Review
Biochemical Research Methods
Stefano Castellana, Tommaso Biagini, Luca Parca, Francesco Petrizzelli, Salvatore Daniele Bianco, Angelo Luigi Vescovi, Massimo Carella, Tommaso Mazza
Summary: This study found that hundreds of human proteins interact with degenerated DNA sequences, and identifying these motifs and genomic sites is a challenging research goal in modern molecular biology and bioinformatics. Over the past twenty years, there has been an explosion of computational tools for this task, and sixteen of them were evaluated for their ability to identify known motifs in simulated sequence datasets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biotechnology & Applied Microbiology
Javad Aminian-Dehkordi, Shadi Rahimi, Mehdi Golzar-Ahmadi, Amritpal Singh, Javiera Lopez, Rodrigo Ledesma-Amaro, Ivan Mijakovic
Summary: Synthetic biology offers new solutions for environmental protection by developing remediation systems using genetically engineered microbes and plants, and utilizing computational methods for design and application to detect and respond to specific pollutants.
BIOTECHNOLOGY ADVANCES
(2023)
Review
Plant Sciences
Elif Gediz Kocaoglan, Dhanya Radhakrishnan, Naomi Nakayama
Summary: Plant morphology and anatomy greatly impact agricultural yield. Genetic engineering has allowed for precise engineering of plant development, but with unpredictable outcomes. Synthetic biology approaches offer the potential for improved plant growth and development, creating climate-resilient agriculture.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biotechnology & Applied Microbiology
Natalie Chia, Sang Yup Lee, Yaojun Tong
Summary: Optogenetics technique provides a solution to chemical induction with dynamic control and low cost. It utilizes genetically encodable light-sensing modules to fine tune gene expression and protein activity. Recent advancements in microbial synthetic biology have been achieved, but more portable optogenetic tools need to be developed.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Biochemical Research Methods
Pengli Cai, Sheng Liu, Dachuan Zhang, Huadong Xing, Mengying Han, Dongliang Liu, Linlin Gong, Qian-Nan Hu
Summary: SynBioTools is a comprehensive tool registry that integrates synthetic biology databases, computational tools, and experimental methods. It provides users with a one-stop facility for searching and selecting synthetic biology tools, including resources not mentioned in bio.tools. The tools are categorized based on their potential biosynthetic applications and detailed comparisons of similar tools are included.
BMC BIOINFORMATICS
(2023)
Article
Engineering, Electrical & Electronic
Andrew Lezia, Arianna Miano, Jeff Hasty
Summary: The design and construction of synthetic gene circuits have made significant progress, with applications in medicine, biosensing, and industrial chemical production. The focus has shifted from isolated circuits to complex systems, and design methods now include detailed models of host genome interaction with synthetic gene circuits.
PROCEEDINGS OF THE IEEE
(2022)
Review
Biochemical Research Methods
Jing Wang, Qinglong Zhang, Junshan Han, Yanpeng Zhao, Caiyun Zhao, Bowei Yan, Chong Dai, Lianlian Wu, Yuqi Wen, Yixin Zhang, Dongjin Leng, Zhongming Wang, Xiaoxi Yang, Song He, Xiaochen Bo
Summary: This review article discusses the recent applications of computational methods in synthetic lethality (SL) prediction. It introduces the concept and screening methods of SL, summarizes various SL-related data resources, and provides an overview of computational methods including statistical-based methods, network-based methods, classical machine learning methods, and deep learning methods for SL prediction. The article also highlights the use of negative sampling methods in these models. Representative tools for SL prediction are introduced, and the challenges and future work for SL prediction are discussed.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Engineering, Electrical & Electronic
Robyn P. Araujo, Sean T. Vittadello, Michael P. H. Stumpf
Summary: Innovations in synthetic biology currently rely on trial and error, domain expertise, and ingenuity, but rational design engineering methods may offer a more efficient approach. Mathematical models of cellular systems are necessary to determine if they can meet intended target behavior. Complementary approaches such as algebraic methods and Bayesian design approaches can help identify general principles and choose models with the highest probability of fulfilling design objectives.
