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)
Review
Biochemistry & Molecular Biology
Catherine E. Scull, Shiba S. Dandpat, Rosa A. Romero, Nils G. Walter
Summary: Transcriptional riboswitches involve RNA aptamers in bacterial mRNAs and control gene expression by altering RNA folding and transcription in response to ligand binding. Integration of cellular processes and environmental conditions across multiple timescales is essential for a successful response to environmental cues.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Ecology
Thorsten B. H. Reusch, Iliana B. Baums, Benjamin Werner
Summary: Somatic genetic variation may have a significant impact on long-lived, modular species, with sexual and asexual processes influencing the accumulation of genetic load and molecular evolution rates. Further research is needed to understand the fitness effects of SoGV, multilevel selection, and asexual selective sweeps.
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Review
Biochemistry & Molecular Biology
Janis Hoetzel, Beatrix Suess
Summary: Synthetic riboswitches, which consolidate sensing and execution functions in a single RNA molecule, are powerful tools in synthetic biology. However, there is a scarcity of in vitro selected aptamers suitable for engineering synthetic riboswitches. Studies have shown that the key characteristics of regulatory active RNAs, such as structural switching abilities and binding dynamics, are insufficiently represented in conventional SELEX approaches. This review proposes a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied in synthetic riboswitch engineering.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Deborah Antunes, Lucianna H. S. Santos, Ernesto Raul Caffarena, Ana Carolina Ramos Guimaraes
Summary: The spread of antibiotic-resistant bacteria poses a significant threat to health, necessitating the search for novel treatment mechanisms. Riboswitches are considered promising targets for antibacterial drugs. Computational biophysics investigations reveal that 2'-dG riboswitches exhibit increased stability and affinity towards nucleoside ligands, with 2'-dG-II riboswitches showing enhanced intramolecular communication and recognition ability for both cognate and noncognate ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Kamila Mustafina, Yoko Nomura, Rachapun Rotrattanadumrong, Yohei Yokobayashi
Summary: Research focuses on implementing chemical regulation of gene expression in mammalian cells by engineering aptazymes combining a self-cleaving ribozyme with an RNA aptamer. Circularly permuted variants of the pistol ribozyme class were explored as a synthetic ribozyme scaffold for designing guanine and tetracycline activated riboswitches with ON/OFF ratios as high as 8.6 in mammalian cells, adding to the limited toolbox for mammalian synthetic biology applications and suggesting potential in exploring ribozymes beyond natural motifs.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Franz Opel, Nina A. Siebert, Sabine Klatt, Adrian Tuellinghoff, Janis G. Hantke, Joerg Toepel, Bruno Buehler, Dennis J. Nuernberg, Stephan Klaehn
Summary: Cyanobacteria have attracted great interest in biotechnology for their potential in sustainable, photosynthesis-driven production of fuels and value-added chemicals. However, compared to heterotrophic microorganisms, cyanobacterial model strains still lag behind in terms of molecular tools for engineering their metabolism. Researchers have developed a new tool called the pSOMA shuttle vector series for comprehensive genetic engineering of cyanobacteria and demonstrated its potential in gene expression and transfer.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Andrea Guedez, Matt Sherman, Youngha Ryu
Summary: The randomized aptamer domain of the theophylline riboswitch yielded a library with millions of variants, leading to the discovery of a caffeine-specific synthetic riboswitch through dual genetic selection. The riboswitch controlled the expression of target genes in the presence of caffeine, demonstrating caffeine-dependent gene regulation effectively.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Guangrong Meng, Liang Hu, Martin Tomanik, Jin-Quan Yu
Summary: Pd-II-catalyzed beta- and gamma-C(sp(3))-H heteroarylation of free carboxylic acids using pyridine-pyridone ligands overcomes limitations in selective functionalization and compatibility with heteroatoms. A sequence of three consecutive C(sp(3))-H activation reactions of pivalic acid constructs diverse quaternary carbon centers containing heteroaryls, offering a valuable tool for breaking new ground in medicinal chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
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)
Review
Oncology
Andes Arboleda-Garcia, Ivan Alarcon-Ruiz, Lissette Boada-Acosta, Yadira Boada, Alejandro Vignoni, Eloisa Jantus-Lewintre
Summary: Synthetic biology aims to transform bacteria cells into powerful tools for cancer therapy by programming them with artificial genetic circuits. The development of new systems that provide localized antitumoral action while minimizing damage to healthy tissues is crucial for reducing the side effects of cancer treatments. Advances in genetic engineering and synthetic biology have improved the safety and efficacy of bacterial therapies.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yaroslav Chushak, Svetlana Harbaugh, Kathryn Zimlich, Bryan Alfred, Jorge Chavez, Nancy Kelley-Loughnane
Summary: Riboswitches are RNA-based regulatory elements that control gene expression through ligand-induced structural changes in mRNA. Synthetic riboswitches have been mainly tested in cell-based systems, but cell-free protein expression systems offer advantages such as eliminating interactions with cellular networks. Studying a theophylline-responsive synthetic riboswitch in E. coli cellular extract and PURE cell-free systems revealed lower protein expression levels due to reduced mRNA fraction in the 'ON' state and lower translation initiation rate compared to a control construct.
