Review
Biochemistry & Molecular Biology
Magdalena Hryhorowicz, Daniel Lipinski, Joanna Zeyland
Summary: The bacteria-derived CRISPR/Cas system is a versatile tool for genome engineering, with wide applications in various fields. However, challenges like immunological reactions and off-target effects remain. This review discusses the current classification of CRISPR systems, new genome-editing technologies, recent applications, as well as limitations, ethical issues, and challenges associated with the CRISPR/Cas system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Issei Nakazato, Miki Okuno, Chang Zhou, Takehiko Itoh, Nobuhiro Tsutsumi, Mizuki Takenaka, Shin-Ichi Arimura
Summary: In addition to their role in respiration, mitochondria in land plants contain important genes whose functions and regulations are not fully understood. Until recently, it has been challenging to analyze and improve these genes due to the lack of methods for stably modifying plant mitochondrial genomes. However, the use of mitochondria-targeting transcription activator-like effector nucleases (mitoTALENs) has provided a breakthrough in gene disruption without causing major changes in genome structure. This study demonstrates the successful use of mitochondria-targeting TALEN-based cytidine deaminase to substitute targeted base pairs in plant mitochondrial genomes, highlighting the potential for precise genetic modifications in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Tao Yao, Guoliang Yuan, Haiwei Lu, Yang Liu, Jin Zhang, Gerald A. Tuskan, Wellington Muchero, Jin-Gui Chen, Xiaohan Yang
Summary: The genus Populus is widely used for various purposes and has become a desirable crop for biofuel production and research. Modern biotechnologies, including CRISPR/Cas9, have been applied to improve its genetic and genomic traits. In this study, CRISPRa and CBE technologies were successfully used for gene expression regulation and precise gene engineering in two Populus species.
HORTICULTURE RESEARCH
(2023)
Review
Plant Sciences
K. T. Ravikiran, R. Thribhuvan, Seema Sheoran, Sandeep Kumar, Amar Kant Kushwaha, T. V. Vineeth, Manisha Saini
Summary: This review discusses the use of genome editing to alter the quality traits in important crops and the challenges faced in maintaining the crop products' quality. Improving product quality is as important as high yield for consumer acceptance and end use. Conventional plant breeding approaches have achieved significant progress, but at a slower rate. To keep up with changing consumer tastes and industry demands, these efforts need to be supplemented with biotechnological tools. Genome editing, particularly with the CRISPR/Cas9 system, has revolutionized trait manipulation and has been applied in various crops for desirable modifications in quality attributes.
Article
Biochemistry & Molecular Biology
Qiupeng Lin, Zixu Zhu, Guanwen Liu, Chao Sun, Dexing Lin, Chenxiao Xue, Shengnan Li, Dandan Zhang, Caixia Gao, Yanpeng Wang, Jin-Long Qiu
Summary: MAD7 is a novel CRISPR-Cas nuclease that can be used for plant genome editing, recognizing T-rich PAM sequences. By developing variants and additional systems, the targeting range and editing efficiency of MAD7 can be enhanced, and it performs well in multiplex gene editing.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Review
Plant Sciences
Niaz Ahmad, Samia Fatima, Muhammad Aamer Mehmood, Qamar U. Zaman, Rana Muhammad Atif, Weijun Zhou, Mehboob-ur Rahman, Rafaqat Ali Gill
Summary: CRISPR-mediated genome editing is a powerful tool for targeted mutations, but limited to model crops with annotated genomes. Important crops like wheat, cotton, rapeseed-mustard, and potato have complex polyploid genomes, hindering progress. Excellent work on Brassica crops shows potential for improving other polyploid crops. This review highlights key examples and considerations for deploying CRISPR-mediated genome editing in other polyploid crops.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Wenliang Hao, Wenjing Cui, Feiya Suo, Laichuang Han, Zhongyi Cheng, Zhemin Zhou
Summary: In this study, a genomic diversification platform was constructed using CRISPR-ABE8e-CDA-nCas9 technology to rapidly evolve bacterial chassis. The platform allows for adjustable conversion efficiency and editable window, enabling editing of any pre-defined genomic loci and generating a diverse repertoire of genomic sequence mutants.
Review
Biotechnology & Applied Microbiology
Jacob S. Antony, John M. Hinz, John J. Wyrick
Summary: The versatile CRISPR-Cas genome editing technology has become a popular tool for research and biotechnology. In this article, the applications and challenges of using CRISPR genome editing in Saccharomyces cerevisiae are discussed.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Zhanglin Lin, Huanhuan Li, Lan He, Yanyun Jing, Marco Pistolozzi, Tingting Wang, Yanrui Ye
Summary: This study demonstrates the efficient genome editing of Pseudomonas aeruginosa using FnCas12a, achieving gene deletion, insertion, and replacement with high efficiency, including the deletion of large DNA fragments and serial deletion of duplicate gene clusters. This work provides a useful and complementary addition to the genome engineering toolbox for the study of P. aeruginosa biology and physiology.
