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
Biochemistry & Molecular Biology
Shelby R. Lennon, Robert T. Batey
Summary: Riboswitches are genetic regulatory elements that use RNA conformational switching mediated by ligand binding to control gene expression. This review focuses on the mechanism of ligand-directed conformational changes in cobalamin riboswitches, a widely distributed class of riboswitches in bacteria. The review discusses the architectural features of cobalamin riboswitches, experimental approaches used to study them, and the importance of studying their folding landscapes in vitro and in a co-transcriptional context. The review highlights the challenges of studying cobalamin riboswitches outside of the transcriptional context and emphasizes the importance of co-transcriptional approaches for understanding their structure-function relationships. This understanding is crucial for the future development and applications of small-molecule guided RNA switches.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
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
Multidisciplinary Sciences
Margrethe A. Boyd, Walter Thavarajah, Julius B. Lucks, Neha P. Kamat
Summary: Cell-free systems utilizing synthetic membranes can encapsulate genetically encoded biosensors for detection of various targets. By modulating membrane composition, the response of the sensors can be tuned and degradation can be prevented. This study demonstrates the potential of bilayer membranes in conferring tunable permeability to genetically encoded sensors and confirms the feasibility of artificial cell platforms for detecting environmentally relevant small molecules.
Article
Plant Sciences
Duan Chu, Lai Wei
Summary: Synonymous codon usage could influence gene expression, as alleles with higher codon optimality tend to have higher expression levels in Arabidopsis hybrids.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Eric Rovira, Beatriz Moreno, Nerea Razquin, Lorea Blazquez, Ruben Hernandez-Alcoceba, Puri Fortes, Fernando Pastor
Summary: Synthetic riboswitches are promising regulatory devices that can finely tune gene expression without the need for external factors. By engineering tetracycline-inducible riboswitches and using a technique called SEREX, we were able to achieve significant inductions in gene expression. Multiplexing riboswitches further enhanced inductions. These U1i-based riboswitches are reversible and dose-dependent, making them attractive tools for gene therapy applications.
Article
Biochemistry & Molecular Biology
Mackenzie M. Johnson, Adam J. Hockenberry, Matthew J. Mcguffie, Luiz Carlos Vieira, Claus O. Wilke
Summary: Variation in gene expression is closely associated with codon usage bias, especially under rapid growth conditions. Growth rate-dependent expression variation is an important constraint that influences the evolution of gene sequences in microorganisms.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Rosa M. Pinto, Albert Bosch
Summary: Codon bias, a common phenomenon in all organisms, is influenced by mutation, drift, and selection. While selection for translation efficiency and accuracy is well recognized, fewer studies have explored the impact of translation rate control on codon usage. Experimental molecular evolution using RNA virus populations is a powerful tool in understanding the mechanisms behind codon bias. Furthermore, experimental studies are encouraged to define the role of selection in codon evolution, as most studies on virus codon usage rely on computational analyses.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Fabio Amadei, Maria Reichenbach, Sofia Gallo, Roland K. O. Sigel
Summary: The RNA structural elements called riboswitches play a critical role in regulating gene expression by responding to specific cellular metabolites. The folding pathway and structure of the moaA riboswitch from E. coli, which responds to the metabolite molybdenum cofactor (Moco), were investigated. The study revealed that low ion concentrations can induce a high degree of structure formation in the riboswitch, and Mg2+ facilitates the compaction of the riboswitch towards its active structure.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Gabriel Wright, Anabel Rodriguez, Jun Li, Tijana Milenkovic, Scott J. Emrich, Patricia L. Clark
Summary: Research has shown that synonymous codon usage can affect various mechanisms related to protein production, especially in co-translational protein folding. Conservation of synonymous codon usage patterns across evolution highlights the potential benefits of matching codon usage patterns from the original organism in heterologous gene expression.
Article
Biochemistry & Molecular Biology
Chengyi Du, Yujie Wang, Sha Gong
Summary: The ThiM riboswitch from Escherichia coli is a typical mRNA device that modulates downstream gene expression by sensing TPP. Its regulatory behavior in cells depends on co-transcriptional folding and a combination of transcription rate, pause, and ligand levels.
Article
Neurosciences
Rekha Khandia, Mohd. Saeed, Ahmed M. Alharbi, Ghulam Md. Ashraf, Nigel H. Greig, Mohammad Amjad Kamal
Summary: Codon usage analysis is important for molecular characterization and understanding gene evolution. This study investigated the association between gene length and various parameters related to codon usage. The findings showed a significant correlation between gene length and codon bias in neurodegeneration-associated genes. However, this association varied depending on the size of gene segments. The study also found that gene length was associated with nucleotide disproportion and codon choices. This analysis provides insights into gene expression and potential interventions in defective gene functioning in clinical settings.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Michael Shaferman, Melis Gencel, Noga Alon, Khawla Alasad, Barak Rotblat, Adrian W. R. Serohijos, Lital Alfonta, Shimon Bershtein
Summary: The variability in codon bias between bacterial genomes can interfere with horizontal gene transfer, which drives bacterial adaptation. This study designed an experimental system to investigate the constraints imposed by codon bias on the integration of transferred genes. It was found that mRNA folding stability plays a dominant role in fitness contribution when horizontal gene transfer leads to overstabilization of the 5'-end mRNA.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Anuj Sharma, Shelly Gupta, Karan Paul
Summary: This study compared the preferred codons, codon usage patterns, dinucleotide and amino acid usage patterns of 76 species of the genus Clostridium. It was found that pathogenic Clostridium species had smaller genome sizes with lower AT-rich content, and their choice of codons was influenced by genomic GC/AT content. Pathogenic species displayed a strict bias in codon usage, employing 35 out of 61 codons encoding for 20 amino acids. They also used amino acids with lower biosynthetic cost. Overall, pathogenic members of the genus Clostridium preferred small, AT-rich codons to reduce biosynthetic costs and match the cellular environment of their AT-rich human host.
