Article
Biochemical Research Methods
Jichen Bao, Enrique de Dios Mateos, Silvan Scheller
Summary: This study developed a genome-editing toolbox using LbCas12a and the endogenous homology-directed repair machinery in M. maripaludis, enabling reliable and efficient genome editing in methanogens. The toolbox demonstrated successful deletion and replacement of target genes, and was applicable for metabolic engineering and flux balancing studies. This CRISPR/LbCas12a toolbox provides a reliable and quick method for genome editing in methanogens.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Jichen Bao, Enrique de Dios Mateos, Silvan Scheller
Summary: A genome-editing toolbox using Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in combination with the endogenous homology-directed repair machinery of M. maripaludis has been designed, allowing reliable and quick genome editing in a methanogen.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Keiji Nishida, Akihiko Kondo
Summary: CRISPR-Cas system offers various modes for DNA editing in metabolic engineering, with consideration of host-dependent repair pathways. The versatility of CRISPR system has led to derivative technologies to complement nuclease-based editing, avoiding cytotoxicity, especially in microorganisms.
METABOLIC ENGINEERING
(2021)
Article
Agricultural Engineering
Byeong-ryool Jeong, Junhwan Jang, EonSeon Jin
Summary: CRISPR-Cas has revolutionized genetic modification with its simplicity and accuracy, and can be applied at the genomic level. Microalgae are excellent feedstocks for biofuels and nutraceuticals due to their high levels of fatty acids, carotenoids, and other metabolites. However, microalgal engineering is not as advanced as other model organisms. This review proposes further genome engineering schemes, including the construction of sgRNA libraries, pan-genomic and epigenomic resources, and mini-genomes, to develop synthetic biology for carbon-based engineering in microalgae.
BIORESOURCE TECHNOLOGY
(2023)
Article
Microbiology
Xueli Zhang, Chaohui Zhang, Caijiao Liang, Bizhou Li, Fanmei Meng, Yuncan Ai
Summary: Bacteriophages, the most abundant organisms in the biosphere, have been sequenced extensively. However, the study of bacteriophage functional genomics has been hindered by a lack of effective research methods. This study designed a phage genome editing platform based on the CRISPR-Cas9 system, and successfully achieved gene editing in Vibrio natriegens phage TT4P2. This platform has the potential to advance research on phage gene diversity and accelerate the development of phage synthetic biology and nanotechnology.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Justin A. Bosch, Gabriel Birchak, Norbert Perrimon
Summary: The study successfully applied prime editing in Drosophila to introduce premature stop codons and achieve efficient germline transmission, demonstrating its potential for studying gene function in Drosophila.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biotechnology & Applied Microbiology
Dongdong Zhao, Xinna Zhu, Hang Zhou, Naxin Sun, Ting Wang, Changhao Bi, Xueli Zhang
Summary: Effective metabolic pathways are crucial for efficient cell factories, and utilizing CRISPR technology in pathway engineering can enhance efficiency, reduce costs, and simplify target customization. This technology has been proven to be robust and effective in various organisms.
METABOLIC ENGINEERING
(2021)
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
Kylie Standage-Beier, Stefan J. Tekel, David A. Brafman, Xiao Wang
Summary: This study introduces a software tool called PINE-CONE which enables high-throughput automated design of pegRNAs and prime editing strategies. By translating edit coordinates and sequences into required designs, PINE-CONE accelerates the application of PE technology in synthetic biology and biomedical research.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Rui Su, Ting Wang, Taidong Bo, Ningyun Cai, Meng Yuan, Chen Wu, Hao Jiang, Huadong Peng, Ning Chen, Yanjun Li
Summary: In this study, a CRISPR-based genome editing technology called RAPID was developed for Corynebacterium glutamicum. This technology enables efficient gene deletion and insertion, and only requires a linear DNA template for gene deletion. This method simplifies the editing process and can be widely applied in genetic manipulations of C. glutamicum.