Article
Biochemical Research Methods
Yicheng Long, Thomas R. Cech
Summary: The use of CRISPR genome editing has greatly advanced mutagenesis studies in human iPSCs, enabling precise gene manipulation for studying physiological functions, disease modeling, drug screening, and therapeutic development. However, comprehensive strategic designs are necessary to consider potential side effects of CRISPR editing. This study presents novel and highly efficient strategies for introducing mutations in human iPSCs, including step-by-step protocols and examples of successful application in different cell types.
Article
Biology
Thomas Thumberger, Tinatini Tavhelidse-Suck, Jose Arturo Gutierrez-Triana, Alex Cornean, Rebekka Medert, Bettina Welz, Marc Freichel, Joachim Wittbrodt
Summary: Precise and targeted genome editing using CRISPR/Cas9 is crucial for basic research and translational applications. Researchers have developed a method called "hei-tag" that enhances the efficiency of Cas9 and base editors by adding a myc-tag linked to an optimized NLS. This method improves editing efficiency and is effective in various model and non-model systems.
Review
Biochemistry & Molecular Biology
Siyoon Shin, Seeun Jang, Donghyun Lim
Summary: CRISPR-based genome-editing technologies have revolutionized various fields, but face challenges such as off-target DNA cleavages. Small molecules can be important tools to address these issues and enable precise control of CRISPR systems.
Review
Medicine, Research & Experimental
Asma Ghaemi, Elnaz Bagheri, Khalil Abnous, Seyed Mohammad Taghdisi, Mohammad Ramezani, Mona Alibolandi
Summary: The prokaryotic CRISPR-Cas systems serve as a revolutionary genome editing tool for modifying, visualizing, and identifying DNA and RNA sequences in live cells of various species. Besides genome editing, the DNA-targeting modifications by CRISPR-Cas offer opportunities for diagnosis, therapy, and genetic disorders investigation. Preclinical studies and CRISPR-Cas9-based therapeutics may encounter challenges, but there is potential for its development in cancer therapy.
Review
Plant Sciences
Dragana Miladinovic, Dulce Antunes, Kubilay Yildirim, Allah Bakhsh, Sandra Cvejic, Ankica Kondic-Spika, Ana Marjanovic Jeromela, Hilde-Gunn Opsahl-Sorteberg, Antonios Zambounis, Zoe Hilioti
Summary: Genome editing technologies have revolutionized plant biology, offering solutions to challenges in plant architecture, food security, nutrient content, environmental adaptation, disease resistance, and production of plant-based materials. The efficiency of site-specific genome editing in plants, with a powerful toolbox of molecular scissors, allows for tailored approaches to plant breeding strategies. The synergies of genome editing with other technological platforms are leading to an exciting era of post-genomic plant research and production, demonstrating the importance of science, technology, and tools in meeting current and future challenges in agriculture.
PLANT CELL REPORTS
(2021)
Article
Microbiology
Sara M. Klose, Nadeeka Wawegama, Fiona M. Sansom, Marc S. Marenda, Glenn F. Browning
Summary: In this study, the researchers used the Mycoplasma gallisepticum CRISPR/Cas system to targeted mutate a nuclease gene, providing insights into the role of this gene and revealing the effectiveness of the system in interfering with gene functions.
VETERINARY MICROBIOLOGY
(2022)
Article
Plant Sciences
Akiyoshi Yoda, Narumi Mori, Kohki Akiyama, Mayu Kikuchi, Xiaonan Xie, Kenji Miura, Kaori Yoneyama, Kanna Sato-Izawa, Shinjiro Yamaguchi, Koichi Yoneyama, David C. Nelson, Takahito Nomura
Summary: The LGS1 gene in sorghum is involved in the synthesis of substances that affect seed germination in root parasitic plants, proposing a novel SL biosynthetic pathway involving sulfo group catalysis and cyclization of 18-OH-CLA.