PROCEEDINGS OF THE IEEE
(2022)
Review
Biotechnology & Applied Microbiology
Angel Leon-Buitimea, Francisco de Jesus Balderas-Cisneros, Cesar Rodolfo Garza-Cardenas, Javier Alberto Garza-Cervantes, Jose Ruben Morones-Ramirez
Summary: With the rise of antibiotic-resistant bacterial infections, there is a global health crisis. Overuse, inappropriate prescribing, and lack of innovation have led to an increase in microorganisms that can overcome traditional antimicrobial treatments. Synthetic biology offers a promising strategy to develop new antimicrobial therapies through the engineering of control systems in microbial cells.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Maria Martin-Pascual, Christos Batianis, Lyon Bruinsma, Enrique Asin-Garcia, Luis Garcia-Morales, Ruud A. Weusthuis, Richard van Kranenburg, Vitor A. P. Martins dos Santos
Summary: Pseudomonas putida is a microbial chassis with great potential for industrial and environmental biotechnology, but the lack of standardization and convergence in tools and methods has led to compartmentalization and inefficient use of resources in biotechnological applications.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Microbiology
Kenneth E. E. Schackart III, Jessica B. Graham, Alise J. Ponsero, Bonnie L. Hurwitz
Summary: In this study, 19 metagenomic phage detection tools were evaluated, and 9 were systematically assessed. The results showed significant differences in the predicted phage communities among the different tools, with tools using a homology approach demonstrating lower false positive rates and robustness to eukaryotic contamination, while tools using a sequence composition approach showed higher sensitivity. The benchmark datasets developed in this study are publicly available for future comparability of new tools.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemical Research Methods
Peter D. Karp, Peter E. Midford, Richard Billington, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Wai Kit Ong, Pallavi Subhraveti, Ron Caspi, Carol Fulcher, Ingrid M. Keseler, Suzanne M. Paley
Summary: The development of Pathway Tools software enables researchers to construct biological knowledge resources more efficiently, develop metabolic flux models, and interpret high-throughput data using pathway information.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Chemistry, Multidisciplinary
Marcelo D. T. Torres, Jicong Cao, Octavio L. Franco, Timothy K. Lu, Cesar de la Fuente-Nunez
Summary: Antibiotic resistance poses a significant global health challenge, with the need for innovative strategies becoming more urgent. Antimicrobial peptides (AMPs) offer a natural template for the discovery, design, and production of antibiotics, potentially leading the way for future advancements in peptide drug discovery through computational and synthetic biology approaches.
Article
Engineering, Electrical & Electronic
Simon Kretschmer, Tanja Kortemme
Summary: Synthetic biology approaches challenges in healthcare and sustainability with an engineering perspective. Designing biomolecular circuits with programmable input-output behaviors is crucial. However, the limited repertoire of natural sensors and difficulties in interfacing with engineered circuits restrict the sensing capabilities. Computational protein design offers the potential to engineer modular and tunable sensors that can be tailored for different applications. This review focuses on recent approaches using the Rosetta software suite to design protein-based sensors for small-molecule inputs and discusses mechanisms for coupling ligand inputs to functional outputs.
PROCEEDINGS OF THE IEEE
(2022)
Review
Plant Sciences
Tawni Bull, Arjun Khakhar
Summary: Synthetic control systems have advanced the study and engineering of unicellular organisms, but applying these tools to multicellular organisms like plants has been challenging. Predictable engineering of plants can help alleviate global problems.
PLANT CELL REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Yadan Zhang, Mario Andrea Marchisio
Summary: The CRISPR-Cas system in prokaryotes serves as an adaptive and inheritable immune response against invading DNA, while anti-CRISPR proteins act as inhibitors of this system. Over the past decade, CRISPR-Cas systems have been harnessed as a genetic-engineering tool, with the type II CRISPR-Cas system being the most popular in biotechnology.
Review
Biotechnology & Applied Microbiology
Michael Dare Asemoloye, Mario Andrea Marchisio, Vijai Kumar Gupta, Lorenzo Pecoraro
Summary: The ability of fungi to produce ligninolytic enzymes for various industrial applications is limited by their natural production levels, but recent advances in synthetic biology and computational design have shown promise in enhancing enzyme synthesis. Different protein engineering methods such as rational, semi-rational, and directed evolution approaches have been utilized to enhance the production of ligninolytic enzymes in fungi. Techniques like metabolic pathway engineering and synthetic biology have been instrumental in optimizing enzyme production and improving their properties for industrial use. The CRISPR-Cas protein systems have emerged as a promising biotechnology for large-scale production of ligninolytic enzymes in fungi.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemical Research Methods
Xingyu Xu, Zhen Zhu, Yingying Wang, Yangye Geng, Feng Xu, Mario A. Marchisio, Zixin Wang, Dejing Pan
Summary: Microfluidic methodologies for replicative lifespan determination of budding yeast cells are highly impacted by the robustness of experimental conditions, especially the design of yeast-trapping structures. In this study, an optimized design, the yeast rotation (YRot) trap, was proposed and validated for stable retention of mother cells and hydrodynamic rotation of buds. The integration of denser YRot traps in microchannels could potentially improve experimental conditions for precise RLS determination in yeast aging studies.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Dawit M. Weldemichael, Kun Zhou, Shi-jia Su, Lin Zhao, Mario Andrea Marchisio, Matthias Bureik
Summary: Among 50 human microsomal CYPs, 38 were found to significantly increase production of superoxide anions (O-2(-center dot)) in the absence of substrate. Some CYPs were intermediate strength O-2(-center dot) producers, while others were even stronger, with CYP2B6, CYP5A1, CYP2A13, CYP51A1, and CYP1A2 being the strongest producers.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Biochemical Research Methods
Yadan Zhang, Mario Andrea Marchisio
Summary: Type II CRISPR-(d)SpCas9 and anti-CRISPR proteins (AcrIIs) exhibit evidence of coevolution and competition between bacteria and phages. In Saccharomyces cerevisiae, using bare dSpCas9 in conjunction with scaffold gRNA (scRNA) appears to be the most efficient activation system. Among the AcrIIs studied, AcrIIA4 demonstrated the highest inhibition strength at low concentrations, while the fusion of activation domains with dSpCas9 limited their interaction with AcrIIs, highlighting the superiority of bare dSpCas9 for building synthetic genetic networks in yeast.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yingying Wang, Zhen Zhu, Ke Liu, Qin Xiao, Yangye Geng, Feng Xu, Shuiping Ouyang, Ke Zheng, Yimin Fan, Nan Jin, Xiangwei Zhao, Mario A. Marchisio, Dejing Pan, Qing-An Huang
Summary: In this study, a high-throughput microfluidic chip for diploid yeast long-term culturing, optical inspection, and cell-aging analysis was developed. The chip features delicate microstructures to ensure cell stability and alleviate stress. Using this chip, the researchers were able to track the replicative lifespan and budding time interval of diploid yeast cells and observe cell desynchronization during aging.