MICROBIAL CELL FACTORIES
(2023)
Review
Plant Sciences
Arya Bagus Boedi Iswanto, Rahul Mahadev Shelake, Minh Huy Vu, Jae-Yean Kim, Sang Hee Kim
Summary: Plasmodesmata play a crucial role in intercellular communication and molecular exchange in plant cells, with potential applications in crop improvement. Researchers suggest that genome editing techniques like CRISPR/Cas offer powerful tools to analyze the function of plasmodesmata components and engineer elite crops.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Janine Pietralla, Niklas Capdeville, Patrick Schindele, Holger Puchta
Summary: ErCas12a is a nuclease derived from Eubacterium rectale with potential applications in plant genome engineering. Optimized through protein engineering, an improved variant named imErCas12a showed significantly enhanced gene editing efficiency in comparison to the wild-type enzyme. This economically attractive alternative demonstrated strong editing efficiencies at lower temperatures and enabled editing of previously inaccessible targets without off-site activity.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Azamat V. Karginov, Marina G. Tarutina, Anastasia R. Lapteva, Maria D. Pakhomova, Artur A. Galliamov, Sergey Y. Filkin, Alexey N. Fedorov, Michael O. Agaphonov
Summary: In this work, an improved plasmid vector set for CRISPR-Cas9 genome editing in methylotrophic yeasts is presented. The vector set includes a plasmid encoding Cas9 with a nuclear localization signal and plasmids with a scaffold for the single guide RNA (sgRNA). Construction of sgRNA gene for a specific target sequence only requires the insertion of a 24 bp oligonucleotide duplex into the scaffold. The functionality of this vector set has been demonstrated in multiple methylotrophic yeast species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Gemma Llargues-Sistac, Laia Bonjoch, Sergi Castellvi-Bel
Summary: The use of next-generation sequencing (NGS) technologies has greatly advanced our understanding of the mutational landscape of complex human diseases such as cancer. Haploid human cell models, such as the HAP1 cell line, have emerged as valuable tools for functional gene studies, especially in combination with CRISPR-Cas9 gene editing technology. This review explores the recent applications of the HAP1 cell line in functional genetic studies and high-throughput genetic screens, highlighting its potential to enhance our understanding of gene function and the genetic basis of human diseases identified through NGS technologies, and its implications for clinical practice and patient care.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Hao Tang, Xiaohui Zhao, Xingyu Jiang
Summary: CRISPR holds great potential in biomedical research and disease therapy but faces challenges in efficient delivery. Various multi-layered non-viral vectors have been developed for CRISPR delivery, with ongoing clinical trials to test their efficacy.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Article
Plant Sciences
Sarbottam Piya, Tracy Hawk, Bhoomi Patel, Logan Baldwin, John H. Rice, C. Neal Stewart, Tarek Hewezi
Summary: The study demonstrates that inactivating protein kinases through kinase-dead mutations can enhance soybean resistance to nematodes, showing the potential of this approach in increasing plant resistance to biotic and abiotic stresses.
MOLECULAR PLANT PATHOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Alessandro Occhialini, Alexander C. Pfotenhauer, Li Li, Stacee A. Harbison, Andrew J. Lail, Jason N. Burris, Cristiano Piasecki, Agnieszka A. Piatek, Henry Daniell, C. Neal Stewart, Scott C. Lenaghan
Summary: A novel synthetic genome structure called the 'mini-synplastome' has been designed and developed, inspired by dinoflagellate plastome organization. It can replicate, be cloned easily, express genes predictably in plastids, not integrate vector sequences into the native plastome, and persist autonomously in plants over generations without external selection pressure. This innovation is anticipated to revolutionize chloroplast biotechnology, facilitate marker-free plastid engineering, and provide an unparalleled platform for one-step metabolic engineering in plants.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Review
Plant Sciences
Mst Shamira Sultana, Reginald J. Millwood, Mitra Mazarei, C. Neal Stewart
Summary: Legume proteinase inhibitors have shown potential for plant protection against herbivores by inhibiting digestive proteinases in insects. Multiple PIs co-expressed in transgenic plants have been found to enhance host defense in an additive manner. Further research is needed to expand PI gene repertoires and improve efficacy against multiple proteinases.
