Article
Microbiology
Bing Fu, Junhui Ying, Qingwei Chen, Qili Zhang, Jiajie Lu, Zhiwen Zhu, Ping Yu
Summary: In this study, the riboflavin-producing strain R1 was constructed by overexpressing five key genes in Escherichia coli BL21. The R2 strain was then constructed by overexpressing another gene in the R1 strain, resulting in an increase of riboflavin production. The deletion of a riboswitch gene in E. coli BL21 further enhanced riboflavin production, leading to the generation of the R4 strain. The results suggest that these genetic modifications can greatly improve riboflavin production.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Immunology
Junwen Lei, Caiyan Xin, Wei Xiao, Wenbi Chen, Zhangyong Song
Summary: This review discusses the roles of riboflavin in infectious diseases, summarizes various antibacterial agents acting as analogues of riboflavin biosynthesis pathway, and describes the effects of exogenous riboflavin on the immune system. Additionally, it highlights the immune response of endogenous riboflavin metabolites in infections.
Article
Biotechnology & Applied Microbiology
Milca Rachel da Costa Ribeiro Lins, Laura Araujo da Silva Amorim, Graciely Gomes Correa, Bruno Willian Picao, Matthias Mack, Marcel Otavio Cerri, Danielle Biscaro Pedrolli
Summary: Researchers have designed and implemented a small RNA tool to target bacterial riboswitches and activate gene expression, which is suitable for regulating gene expression in both cell-free and cellular systems. The synthetic rtRNA targets riboswitches to promote antitermination folding, preventing transcription termination and increasing gene expression.
METABOLIC ENGINEERING
(2021)
Article
Chemistry, Medicinal
Bhaiyyasaheb Harale, Saqib Kidwai, Divya Ojha, Manisha Singh, Dwarika Kumar Chouhan, Ramandeep Singh, Vijay Khedkar, Ambadas B. Rode
Summary: Riboflavin derivatives showed promising antimycobacterial activity, with compound 5a being a lead candidate due to its potency and low toxicity. These compounds may exert their antimycobacterial effects through inhibition of riboflavin biosynthesis pathway via FMN riboswitch.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2021)
Review
Infectious Diseases
Nikoleta Giarimoglou, Adamantia Kouvela, Alexandros Maniatis, Athanasios Papakyriakou, Jinwei Zhang, Vassiliki Stamatopoulou, Constantinos Stathopoulos
Summary: Riboswitches are non-coding RNAs that can regulate transcription and translation by changing their structures, and they are considered as ideal targets for the development of new antibacterials.
Article
Microbiology
Inaki Diez-Ozaeta, Lucia Martin-Loarte, Mari Luz Mohedano, Mercedes Tamame, Jose Angel Ruiz-Maso, Gloria del Solar, Maria Teresa Duenas, Paloma Lopez
Summary: This study developed a new method to select riboflavin-overproducing strains of Weissella cibaria using resistance to roseoflavin as a marker. DNA sequencing revealed mutations in the FMN riboswitch, potentially deregulating riboflavin synthesis. The selected mutants showed promising riboflavin production and potential applications in the food and health industry.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lin Wu, Zhijun Liu, Yu Liu
Summary: This study investigated the ligand-induced switch of adenine riboswitch between 10 and 45 degrees C using a combination of experimental techniques. It was found that temperature played a crucial role in the structural and functional diversity of the riboswitch, exerting opposite effects on ligand binding and gene regulation. The distinct thermodynamics of adenine riboswitch exposed in this research may have implications for RNA sensors and drug design.
Article
Agricultural Engineering
Yuxuan Du, Xinyi Zhang, Hengwei Zhang, Rongshuai Zhu, Zhenqiang Zhao, Jin Han, Di Zhang, Xiaoling Zhang, Xian Zhang, Xuewei Pan, Jiajia You, Zhiming Rao
Summary: A biosensor based on FMN riboswitch was used to construct a high-throughput screening platform for improving the activity of riboflavin kinase gene ribC mutants. Mutants screened using this platform showed an 8-fold increase in FMN yield, indicating its effectiveness in improving the activity of target enzymes and providing a new route for screening industrial enzymes.