Article
Biochemistry & Molecular Biology
Islam M. Y. Abdellatif, Shaoze Yuan, Renhu Na, Shizue Yoshihara, Haruyasu Hamada, Takuya Suzaki, Hiroshi Ezura, Kenji Miura
Summary: Heat stress is a prevalent negative factor affecting plant growth and development. In this study, the response of tomato phyA and phyB1B2 mutants to high temperatures at different growth stages was investigated. The mutants showed tolerance to heat stress during the seed germination and vegetative growth stages, while their response during the flowering stage was dependent on the duration of heat exposure. The vegetative growth stage demonstrated the highest tolerance, with increased membrane stability and water preservation achieved through stomatal closure regulation. Additionally, both mutants upregulated heat-responsive genes and the phyA mutant showed enhanced proline levels and lower malondialdehyde accumulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biotechnology & Applied Microbiology
Shohei Nosaki, Ken Hoshikawa, Hiroshi Ezura, Kenji Miura
Summary: Production of recombinant proteins is crucial for academic research and various industries. Plant-based expression systems offer cost-effective, scalable, and sustainable solutions for producing high-quality proteins. The development of transient expression systems has significantly improved efficiency and yield in plant-based production of recombinant proteins.
PLANT BIOTECHNOLOGY
(2021)
Article
Plant Sciences
Sachiko Kashojiya, Yu Lu, Mariko Takayama, Hiroki Komatsu, Luyen Hieu Thi Minh, Keiji Nishida, Kenta Shirasawa, Kenji Miura, Satoko Nonaka, Jun-ichiro Masuda, Akihiko Kondo, Hiroshi Ezura, Tohru Ariizumi
Summary: Target-AID is a CRISPR/Cas9-based genome-editing tool that confers base-editing capability on the Cas9 system. In this study, we successfully applied the Target-AID system to edit negative regulators of the plant hormone signaling pathway in tomatoes, demonstrating its potential for molecular breeding in tomato crops.
HORTICULTURE RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Lalhaba Oinam, Ryoma Hayashi, Keiko Hiemori, Kayo Kiyoi, Kimiyo Sage-Ono, Kenji Miura, Michiyuki Ono, Hiroaki Tateno
Summary: In this study, recombinant Concanavalin A (ConA) was successfully produced in lettuce using the Agrobacterium tumefaciens-mediated transient expression system. The recombinant ConA showed similar glycan-binding specificity and affinity to the native ConA. This study provides a new approach for the recombinant expression of ConA.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Fumika Misawa, Momoyo Ito, Shohei Nosaki, Hanna Nishida, Masahiro Watanabe, Takamasa Suzuki, Kenji Miura, Masayoshi Kawaguchi, Takuya Suzaki
Summary: In this study, researchers discovered that LjNRT2.1 plays a crucial role in the LjNLP1-LjNLP4 signaling pathway by controlling nitrate uptake/transport to regulate nodulation. LjNLP1 and LjNRT2.1 are both important regulators in nodulation. These findings reveal a plant strategy in regulating nitrogen acquisition.
Article
Food Science & Technology
Thi Bao Chau Bui, Mito Kokawa, Thu Tra Tran, Shohei Nosaki, Kenji Miura, Yutaka Kitamura
Summary: This study presents a new extraction method called simultaneous stone-milling and extraction (SME) that enables efficient one-step extraction of hard-to-crush materials. Compared to other extraction methods, SME extracts contain comparable or higher concentrations of general and specific bioactive compounds, contributing to the advancement of plant extraction and plant-derived phytochemical studies.
INNOVATIVE FOOD SCIENCE & EMERGING TECHNOLOGIES
(2022)
Article
Plant Sciences
Akira Yata, Shohei Nosaki, Akiyoshi Yoda, Takahito Nomura, Kenji Miura
Summary: In this study, we demonstrated the successful production of a large amount of 4-deoxyorobanchol (4DO) in tobacco leaves using a transient expression system. We also found that the stability of 4DO can be maintained in dried leaves for an extended period of time.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Jutapat Romsuk, Shuhei Yasumoto, Ery Odette Fukushima, Kenji Miura, Toshiya Muranaka, Hikaru Seki
Summary: This study established a method for producing oleanolic acid in substantial quantities via heterologous expression of pathway enzymes in Nicotiana benthamiana, and demonstrated the advantage of the Tsukuba system. The production yield of oleanolic acid and other triterpenoids was significantly improved compared to previous reports.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Islam M. Y. Abdellatif, Shaoze Yuan, Shizue Yoshihara, Takuya Suzaki, Hiroshi Ezura, Kenji Miura
Summary: The study finds that PHY photoreceptors play an important role in the drought response of tomato plants. The mutant lines of PHYA and PHYB in tomatoes show enhanced drought tolerance through reduced membrane damage, increased expression of ROS scavenger genes, inhibition of H2O2 accumulation, and enhanced antioxidant activities. These mutants also exhibit higher expression levels of aquaporins and higher relative water content, indicating improved hydration status under drought stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Sheng Wu, Anqi Zhou, Kozue Hiugano, Akiyoshi Yoda, Xiaonan Xie, Kenji Yamane, Kenji Miura, Takahito Nomura, Yanran Li
Summary: We identified a strigol synthase (cytochrome P450 711A enzyme) in the Prunus genus through gene screening and confirmed its unique catalytic activity. We reconstructed the biosynthetic pathway of strigol in Nicotiana benthamiana and reported the total biosynthesis of strigol from xylose in the Escherichia coli-yeast consortium, enabling large-scale production.