Article
Biochemistry & Molecular Biology
Patrick St-Pierre, Euan Shaw, Samuel Jacques, Paul A. Dalgarno, Cibran Perez-Gonzalez, Frederic Picard-Jean, J. Carlos Penedo, Daniel A. Lafontaine
Summary: Experimental evidence reveals the presence of a structural intermediate in the folding pathway of the adenine riboswitch, which acts as an open conformation to ensure ligand accessibility and eventually folds into a structure nearly identical to the ligand-bound complex. This study demonstrates that the adenine riboswitch relies on the folding of a structural intermediate to facilitate efficient metabolite sensing and genetic regulation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
R. Kent, N. Dixon
ACS SYNTHETIC BIOLOGY
(2019)
Review
Biotechnology & Applied Microbiology
Guadalupe Alvarez-Gonzalez, Neil Dixon
BIOTECHNOLOGY FOR BIOFUELS
(2019)
Review
Biotechnology & Applied Microbiology
Ross Kent, Neil Dixon
TRENDS IN BIOTECHNOLOGY
(2020)
Article
Biochemical Research Methods
Leopoldo F. M. Machado, Andrew Currin, Neil Dixon
JOURNAL OF BIOLOGICAL ENGINEERING
(2019)
Article
Biochemical Research Methods
Adokiye Berepiki, Ross Kent, Leopoldo F. M. Machado, Neil Dixon
ACS SYNTHETIC BIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Geizecler Tomazetto, Agnes C. Pimentel, Daniel Wibberg, Neil Dixon, Fabio M. Squina
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2020)
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
Biochemistry & Molecular Biology
Soumitra Samanta, Steve O'Hagan, Neil Swainston, Timothy J. Roberts, Douglas B. Kell
Article
Materials Science, Multidisciplinary
Rakesh K. Gupta, Faisal H. Alqahtani, Omar M. Dawood, Marco Carini, Alejandro Criado, Maurizio Prato, Suresh K. Garlapati, Gareth Jones, James Sexton, Krishna C. Persaud, Caroline Dang, Umberto Monteverde, Mohamed Missous, Robert J. Young, Stephen Boult, Neil Dixon, Leszek Majewski, Max A. Migliorato
Summary: The successful fabrication of a suspended graphene array sensor chip has the potential for sensitive and selective gas sensing applications, marking a significant technological advancement in the development of electronic noses.
Review
Biochemistry & Molecular Biology
Jan Range, Colin Halupczok, Jens Lohmann, Neil Swainston, Carsten Kettner, Frank T. Bergmann, Andreas Weidemann, Ulrike Wittig, Santiago Schnell, Jurgen Pleiss
Summary: EnzymeML is an XML-based data exchange format that supports comprehensive documentation of enzymatic data, extended by implementing the STRENDA Guidelines. It supports the scientific community with a standardized data exchange format and integrates software tools through a Python API.
Correction
Biotechnology & Applied Microbiology
Fenryco Pratama, Dennis Linton, Neil Dixon
MICROBIAL CELL FACTORIES
(2021)
Article
Biotechnology & Applied Microbiology
Fenryco Pratama, Dennis Linton, Neil Dixon
Summary: This study demonstrates that improved protein glycosylation in a heterologous host can be achieved by mimicking the coordination between protein translocation, folding, and glycosylation observed in native hosts like Campylobacter jejuni and mammalian cells. Furthermore, it provides insight into strain engineering and bioprocess strategies to improve glycoprotein yield and titre while avoiding the physiological burden of unfolded protein stress on cell growth. The process and genetic strategies identified here will help in further optimizing and scaling up heterologous recombinant N-glycoprotein production.
MICROBIAL CELL FACTORIES
(2021)
Article
Multidisciplinary Sciences
Trishnamoni Gautom, Dharmendra Dheeman, Colin Levy, Thomas Butterfield, Guadalupe Alvarez Gonzalez, Philip Le Roy, Lewis Caiger, Karl Fisher, Linus Johannissen, Neil Dixon
Summary: The study demonstrates that the presence of the gene encoding the solute binding protein TphC enables the uptake of terephthalate (TPA), allowing for the biological degradation of Polyethylene terephthalate (PET) plastic. The analysis reveals the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Rosa Morra, Fenryco Pratama, Thomas Butterfield, Geizecler Tomazetto, Kate Young, Ruth Lopez, Neil Dixon
Summary: Excretion of cytoplasmic protein (ECP) is a commonly observed phenomenon in bacteria, and this partial extracellular localization of the intracellular proteome has been implicated in a variety of stress response mechanisms. The genes mscL and arfA are commonly co-located on the genomes of Gammaproteobacteria and display overlap in their respective 3' UTR and 3' CDS, allowing for an antisense RNA-mediated regulatory control.
LIFE SCIENCE ALLIANCE
(2023)
Article
Chemistry, Multidisciplinary
Robson Tramontina, James L. Galman, Fabio Parmeggiani, Sasha R. Derrington, Timothy D. H. Bugg, Nicholas J. Turner, Fabio M. Squina, Neil Dixon