BIORESOURCE TECHNOLOGY
(2023)
Article
Plant Sciences
Kamonthip Jiadkong, Mami Nampei, Sumana Wangsawang, Akihiro Ueda
Summary: This study reveals that riboflavin treatment can enhance salt tolerance in a salt-sensitive rice cultivar by regulating Na+ and K+ uptake, altering mineral concentrations in roots and leaf blades, and reducing the Na+/K+ ratio in leaf blades.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Biochemistry & Molecular Biology
Marta Irla, Sigrid Hakvag, Trygve Brautaset
Summary: Genome-wide transcriptomic data from RNA-seq experiments can help identify novel regulatory elements. Riboswitches, such as the lysine riboswitch in Bacillus methanolicus, are useful tools for regulating gene expression. Promoters are easily identifiable in prokaryotic genomes and can be combined with riboswitches to create novel tools for inducible gene expression, as demonstrated in this study.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Bo Yu, Pan Li, Qiangfeng Cliff Zhang, Lin Hou
Summary: DiffScan is a computational framework for normalization and differential analysis of RNA structure probing data, which can accurately identify SVRs at nucleotide resolution, demonstrating its compatibility with various structure probing platforms.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Adrien Chauvier, Patrick St-Pierre, Jean-Francois Nadon, Elsa D. M. Hien, Cibran Perez-Gonzalez, Sebastien H. Eschbach, Anne-Marie Lamontagne, J. Carlos Penedo, Daniel A. Lafontaine
Summary: The researchers presented a new approach for site-specific labeling and smFRET studies of kilobase-length transcripts within native bacterial complexes, revealing the relationship between RNA folding and gene regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Sumit Mukherjee, Matan Drory Retwitzer, Sara M. Hubbell, Michelle M. Meyer, Danny Barash
Summary: Riboswitches are conserved RNA sensors that mainly regulate genes/operons in bacteria. The challenge is to discover riboswitch classes in eukaryotes and understand the evolution of bacterial riboswitches. A novel approach based on inverse RNA folding was developed to identify potential structural candidates in fungi that could be distant homologs of bacterial riboswitches. This method transforms a structure-based search into a sequence-based search, considering the conservation of secondary structure shape and ligand-binding residues.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Microbiology
Kristopher J. Kennedy, Florian J. Widner, Olga M. Sokolovskaya, Lina Innocent, Rebecca R. Procknow, Kenny C. Mok, Michiko E. Taga
Summary: In bacteria, riboswitches are gene regulatory RNAs that directly bind and detect metabolites, controlling many essential metabolic processes. Cobalamin riboswitches are an exception as they can respond to multiple variants of cobalamin (vitamin B-12), known as corrinoids. This study found that cobalamin riboswitches vary in their specificity for corrinoids, with some being broadly responsive and others being more selective. Analyses and models suggest that cobalamin riboswitches indirectly differentiate among corrinoids by sensing differences in their structural conformation. These findings provide insights into how bacteria can sense and respond to the chemical diversity of essential metabolites.
Article
Chemistry, Multidisciplinary
Shai Zilberzwige-Tal, Danielle Gazit, Hanaa Adsi, Myra Gartner, Rahat Behl, Dana Laor Bar-Yosef, Ehud Gazit
Summary: Both DNA and RNA nanotechnologies have great potential for in vitro molecular engineering, but their degradation sensitivity and loss of function limit their applications outside the lab. Inspired by the protective mechanism of viruses, researchers have developed RNA-virus-like particles (VLPs) as nanocarriers that can effectively resist degradation. By harnessing biological recognition elements, engineered riboswitch nanocarriers have been shown to have potential as a treatment for genetic metabolic disorders. These nanocarriers selectively bind metabolites and inhibit their self-assembly process, resulting in significant inhibition of sensitivity to adenine feeding and reduction of cytotoxic structures. This RNA therapeutic technology can be easily adapted for other conditions and diseases.