Article
Biochemical Research Methods
Svetlana V. Harbaugh, Adam D. Silverman, Yaroslav G. Chushak, Kathryn Zimlich, Monica Wolfe, Walter Thavarajah, Michael C. Jewett, Julius B. Lucks, Jorge L. Chavez
Summary: By converting RNA aptamers into functional riboswitches, direct detection and control of gene expression for analytes such as dopamine can be achieved. This research is expected to have broad applicability for the conversion of in vitro-generated RNA aptamers into fieldable molecular diagnostics.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biology
Lin Chou, Yu-Chen Lin, Mindia Haryono, Mary Nia M. Santos, Shu-Ting Cho, Alexandra J. Weisberg, Chih-Feng Wu, Jeff H. Chang, Erh-Min Lai, Chih-Horng Kuo
Summary: This study focused on the Agrobacterium tumefaciens species complex, revealing its genetic diversity and evolutionary patterns. The research demonstrated that a phylogeny-guided sampling scheme combined with high-quality assemblies is a cost-effective approach for evolutionary genomics analysis. Additionally, the study identified novel diversity in key genes related to pathogenicity and interbacterial competition, providing insights into the evolution of species complexes.
Article
Biochemical Research Methods
Laszlo Mozsik, Carsten Pohl, Vera Meyer, Roel A. L. Bovenberg, Yvonne Nygard, Arnold J. M. Driessen
Summary: This paper presents a collection of 96 genetic parts that can be used in synthetic biology research in fungi, allowing for the assembly of complex multipartite components. It provides a standardized and modular approach for the rapid assembly of synthetic transcription units.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Christopher J. Robinson, Pablo Carbonell, Adrian J. Jervis, Cunyu Yan, Katherine A. Hollywood, Mark S. Dunstan, Andrew Currin, Neil Swainston, Reynard Spiess, Sandra Taylor, Paul Mulherin, Steven Parker, William Rowe, Nicholas E. Matthews, Kirk J. Malone, Rosalind Le Feuvre, Philip Shapira, Perdita Barran, Nicholas J. Turner, Jason Micklefield, Rainer Breitling, Eriko Takano, Nigel S. Scrutton
METABOLIC ENGINEERING
(2020)
Article
Biotechnology & Applied Microbiology
Adrian J. Jervis, Erik K. R. Hanko, Mark S. Dunstan, Christopher J. Robinson, Eriko Takano, Nigel S. Scrutton
Summary: CRISPR technologies, originally from bacteria, have become standard tools for genetic manipulations in various organisms. While the development of CRISPR tools for engineering bacteria has been slower, their functions and applications in genome editing and gene regulation have been demonstrated in different bacteria, leading to wider adoption. The provided plasmid-based systems allow efficient genome editing, integration, and CRISPRi in E. coli, making the adoption of CRISPR technology easier for any laboratory.
MICROBIAL BIOTECHNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Andrew Currin, Steven Parker, Christopher J. Robinson, Eriko Takano, Nigel S. Scrutton, Rainer Breitling
Summary: The ability to engineer biological systems is crucial in biotechnology and synthetic biology. Generating genetic diversity is essential to explore variations in phenotype, and recent advancements in DNA synthesis technology have enhanced our ability to create variant libraries. This review focuses on approaches to create diversity from enzyme level to entire pathways in vitro, emphasizing the creation of combinatorial libraries for significant improvements in function.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Multidisciplinary Sciences
Michael Winn, Michael Rowlinson, Fanghua Wang, Luis Bering, Daniel Francis, Colin Levy, Jason Micklefield
Summary: Coronatine and related bacterial phytotoxins mimic plant hormone JA-Ile and disrupt important plant physiological signaling pathways. The enzyme CfaL can synthesize JA-Ile and a variety of amides, showing potential for applications in agrochemicals and pharmaceuticals.