PLANT CELL REPORTS
(2022)
Article
Plant Sciences
Yaping Xu, Vivek Shrestha, Cristiano Piasecki, Benjamin Wolfe, Lance Hamilton, Reginald J. Millwood, Mitra Mazarei, Charles Neal Stewart
Summary: The study utilized UAV-based remote sensing for automated phenotyping of field-grown switchgrass, exploring the potential of multiple sustainable traits and developing statistical models for each trait. The accuracy of the UAV models was verified by ground-truthing, providing a new method for high-throughput phenotyping of switchgrass.
Article
Plant Sciences
Jun Liu, Qidi Zhao, Haiyan Huang, Rongjian Ye, Charles Neal Stewart, Junming Wang
Summary: The production and movement of seeds are crucial for the spread of glyphosate-resistant horseweed. However, there is a lack of experimental data on seed production and dispersion. This study provides insights into the dynamic emission, dispersion, and deposition of horseweed seeds throughout a seed-shedding season, showing that wind speed plays a major role in seed emission and transport. The results of this study will be valuable for the management of glyphosate-resistant horseweed.
Review
Plant Sciences
Romesh K. Salgotra, Charles Neal Stewart
Summary: Recent advances in next generation sequencing technologies have greatly increased the genomic resources for legume crops. High throughput genotyping and high throughput phenotyping enable more precise and efficient improvement of legume crops. Molecular breeding approaches are currently being used to enhance important legume crops, and future developments will support the customization of legume crop varieties through haplotype-based breeding.
Editorial Material
Multidisciplinary Sciences
Fred Gould, Richard M. Amasino, Dominique Brossard, C. Robin Buell, Richard A. Dixon, Jose B. Falck-Zepeda, Michael A. Gallo, Ken E. Giller, Leland L. Glenna, Timothy Griffin, Daniel Magraw, Carol Mallory-Smith, Kevin V. Pixley, Elizabeth P. Ransom, David M. Stelly, C. Neal Stewart
Review
Biotechnology & Applied Microbiology
Yongil Yang, Timothy Alexander Chaffin, Amir H. Ahkami, Eduardo Blumwald, Charles Neal Stewart
Summary: Plant-based biosynthesis plays a crucial role in environmental sustainability by reducing greenhouse gas emissions, water pollution, and biodiversity loss. Recent advancements in genetic editing, synthetic promoter development, and single-cell omics have improved our understanding of cell-type-specific mechanisms and enhanced bioproduction.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Robert G. Sears, Stephen B. Rigoulot, Alessandro Occhialini, Britany Morgan, Tayebeh Kakeshpour, Holly Brabazon, Caitlin N. Barnes, Erin M. Seaberry, Brianna Jacobs, Chandler Brown, Yongil Yang, Tayler M. Schimel, Scott C. Lenaghan, C. Neal Stewart
Summary: Nuclear energy is expected to grow in order to meet climate goals, leading to an increased need to detect leakage from nuclear plants and assess their impact on ecosystems. Mechanical sensors currently used to detect gamma radiation have limitations, prompting the development of a plant biosensor that utilizes synthetic biology to detect low-dose ionizing radiation. The radiation phytosensor has shown promising results in detecting gamma radiation exposure and functioning effectively in real-world scenarios.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Mst Shamira Sultana, Mitra Mazarei, Juan Luis Jurat-Fuentes, Tarek Hewezi, Reginald J. J. Millwood, C. Neal Stewart
Summary: Trypsin inhibitors (TIs) in plants play a protective role against herbivores by reducing the biological activity of trypsin. Soybean contains two major TI classes, Kunitz trypsin inhibitor (KTI) and Bowman-Birk inhibitor (BBI). This study investigated the potential role of soybean TIs in plant defense against insects and nematodes. Overexpression of TI genes in soybean and Arabidopsis led to significant increase in trypsin and chymotrypsin inhibitory activities and reduced larvae weight of corn earworm (Helicoverpa zea). However, no differences were observed in soybean cyst nematode (SCN) female index between transgenic and non-transgenic plants. The study highlights the potential applications of TI genes for insect resistance improvement in plants.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Mitra Mazarei, Pratyush Routray, Sarbottam Piya, C. Neal Stewart Jr, Tarek Hewezi
Summary: In this study, a transcriptome analysis of RNA-seq data was performed to select candidate genes associated with root growth and development in soybean. Overexpression of the GmNAC19 and GmGRAB1 transcription factors in transgenic composite plants significantly increased root growth, biomass, and seed yield. Additionally, GmNAC19 overexpression enhanced water stress tolerance in the transgenic plants.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Alexander C. Pfotenhauer, Alessandro Occhialini, Stacee A. Harbison, Li Li, Agnieszka A. Piatek, Curtis R. Luckett, Yongil Yang, C. Neal Stewart, Scott C. Lenaghan
Summary: Genome editing technology has been used to improve staple food crops, such as potato, by increasing their yield. In this study, CRISPR/Cas9 was used to edit the genome of potato and successfully increased the size of starch granules in tubers, resulting in increased yield. The results of this study demonstrate the enormous potential of genome editing technology for crop improvement.
