Biology
Andrew C. Read, Mathilde Hutin, Matthew J. Moscou, Fabio C. Rinaldi, Adam J. Bogdanove
MOLECULAR PLANT-MICROBE INTERACTIONS
(2020)
Article
Multidisciplinary Sciences
Morgan E. Carter, Sara C. D. Carpenter, Zoe E. Dubrow, Mark R. Sabol, Fabio C. Rinaldi, Olga A. Lastovetsky, Stephen J. Mondo, Teresa E. Pawlowska, Adam J. Bogdanove
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Genetics & Heredity
Alison D. Scott, Aleksey V. Zimin, Daniela Puiu, Rachael Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily Burns, Jill Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
G3-GENES GENOMES GENETICS
(2020)
Article
Microbiology
Sara C. D. Carpenter, Prashant Mishra, Chandrika Ghoshal, Prasanta K. Dash, Li Wang, Samriti Midha, Gouri S. Laha, Jagjeet S. Lore, Wichai Kositratana, Nagendra K. Singh, Kuldeep Singh, Prabhu B. Patil, Ricardo Oliva, Sujin Patarapuwadol, Adam J. Bogdanove, Rhitu Rai
FRONTIERS IN MICROBIOLOGY
(2020)
Review
Plant Sciences
Zoe E. Dubrow, Adam J. Bogdanove
Summary: Xanthomonas campestris pv. campestris, the causal agent of black rot of crucifers, was one of the first bacterial plant pathogens ever identified. 130 years later, black rot still poses a threat to Brassica crops worldwide. Recent genomic and genetic data are enhancing our understanding of X. campestris taxonomy, dissemination, inoculum sources, and virulence factors, with the potential to impact resistance breeding and management strategies.
JOURNAL OF GENERAL PLANT PATHOLOGY
(2021)
Article
Agronomy
Marlene Lachaux, Emilie Thomas, Adam J. Bogdanove, Boris Szurek, Mathilde Hutin
Summary: We identified and characterized TalD and TalI as two African Xoo TALEs with avirulence activity on IR64 and CT13432 respectively. Resistance of CT13432 against African Xoo results from the combination of two mechanisms, one relying on the TalI-mediated induction of an unknown executor gene and the other on an Xa1-like gene or allele.
Article
Microbiology
Matthew A. Tancos, Zoe E. Dubrow, Sara C. D. Carpenter, Adam J. Bogdanove
Summary: Xanthomonas campestris strain FDWSRU 18048, which is closely related to X. campestris pv. incanae strain CFBP2527, has been reported to infect nonnative, invasive garlic mustard populations in the eastern United States.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Biochemistry & Molecular Biology
Madison A. Kennedy, Christopher J. Hosford, Caleigh M. Azumaya, Yvette A. Luyten, Minyong Chen, Richard D. Morgan, Barry L. Stoddard
Summary: Type IIS restriction endonucleases cleave substrates outside target sequences. This study examines the PaqCI endonuclease's DNA cleavage and molecular structures with or without multiple bound DNA targets. The enzyme maintains a tetrameric organization in the absence or presence of substrate, but undergoes significant domain repositioning in a trapped DNA-bound complex. While PaqCI and FokI share similar DNA cleavage mechanisms, they differ in domain organization and quaternary architecture.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Betty W. Shen, Lindsey A. Doyle, Rachel Werther, Abigail A. Westburg, Daniel P. Bies, Stephanie Walter, Yvette A. Luyten, Richard D. Morgan, Barry L. Stoddard, Brett K. Kaiser
Summary: Bacteriophage exclusion (BREX) systems, encoded by bacteria and archaea, limit phage infection via an unknown mechanism. One component, BrxL, shares sequence similarity with AAA+ proteins like Lon protease. CryoEM structures reveal BrxL as a chambered, ATP-dependent DNA binding protein. Mutations affecting ATPase activity disrupt various in vitro behaviors, but only mutations disrupting the ATPase active site completely eliminate phage restriction, suggesting possible collaboration between BrxL and other BREX factors in disrupting phage DNA replication initiation.
NUCLEIC ACIDS RESEARCH
(2023)