Review
Biochemistry & Molecular Biology
Hyun-Min Kim, Yebin Hong, Jiani Chen
Summary: CRISPR-Cas enables highly efficient genome editing, allowing the introduction of desired modifications such as mutations and deletions. C. elegans has emerged as a significant model organism for CRISPR-Cas, with numerous strategies established. However, the abundance of methods makes it challenging to choose the correct approach, highlighting the importance of selecting appropriate screening methods for genome modification planning.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Ming Zhao, Miaomiao Gao, Liangbin Xiong, Yongjun Liu, Xinyi Tao, Bei Gao, Min Liu, Feng-Qing Wang, Dong-Zhi Wei
Summary: Genome mutagenesis plays a crucial role in driving organism evolution. In this study, a CRISPR-Cas assisted random mutation (CARM) technique was developed to induce whole-genome mutagenesis in a controllable manner. The method involved using a random gRNA library and SpCas9-NG to randomly damage genomes, leading to diverse and abundant mutations through low-fidelity repair. The technique was successfully applied to evolve the metabolic capacity and production of specific compounds in Saccharomyces cerevisiae strains. The results demonstrate the potential of CARM in increasing genetic diversity and discovering new phenotypes for further investigation through reverse engineering.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Plant Sciences
Marta Vazquez-Vilar, Victor Garcia-Carpintero, Sara Selma, Joan M. Bernabe-Orts, Javier Sanchez-Vicente, Blanca Salazar-Sarasua, Arianna Ressa, Carmine de Paola, Maria Ajenjo, Jose Carlos Quintela, Asun Fernandez-del-Carmen, Antonio Granell, Diego Orzaez
Summary: The ability of CRISPR/Cas to target multiple loci simultaneously is a game-changer in plant breeding, accelerating trait stacking and revealing hidden traits. However, the design and assembly of multiplex constructs comprising tandemly arrayed guide RNAs can be troublesome due to the presence of repetitive sequences, hindering more widespread use.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Chemistry, Physical
Noshad Peyravian, Maziar Malekzadeh Kebria, Jafar Kiani, Peiman Brouki Milan, Masoud Mozafari
Summary: This review focuses on the recent advancements of microfluidic systems to deliver CRISPR/Cas systems in clinical and therapy investigations, highlighting the limitations of conventional delivery tools and the advantages of microfluidic systems in in vitro delivery.
Article
Environmental Sciences
V. Yamini, V. Devi Rajeswari
Summary: Bioremediation, especially microbial-based bioremediation, has become a widely used technology for eliminating contaminants. Microbes, such as bacteria, algae, fungi, and yeast, have shown great potential for effectively degrading polycyclic aromatic hydrocarbon and recovering contaminated soil due to their versatile metabolic capacity and ability to survive in harsh environmental conditions.
Review
Biotechnology & Applied Microbiology
Jing Wang, Xifang Yang, Xueliang Wang, Wanhe Wang
Summary: CRISPR/Cas-based biosensors have been widely used for nucleic acid detection, but their applications for protein detection have been overlooked. Recent studies show that CRISPR/Cas-based biosensors not only analyze proteins, but also enhance the sensitivity and specificity of protein detection. However, there is a lack of comprehensive reviews and elucidation of the mechanisms of CRISPR/Cas-based biosensors for protein detection, which hinders the development of better protein biosensors.
BIOENGINEERING-BASEL
(2022)
Article
Biophysics
Quynh Anh Phan, Linh B. Truong, David Medina-Cruz, Can Dincer, Ebrahim Mostafavi
Summary: CRISPR-Dx offers broad enhancements compared to traditional nanobiosensors by utilizing the trans-cleavage activity of the CRISPR/Cas systems. However, the current singlestranded DNA/RNA reporters of CRISPR-Dx have poor stability and limited sensitivity. Research is shifting towards using the trans-cleavage activity of CRISPR/Cas effectors on metal nanoparticles to develop novel nanobiosensors with high accuracy, sensitivity, selectivity, and versatility.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Chemistry, Physical
Songcheng Yu, Shengnan Cao, Sitian He, Kaixiang Zhang
Summary: DNA methylation is an important epigenetic characteristic that can result in heritable and revisable changes in phenotype without altering the DNA sequence. Aberrant methylation at specific loci has been linked to various diseases. The use of Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems as biosensors has shown potential for detecting locus-specific DNA methylation.