Article
Multidisciplinary Sciences
John A. Howe, Hao Wang, Thierry O. Fischmann, Carl J. Balibar, Li Xiao, Andrew M. Galgoci, Juliana C. Malinverni, Todd Mayhood, Artjohn Villafania, Ali Nahvi, Nicholas Murgolo, Christopher M. Barbieri, Paul A. Mann, Donna Carr, Ellen Xia, Paul Zuck, Dan Riley, Ronald E. Painter, Scott S. Walker, Brad Sherborne, Reynalda de Jesus, Weidong Pan, Michael A. Plotkin, Jin Wu, Diane Rindgen, John Cummings, Charles G. Garlisi, Rumin Zhang, Payal R. Sheth, Charles J. Gill, Haifeng Tang, Terry Roemer
Article
Pharmacology & Pharmacy
Christopher M. Barbieri, Xinkang Wang, Weizhen Wu, Xueping Zhou, Aimie M. Ogawa, Kim O'Neill, Donald Chu, Gino Castriota, Dietmar A. Seiffert, David E. Gutstein, Zhu Chen
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS
(2017)
Article
Biochemical Research Methods
Christopher M. Barbieri, Ann M. Stock
ANALYTICAL BIOCHEMISTRY
(2008)
Review
Biochemistry & Molecular Biology
Daniel S. Pilch, Christopher M. Barbieri, Suzanne G. Rzuczek, Edmond J. LaVoie, Joseph E. Rice
Article
Biochemistry & Molecular Biology
Christopher M. Barbieri, Timothy R. Mack, Victoria L. Robinson, Matthew T. Miller, Ann M. Stock
JOURNAL OF BIOLOGICAL CHEMISTRY
(2010)
Article
Biochemistry & Molecular Biology
Christopher M. Barbieri, Ti Wu, Ann M. Stock
JOURNAL OF MOLECULAR BIOLOGY
(2013)
Article
Biochemistry & Molecular Biology
Paolo Rossi, Christopher M. Barbieri, James M. Aramini, Elisabetta Bini, Hsiau-Wei Lee, Haleema Janjua, Rong Xiao, Thomas B. Acton, Gaetano T. Montelione
NUCLEIC ACIDS RESEARCH
(2013)
Article
Biochemistry & Molecular Biology
Paolo Rossi, Lei Shi, Gaohua Liu, Christopher M. Barbieri, Hsiau-Wei Lee, Thomas D. Grant, Joseph R. Luft, Rong Xiao, Thomas B. Acton, Edward H. Snell, Gaetano T. Montelione, David Baker, Oliver F. Lange, Nikolaos G. Sgourakis
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2015)
Article
Biochemistry & Molecular Biology
David J. Sidote, Christopher M. Barbieri, Ti Wu, Ann M. Stock
Article
Biochemistry & Molecular Biology
Hao Wang, Paul A. Mann, Li Xiao, Charles Gill, Andrew M. Galgoci, John A. Howe, Artjohn Villafania, Christopher M. Barbieri, Juliana C. Malinverni, Xinwei Sher, Todd Mayhood, Megan D. McCurry, Nicholas Murgolo, Amy Flattery, Matthias Mack, Terry Roemer
CELL CHEMICAL BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Jiro Kondo, Mariana Hainrichson, Igor Nudelman, Dalia Shallom-Shezifi, Christopher M. Barbieri, Daniel S. Pilch, Eric Westhof, Timor Baasov
Article
Biochemistry & Molecular Biology
Malvika Kaul, Christopher M. Barbieri, Annankoil R. Srinivasan, Daniel S. Pilch
JOURNAL OF MOLECULAR BIOLOGY
(2007)
Article
Microbiology
Christopher M. Barbieri, Malvika Kaul, Melanie Bozza-Hingos, Fang Zhao, Yitzhak Tor, Thomas Hermann, Daniel S. Pilch
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2007)
Article
Biochemistry & Molecular Biology
Christopher M. Barbieri, Annankoil R. Srinivasan, Suzanne G. Rzuczek, Joseph E. Rice, Edmond J. LaVoie, Daniel S. Pilch
NUCLEIC ACIDS RESEARCH
(2007)