Article
Plant Sciences
Zheng-Jun Guan, Min Zheng, Zhi-Xi Tang, Wei Wei, C. Neal Stewart Jr
Summary: In this study, differential expression of total protein in leaves of two transgenic oilseed rape lines and their non-transgenic parent plant was analyzed. Fourteen differential protein spots were identified, including eleven upregulated and three downregulated proteins, involved in photosynthesis, transporter function, metabolism, protein synthesis, and cell growth and differentiation. These changes in protein spots may be attributed to the insertion of foreign transgenes in transgenic oilseed rape, but transgenic manipulation does not necessarily cause significant changes in the proteomes of oilseed rape.
Article
Plant Sciences
Britany Lauren Morgan, Tayebeh Kakeshpour, Alessandro Occhialini, Gabriella King, Megan Sichterman, Stacee A. Harbison, Stephen B. Rigoulot, Holly Brabazon, Charles Neal Stewart Jr, Scott C. Lenaghan
Summary: The heterologous expression of the Escherichia coli OtsB gene in potato significantly improves the plant's resilience to various stress factors, including heat, photoperiod, herbivory, and competition. This increase in stress tolerance leads to higher tuber yield and overall stability in crop plants.
Editorial Material
Plant Sciences
Wei Wei, Charles Neal Stewart Jr
Article
Biochemistry & Molecular Biology
Yanru Feng, Muhammad Shahedul Alam, Feng Yan, Michael Frei
Summary: Tropospheric ozone has significant effects on the remobilization and allocation efficiency of aboveground biomass and nutrients in cereal crops. Long-term ozone exposure increases straw C:N ratio and affects grain C:N ratio. Grain N concentrations increase significantly under ozone stress, but N yield declines due to grain yield losses. Various indicators of N use efficiency are reduced, indicating reduced N absorption from soil and allocation from vegetative to reproductive organs. Straw C:N ratio is not suitable for predicting wheat productivity. Nitrogen harvest index (NHI) is not affected by ozone stress, but the relationship between harvest index (HI) and NHI is changed by elevated ozone concentration.
Article
Biochemistry & Molecular Biology
Cong Guan, Wei Li, Guoliang Wang, Ruimei Yang, Jinglei Zhang, Jinhong Zhang, Bo Wu, Run Gao, Chunlin Jia
Summary: This study characterized the expression profiles of mRNAs and ncRNAs in switchgrass under drought stress. The up-regulated mRNAs were enriched in starch and sucrose metabolism pathway, while the differentially expressed lncRNAs potentially regulated protein-coding genes. The study also constructed regulatory networks and validated the functionality of the target gene PvSS4 in enhancing drought tolerance.
Article
Biochemistry & Molecular Biology
Juan Nicolas-Espinosa, Lucia Yepes-Molina, Fuensanta Martinez-Bernal, Miriam Fernandez-Pozurama, Micaela Carvajal
Summary: This study aimed to investigate the physiological response of broccoli leaves to abiotic stresses such as salinity and boron toxicity/deficiency. The results showed that the combined stress of salinity and boron deficiency resulted in a significant reduction in plant biomass, and the adaptation mechanisms were associated with water and boron concentration in the leaves. The expression patterns of PIP aquaporins varied among the different stress treatments, and their presence in the plasma membrane and interaction with the lipid environment played potential regulatory roles in facilitating salinity-boron stress adaptation mechanisms.