Article
Biochemical Research Methods
Junhua Dong, Cen Chen, Yuepeng Liu, Jingen Zhu, Mengling Li, Venigalla B. Rao, Pan Tao
Summary: Bacteriophage T4 shows great potential for biomedical applications due to its unique characteristics, though genetic engineering of its modified genome is challenging. The CRISPR-Cas12a system proves to be more efficient in cleaving the modified genome compared to the traditional CRISPR-Cas9 system, allowing for the generation of recombinant T4 phages. This CRISPR-inspired approach has the potential to expand the use of phages in various basic and translational research projects.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Pharmacology & Pharmacy
Abhijit Dey
Summary: Medicinal plants have been historically significant for human use, and the CRISPR/Cas9 genome editing tool has been successfully applied to engineer plant secondary metabolic pathways, enhancing the production of genetically-engineered medicinal crops with advanced traits.
PHARMACOLOGICAL RESEARCH
(2021)
Review
Biotechnology & Applied Microbiology
Lu Shan, Zongjie Dai, Qinhong Wang
Summary: Non-conventional yeasts have attracted attention for their excellent characteristics, with advancements in genome editing efficiency and accuracy due to the emergence of CRISPR/Cas technology. Different strategies for optimizing CRISPR/Cas systems in various non-conventional yeasts and their biotechnological applications have been summarized, along with potential directions for broadening and improving the use of CRISPR/Cas technology in this field.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Review
Biochemical Research Methods
Niklas Capdeville, Patrick Schindele, Holger Puchta
Summary: Since their first adaptation for plant genome editing, CRISPR-Cas system nucleases and tools have revolutionized the field, enabling precise induction of predefined modifications and the generation of more efficient base editors. Prime editors have also been optimized for plant applications, allowing accurate substitutions, insertions, and deletions. Recent progress in chromosome restructuring allows not only genetic linkages and breakage, but also promoter swapping.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Entomology
Gabriela-Maria Baci, Alexandra-Antonia Cucu, Alexandru-Ioan Giurgiu, Adriana-Sebastiana Musca, Lilla Bagameri, Adela Ramona Moise, Otilia Bobis, Attila Cristian Ratiu, Daniel Severus Dezmirean
Summary: CRISPR-Cas is a powerful gene editing tool that has made remarkable progress in B. mori genome editing, advancing research in the fields of entomology and biological sciences.
Review
Plant Sciences
Niklas Capdeville, Laura Merker, Patrick Schindele, Holger Puchta
Summary: In recent years, the advancement of CRISPR/Cas technology has greatly expanded the possibilities and precision of plant genome engineering. From single nucleotide changes to alterations spanning millions of base pairs, precise and targeted modifications have become achievable, opening up new avenues for crop improvement.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Jongbeom Park, In Jung Kim, Soo Rin Kim
Summary: Petroleum-based chemical synthesis of industrial products causes environmental and societal issues. Using microorganisms for biotechnological production is a sustainable alternative. Saccharomyces cerevisiae is commonly used to produce biofuels and biomaterials, but its product profiles are restricted. Developing alternative stress-resistant microbial platforms can enhance ethanol production from lignocellulose. Nonconventional yeasts (NCY) show promise as alternative microbial platforms due to desirable metabolic pathways and resistance to stress factors. However, limited genetic information and gene editing tools hinder scaled-up applications. The CRISPR-Cas9 system is a powerful gene editing tool for NCYs. This review discusses the current status and recent advances in promising NCYs and highlights metabolic engineering strategies using the CRISPR-Cas9 system, providing a basis for novel yeast applications.
