Article
Biotechnology & Applied Microbiology
Xuekun Wang, Mario Andrea Marchisio
Summary: This study highlights the importance of coordinated, high-level, and stable expression of multiple genes for engineering biosynthetic circuits and metabolic pathways. The use of IRES and 2 A peptides allows for co-expression of various genes in polycistronic vectors, enabling reliable expression in eukaryotic cells. Ribosome-skipping events mediated by 2 A peptides facilitate the generation of multiple independent proteins from a single open reading frame.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2021)
Article
Microbiology
Kenneth Rachwalski, Michael J. Ellis, Madeline Tong, Eric D. Brown
Summary: sRNAs are critical mechanisms in bacteria's response to stress, but uncovering their growth phenotypes in E. coli and related bacteria has been challenging. In contrast, deleting the chaperone hfq, required for the activity of many sRNAs in E. coli, results in significant growth defects. This study investigates the genetic interactions among sRNA genes and sheds light on the complex networks of sRNA regulation that support bacterial survival.
Review
Biology
Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Konstantinos Papadopoulos, Ioanna Tsotra, Vassiliki A. Iconomidou, Ioannis Michalopoulos
Summary: Gene coexpression analysis is a method to discover coexpressed genes from a large variety of transcriptomic experiments. By constructing gene coexpression networks and performing enrichment analysis, the predominant biological roles of coexpressed genes can be determined. This analysis involves multiple intricate procedures, including data collection, preprocessing, similarity calculation, and evaluation. This review provides a comprehensive account of the steps required for gene coexpression analysis, as well as key issues and popular tools.
Article
Plant Sciences
Arjun Khakhar, Daniel F. Voytas
Summary: The tools of synthetic biology offer great potential to uncover fundamental mechanisms in plant development and metabolism, but typically require transgenesis. Delivery of foreign genetic material to plants using systemically mobile RNA virus vectors can minimize transgenesis, revolutionizing plant synthetic biology by reducing costs, accelerating experimental timescales, and making genetic manipulation easier.
FRONTIERS IN PLANT SCIENCE
(2021)
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
Biochemical Research Methods
Kristoffer Bach Falkenberg, Vivienne Mol, Arrate Sainz de la Maza Larrea, Ivan Pogrebnyakov, Morten H. H. Norholm, Alex Toftgaard Nielsen, Sheila Ingemann Jensen
Summary: Versatile DNA assembly standards and well-characterized part libraries are crucial tools in synthetic biology. Despite limitations in vector standards for Gram-positive hosts, the ProUSER2.0 toolbox provides a standardized platform for creating shuttle vectors in Bacillus subtilis. This system is semi-compatible with previously developed standards and allows for efficient insertion of cargo sequences. Through thorough characterization of integration sites and promoters, the toolbox facilitates the construction of signal peptide libraries for industrial proteins. Overall, the ProUSER2.0 toolbox is a powerful and flexible framework for use in B. subtilis.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Christoph Kaiser, Jeannine Schneider, Florian Groher, Beatrix Suess, Josef Wachtveitl
Summary: Among the many in vitro-selected aptamers, only a small fraction can be applied for synthetic riboswitch engineering. A comparative study was conducted on three aptamers binding to ciprofloxacin, revealing differences in binding kinetics between regulating and non-regulating aptamers. The study suggests that a highly favored structural adaptation of RNA to the ligand during the final binding step is essential for turning an aptamer into a riboswitch.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Yining Liu, Lei Chen, Tianqi Liu, Xiangqian Su, Lin Peng, Jiangbo Chen, Fei Tan, Pu Xing, Zaozao Wang, Jiabo Di, Beihai Jiang, Hong Qu
Summary: This study identified 694 circRNA-mRNA pairs in colorectal cancer patients, showing the regulatory roles between circular RNAs and their corresponding mRNAs, with some of them associated with patient survival time.
Article
Biochemical Research Methods
Michael T. A. Nguyen, Georgios Pothoulakis, Ebbe S. Andersen
Summary: This study presents an approach for regulating translation in Escherichia coli using the MS2 and PP7 aptamer and coat-protein pairs. It demonstrates that RNA origami scaffolds can activate protein expression, and also shows the regulation of multiple proteins using a single MS2 coat protein fusion.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biology
Hideyuki Nakanishi
Summary: Synthetic mRNAs produced by in vitro transcription can express any transgenes without the risk of insertional mutagenesis. Preclinical studies have developed translational regulation systems to ensure high efficacy and low adverse effects by producing the appropriate amount of therapeutic proteins.
Review
Biotechnology & Applied Microbiology
Wen-Hai Xie, Hong-Kuan Deng, Jie Hou, Li-Juan Wang
Summary: Key points center dot Synthetic sRNAs can be rationally designed based on modular structures of natural sRNAs. center dot Synthetic sRNAs were widely used for metabolic engineering in various microorganisms. center dot Several technological improvements made the synthetic sRNA strategy more applicable.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Review
Pharmacology & Pharmacy
Malvin L. Pardi, Juanqi Wu, Shunsuke Kawasaki, Hirohide Saito
Summary: This review discusses recent developments of RNA-based synthetic genetic circuits in mammalian cells, including post-transcriptional control methods and auxiliary components, as well as their applications in biomedical and preclinical settings.
ADVANCED DRUG DELIVERY REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Elena Bencurova, Aman Akash, Renwick C. J. Dobson, Thomas Dandekar
Summary: In this article, the fundamental aspects of DNA storage and recent advances in this field are discussed, with a focus on natural processes and solutions that can be utilized. New methods for efficient DNA and nucleotide storage inspired by nature are highlighted. Within a few years, DNA-based information storage may become a complement to current electronic data storage systems. Various aspects, such as rapid and directed access, regulatory signals and modulation, and integrated high-density storage and processing modules, are examined. DNA storage has practical applications in biotechnology and human genetics. The potential of DNA storage in synthetic biology and its advantages in direct storage operations are also explored. The use of biology concepts from chromosomal storage, nucleic acid processing, and polymer material sciences will lead to new applications gradually replacing classical information storage methods over time (decades).
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemical Research Methods
Nadia Taou, Michael Lones
Summary: This study introduces a method using synthetic regulatory networks to control and respond to the dynamics of a cell's native regulatory network, with the structure and parameters of the synthetic network optimized using Boolean networks and an evolutionary algorithm. Results show that controllers are effective in driving the target system to specified steady states, with scalability demonstrated for larger controlled networks through experiments with random Boolean networks.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Chemistry, Medicinal
Chloe Maucort, Duc Duy Vo, Samy Aouad, Coralie Charrat, Stephane Azoulay, Audrey Di Giorgio, Maria Duca
Summary: Targeting RNAs with small molecules is a promising field in medicinal chemistry, with microRNAs being particularly interesting targets due to their involvement in pathologies such as cancer.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Review
Biochemical Research Methods
Pei-Ru Chen, Peng-Fei Xia
Summary: Carbon dioxide plays a crucial role in mitigating global climate change and supporting life on Earth. Synthetic biology and metabolic engineering offer a promising approach to enhance CO2 fixation by combining the advantages of autotrophic and heterotrophic organisms. This article reviews the current progress in constructing synthetic CO2 fixation pathways, discusses the underlying design principles and challenges, and provides insights into the future of carbon recycling through engineered synthetic carbon fixation pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2024)