Review
Biochemistry & Molecular Biology
Wen-Feng Huang, Juan Li, Jian-An Huang, Zhong-Hua Liu, Li-Gui Xiong
Summary: This review examines the seasonal trends of phyllosphere microorganisms in woody and herbaceous plants and explores the factors influencing these trends. While herbaceous and woody plants share some similarities and differences in their phyllosphere microbiomes, further experimental validation is needed.
Article
Biochemistry & Molecular Biology
Changguang Liao, Hui Shen, Zihan Gao, Yunshu Wang, Zhiguo Zhu, Qiaoli Xie, Ting Wu, Guoping Chen, Zongli Hu
Summary: The novel CRF, SlCRF6, plays a crucial role in regulating tomato plant morphology, leaf development, and the accumulation of photosynthetic products.
Article
Biochemistry & Molecular Biology
Alok Madhu, Alok Sharma, Amandeep Kaur, Kashmir Singh, Santosh Kumar Upadhyay
Summary: In this study, 15 TaMDHAR genes were identified in bread wheat and their crucial roles in antioxidants, growth and development, and stress responses were revealed.
Article
Biochemistry & Molecular Biology
Kai Zheng, Yongsheng Cai, Yanying Qu, Lu Teng, Chaoyue Wang, Jie Gao, Quanjia Chen
Summary: In this study, the whole genome identification and bioinformatics analysis of the HCT gene family were performed in G. barbadense. The results showed that the GbHCT114 gene regulates plant trichome development, which is closely related to cotton fiber quality. Gene silencing and overexpression experiments confirmed the important role of GbHCT114 gene in cotton fiber morphology, lignin content, and secondary xylem duct cell wall development. Transcriptomic analysis identified differentially expressed genes associated with lignin synthesis and fiber development.
Review
Biochemistry & Molecular Biology
Tanashvi Seth, Sejal Asija, Shahid Umar, Ravi Gupta
Summary: Plants activate a sophisticated signaling cascade in response to pests and pathogens, with lipids playing a crucial role in mediating these defense responses. Different types of lipids are involved in cell signaling during plant-pathogen interaction and each lipid has specific relevance and contributes to specific signaling cascades. Lipid biosynthetic enzymes, including phospholipases, are involved in the production of defense signaling molecules. Lipids participate in stress signaling by mediating signal transduction, acting as precursors for bioactive molecules, regulating ROS formation, and interacting with phytohormones.
Article
Biochemistry & Molecular Biology
Yangyang Chen, Xiao Wu, Xiaohua Wang, Qionghou Li, Hao Yin, Shaoling Zhang
Summary: 'Nanguo' pears emit a rich aroma when fully ripe, and the important volatile components are the six-carbon compounds derived from the lipoxygenase pathway. This study identified a highly expressed bZIP transcription factor that is induced during the mature stage of 'Nanguo' pears, and demonstrated its regulatory role in fatty acid-derived volatile biosynthesis.
Article
Biochemistry & Molecular Biology
Zhao Geng, Haikuan Dou, Jianguang Liu, Guiyuan Zhao, Linlin Liu, Ning Zhao, Hanshuang Zhang, Yongqiang Wang, Zetong An
Summary: The overexpression of GhFB15 gene decreases the salt tolerance of Arabidopsis plants, while silencing the gene improves the salt tolerance of cotton plants. Furthermore, GhFB15 regulates the accumulation of flavonoids and the levels of ROS.
Article
Biochemistry & Molecular Biology
Linjun Cai, Ancheng Ma, Jiao Lei, Chongsheng He
Summary: METTL4 is identified as a plant DNA 6mA methyltransferase in Arabidopsis thaliana and plays a crucial role in regulating heat stress response.
Article
Biochemistry & Molecular Biology
Zailong Tian, Kun Li, Yaru Sun, Baojun Chen, Zhaoe Pan, Zhenzhen Wang, Baoyin Pang, Shoupu He, Yuchen Miao, Xiongming Du
Summary: Plants have evolved a mechanism called 'stress memory' to survive in various environmental stresses. This study reveals the physiological, biochemical, and molecular mechanisms underlying drought stress memory formation in cotton, highlighting the role of histone modification H3K4me3 in regulating transcriptional memory. It also investigates the intergenerational inheritance of drought stress memory in cotton, providing theoretical guidance for cotton breeding.