JOURNAL OF NANOBIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Biruck Woldai Abraha, Mario Andrea Marchisio
Summary: This article presents a method for the visual design and modular modeling of synthetic gene circuits using SBML Level 3. It demonstrates the wet-lab implementation of Boolean NOT gates using the bacterial ClpX-ClpP system for protein degradation. The study serves as the starting point for the development of new software for modular design of eukaryotic gene circuits and provides an alternative approach to building genetic Boolean gates.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yadan Zhang, Huanhuan Ge, Mario Andrea Marchisio
Summary: CRISPR-Cas systems are powerful tools for genetic manipulation and gene expression regulation. In this study, Nme1Cas9 was mutated to d(16A)Nme1Cas9, which retained the active HNH domain and functioned as a functional RNase in vivo. However, LwaCas13a and RfxCas13d did not show functional activity in Saccharomyces cerevisiae.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Environmental Sciences
Michael Dare Asemoloye, Mario Andrea Marchisio
Summary: Fungal laccase (Lac) has become an important biocatalyst in various industries, and in this study, engineered yeast strains showed significant response to different carbon and nitrogen sources, as well as efficient degradation of complex hydrocarbon mixtures.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Review
Chemistry, Multidisciplinary
Tsigereda Weldemichael, Michael Dare Asemoloye, Mario Andrea Marchisio
Summary: Feedforward loops (FFLs) are simple network motifs composed of three genes, and they have been found in many organisms. FFLs enable cells to survive critical environmental conditions. The most common types are coherent 1 and incoherent 1 FFLs, which have different functions. Only a few synthetic FFLs have been engineered so far, and they differ greatly from natural FFLs.
APPLIED SCIENCES-BASEL
(2022)
Article
Biophysics
Michael Dare Asemoloye, Mario Andrea Marchisio
Summary: Yeast-based biosensors have the potential for various applications, and this work contributes to the understanding of detectable chemicals and the development of modular yeast biosensors. By using bacterial transcription factors, transducer circuits were built in Saccharomyces cerevisiae for the detection of specific chemicals. These engineered strains showed fast response time and strong signal output to a wide range of chemical concentrations, and were capable of operating in complex media.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Biochemistry & Molecular Biology
Lifang Yu, Mario Andrea Marchisio
Summary: This study presents an efficient tool to induce mRNA degradation in yeast using CRISPR-(d)Cas system, specifically (d)Cas12a. The study highlights the potential of V-A Cas proteins in yeast and demonstrates their applications in constructing Boolean logic gates.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Tian Zhou, Zhiying Liang, Mario Andrea Marchisio
Summary: In this study, the working of a ss-estradiol-sensing device was optimized by engineering both the chimeric activator and the reporter protein expression cassette. The researchers found a configuration that functions as a highly sensitive biosensor and a sharp switch depending on the concentration of the chimeric activator and the strength of its activation domain.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Xuekun Wang, Ximing Tian, Mario Andrea Marchisio
Summary: Gene digital circuits have various applications and are the subject of many studies in Synthetic Biology. They utilize small genetic components that mimic Boolean gates to perform complex logic functions. In this study, three bacterial repressors (TetR, LexA, and LacI) were coexpressed in the yeast Saccharomyces cerevisiae using synthetic polycistronic cassettes based on 2A peptide sequences. By modifying the original 2A peptides, we successfully constructed single and two-input Boolean gates, and eventually developed a tricistronic vector that enabled the implementation of three-input circuits containing AND and OR gates. Overall, polycistronic constructs simplify the cloning and coexpression of multiple proteins, reducing the complexity of gene digital circuits.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lifang Yu, Yadan Zhang, Mario Andrea Marchisio
Summary: Synthetic gene Boolean gates and digital circuits have diverse applications, and the discovery of CRISPR-Cas systems and their natural inhibitors-Acrs-provides a new tool for designing and implementing in vivo gene digital circuits. This article presents a protocol for establishing small transcriptional networks in Saccharomyces cerevisiae using dCas9/dCas12a and their corresponding Acrs. The results highlight the properties of these Cas proteins as transcription factors and demonstrate how to build Boolean gates based on the CRISPR-dCas-Acr interaction.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
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)