Article
Chemistry, Physical
Elliott J. Craven, Jonathan Latham, Sarah A. Shepherd, Imtiaz Khan, Alba Diaz-Rodriguez, Michael F. Greaney, Jason Micklefield
Summary: New chemo- and biocatalytic methodologies are crucial for the sustainable synthesis of essential molecules in the future. Transition metal catalysis allows for late-stage C-H functionalization of complex molecular scaffolds, while enzymes provide exquisite regioselectivity but access to fewer functionalities compared to more divergent chemocatalysis.
Review
Biochemistry & Molecular Biology
Christopher J. Robinson, Jonathan Tellechea-Luzardo, Pablo Carbonell, Adrian J. Jervis, Cunyu Yan, Katherine A. Hollywood, Mark S. Dunstan, Andrew Currin, Eriko Takano, Nigel S. Scrutton
Summary: Metabolic engineering technologies have been successfully employed for the engineering and optimization of industrial host strains over the past three decades. Design-Build-Test-Learn pipelines are being established to rapidly deliver diverse chemical targets through iterative optimization of microbial production strains. Biofoundries are using in silico tools for genetic design and combinatorial design of experiments to optimize selection within the potential design space based on multi-criteria objectives.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2021)
Article
Multidisciplinary Sciences
Wei Li Thong, Yingxin Zhang, Ying Zhuo, Katherine J. Robins, Joanna K. Fyans, Abigail J. Herbert, Brian J. C. Law, Jason Micklefield
Summary: Engineering biosynthetic assembly lines, especially megasynthases like NRPS, using CRISPR-Cas9 technology can rapidly create new natural products with altered substrate selectivity. This method allows for the generation of diverse lipopeptide variants in good yields compared to traditional homologous recombination-mediated approaches.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Luis Bering, Elliott J. Craven, Stanley A. Sowerby Thomas, Sarah A. Shepherd, Jason Micklefield
Summary: Amides are essential chemical bonds in nature and commonly found in proteins, metabolites, and synthetic products. This study presents an integrated multi-catalytic system that combines nitrile hydratase enzymes with a Cu-catalysed N-arylation reaction for the synthesis of amide bonds. The method offers high substrate loading, broad applicability, and excellent functional group tolerance, enabling the efficient synthesis of natural product derivatives, drug molecules, and challenging chiral amides under environmentally friendly conditions.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Tiia Kittila, Patricia Calero, Folmer Fredslund, Phillip T. Lowe, David Teze, Manuel Nieto-Dominguez, David O'Hagan, Pablo Nikel, Ditte H. Welner
Summary: This study explores the effect of oligomerization status on the catalytic properties of fluorinase and reveals that hexamerization is not necessary for fluorination activity. Oligomerization has a long-range effect on substrate binding, decreasing substrate dissociation and release. In addition, the practical application of trimeric fluorinase in in vitro fluorometabolite synthesis is demonstrated.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Juan Pablo Gomez-Escribano, Lis Algora Gallardo, Kenan A. J. Bozhuyuk, Steven G. Kendrew, Benjamin D. Huckle, Nicola A. Crowhurst, Mervyn J. Bibb, Andrew J. Collis, Jason Micklefield, Paul R. Herron, Barrie Wilkinson
Summary: Streptomyces clavuligerus is an industrially important actinomycete with genetic manipulation limitations. Through Cas9-mediated genome editing, successful curing of pSCL4 revealed its crucial role in the structural stability of the linear chromosome.
MICROBIAL GENOMICS
(2021)
Review
Chemistry, Multidisciplinary
Phillip T. Lowe, David O'Hagan
Summary: This review discusses the history and development of 4'-fluoro-nucleosides, tracing their origin from the discovery of the rare fluorine-containing natural product nucleocidin. Nucleocidin, which contains a fluorine atom at the 4'-position of its ribose ring, has played an important role in inspiring the exploration of 4'-fluoro-nucleosides as a privileged motif for nucleoside-based therapeutics.
CHEMICAL SOCIETY REVIEWS
(2023)
Review
Chemistry, Multidisciplinary
Luis Bering, Joseph Thompson, Jason Micklefield
Summary: Integrated catalysis is a powerful approach to develop new routes towards important products under mild and environmentally benign conditions. By combining chemo- and biocatalysts, overall synthetic efficiency can be improved and otherwise challenging transformations can be performed.
TRENDS IN CHEMISTRY
(2022)
Article
Biochemical Research Methods
Mark S. Dunstan, Christopher J. Robinson, Adrian J. Jervis, Cunyu Yan, Pablo Carbonell, Katherine A. Hollywood, Andrew Currin, Neil Swainston, Rosalind Le Feuvre, Jason Micklefield, Jean-Loup Faulon, Rainer Breitling, Nicholas Turner, Eriko Takano, Nigel S. Scrutton