FERMENTATION-BASEL
(2022)
Article
Multidisciplinary Sciences
Rosanna Puopolo, Ilaria Sorrentino, Giovanni Gallo, Alessandra Piscitelli, Paola Giardina, Alan Le Goff, Gabriella Fiorentino
Summary: The research focused on the immobilization of enzymes on nanosurfaces is crucial for biosensor development, with the study presenting two versions of chimeric proteins that showed promising immobilization properties and reactivity for detecting As(III). The results indicate that these chimeric proteins, when immobilized on gold electrodes, can be utilized as potential electrochemical biosensors for As(III) detection.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Martina Aulitto, Giovanni Gallo, Rosanna Puopolo, Angela Mormone, Danila Limauro, Patrizia Contursi, Monica Piochi, Simonetta Bartolucci, Gabriella Fiorentino
Summary: Extreme environments harbor microorganisms capable of tolerating extreme conditions and heavy metals. The study focused on the isolation and genomic exploration of a new arsenic-tolerant microorganism, Alicyclobacillus mali FL18, which showed high tolerance to arsenite and other metals. Genomic analysis revealed signatures of arsenic resistance genes as well as multidrug resistance efflux transporters in the bacterium's genome.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Giovanni Gallo, Ioannis Mougiakos, Mauricio Bianco, Miriam Carbonaro, Andrea Carpentieri, Anna Illiano, Pietro Pucci, Simonetta Bartolucci, John van der Oost, Gabriella Fiorentino
Summary: This study discovered a novel enzyme through a proteomics approach, interacting with a transcriptional regulator to isolate TtArsM, the first thermophilic prokaryotic arsenite methyltransferase. TtArsM methylates arsenite to produce MMAs and DMAs. Additionally, a highly efficient genome-editing tool was developed to confirm the critical role of TtArsM in arsenite detoxification and create a sensitive whole-cell bioreporter for arsenic ions.
Article
Multidisciplinary Sciences
Giovanni Gallo, Martina Aulitto, Patrizia Contursi, Danila Limauro, Simonetta Bartolucci, Gabriella Fiorentino
Summary: Geothermal springs are rich in various metal ions due to interaction between rock and water, leading to seasonal fluctuations in element composition influencing environmental microbial communities. Extremophilic microorganisms in volcanic thermal vents have developed resistance mechanisms for metal ions and play a role in complex metal biogeochemical cycles. Isolation and characterization of extremophilic microorganisms from hot springs have practical applications in environmental monitoring and bioremediation.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Martina Aulitto, Laura Martinez-Alvarez, Gabriella Fiorentino, Danila Limauro, Xu Peng, Patrizia Contursi
Summary: This study presents a comparative genomic analysis of nine strains of Weizmannia coagulans, focusing on their repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms. The study also analyzes the CRISPR immune system and CRISPR-associated (Cas) genes. Overall, this research provides valuable insights into the genomic diversity of W. coagulans and its potential applications in biotechnology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Rosanna Puopolo, Giovanni Gallo, Danila Limauro, Patrizia Contursi, Gabriella Fiorentino
Summary: Arsenic pollution is a global issue, and biosensors based on enzymatic inhibition have been developed for arsenic detection. The study found that both As(V) and As(III) act as non-competitive inhibitors on the phosphatase activity of TtArsC, with As(V) showing a stronger inhibitory effect. The inhibition-based biosystem is selective for As(V) and exhibits good sensitivity and a low detection limit.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Miriam Carbonaro, Martina Aulitto, Giovanni Gallo, Patrizia Contursi, Danila Limauro, Gabriella Fiorentino
Summary: A newly discovered enzyme, AmCel9, from a thermophilic microorganism was found to have broad substrate specificity and good catalytic activity, making it a promising biocatalyst for lignocellulose deconstruction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Flora Salzano, Martina Aulitto, Gabriella Fiorentino, Emilia Pedone, Patrizia Contursi, Danila Limauro
Summary: A thermo-acidophilic bacterium, Alicyclobacillus mali FL18, was isolated from a hot spring in Italy, and a novel putative beta-xylosidase, Am beta Xyl, belonging to the glycosyl hydrolase family 3, was identified. The enzyme showed high stability and catalytic activity at high temperatures and acidic conditions, and exhibited excellent tolerance to organic solvents and monosaccharides. These characteristics suggest potential applications of Am beta Xyl in various industrial fields.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Giovanni Gallo, Domenico Zannini, Barbara Immirzi, Alessandra De Bruno, Gabriella Fiorentino, Giovanni Dal Poggetto
Summary: The aim of this study was to extract antioxidant molecules from the pectin purification process of citrus lemon waste and encapsulate them in stable pectin films for a green and circular economy process. Seven molecules were recovered, identified, and quantified, and their antioxidant power and stability over time were evaluated. The stability and thermal properties of the bioactive fraction were improved by complexing it with 2-hydroxypropyl-beta-cyclodextrin (HP-beta-CD). The most promising complexes showed increased stability over time compared to uncomplexed antioxidants when incorporated into a pectin film, demonstrating potential for the delivery of antioxidant molecules.