Article
Plant Sciences
Akiyoshi Yoda, Xiaonan Xie, Kaori Yoneyama, Kenji Miura, Christopher S. P. McErlean, Takahito Nomura
Summary: Seeds of root parasitic plants are induced to germinate by strigolactones exudated from host roots. The biosynthesis pathway of 5-deoxystrigol, a major strigolactone, has not been fully understood. In this study, researchers identified Sobic.005G213500 as a regulator that affects the stereoselective biosynthesis of 5-deoxystrigol and provides insights into how different strigolactones are produced to combat parasitic weed infestations.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Biodiversity Conservation
Takatoshi Wakabayashi, Megumi Nakayama, Yurie Kitano, Masato Homma, Kenji Miura, Hirosato Takikawa, Masaharu Mizutani, Yukihiro Sugimoto
Summary: Parasitic witchweeds (Striga species) are a serious threat to food security in Africa, attacking cereal grains and legumes. The chemicals released from host roots, known as germination stimulants, mainly strigolactones (SLs), were first identified in cotton root exudates over 50 years ago. This discovery of a complete biosynthesis pathway for strigolactones in cotton has the potential to enhance our understanding of SL-mediated rhizosphere interactions and improve cotton's effectiveness as a trap crop.
PLANTS PEOPLE PLANET
(2023)
Article
Plant Sciences
Shohei Nosaki, Nobutaka Mitsuda, Shingo Sakamoto, Kazuki Kusubayashi, Ayumi Yamagami, Yuqun Xu, Thi Bao Chau Bui, Tohru Terada, Kenji Miura, Takeshi Nakano, Masaru Tanokura, Takuya Miyakawa
Summary: The transcription factor BIL1/BZR1 is involved in regulating gene expression in response to brassinosteroid hormones in plants. This study reveals that BIL1/BZR1 can repress the transcription of certain genes by binding tightly to specific regions on the DNA. Furthermore, the study demonstrates that BIL1/BZR1 achieves selectivity for particular DNA sequences by reading the shape of the DNA rather than directly recognizing the nucleobases. These findings provide valuable insights into the molecular and structural basis of transcriptional repression by BIL1/BZR1 and its role in gene regulation.
Review
Biochemistry & Molecular Biology
Xiaohan Li, Siyan Xu, Martina Bianca Fuhrmann-Aoyagi, Shaoze Yuan, Takeru Iwama, Misaki Kobayashi, Kenji Miura
Summary: Global warming and climate change have had a significant impact on plant growth and food production. To ensure sustainable crop yields, it is crucial to minimize these effects. The use of genome-editing technologies, such as CRISPR/Cas9 and TALENs, has recently gained attention in plant breeding for genetic modification. These technologies have the potential to enhance our understanding of gene function and improve crops' tolerance to abiotic stresses.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Plant Sciences
Wanli You, Jinglin Zhang, Xueyin Ru, Feng Xu, Zhengguo Wu, Peng Jin, Yonghua Zheng, Shifeng Cao
Summary: This study investigated the effect of calcium chloride (CaCl2) treatment on GABA accumulation in fresh-cut cantaloupe and the underlying mechanisms. The results showed that CaCl2 treatment increased GABA content and the activities of GAD and SSADH enzymes, while reducing glutamate content and GABA-T activity. Additionally, CaCl2 treatment upregulated the expressions of CmCML11 and CmCAMTA5, as well as several GABA shunt genes, through the transcriptional activation by CmCAMTA5. Furthermore, the interaction between CmCML11 and CmCAMTA5 enhanced the transcriptional activation of GABA shunt genes. Overall, this study reveals that CaCl2 treatment promotes GABA accumulation in fresh-cut cantaloupe through the combined effect of CmCML11 and CmCAMTA5 in regulating the expressions of GABA shunt genes.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2024)
Article
Plant Sciences
Min Wang, Yupeng Wang, Xiaohui Wang, Guangwei Wei, Huiyi Yang, Xi Yang, Tinghai Shen, Huijie Qu, Sheng Fang, Ziming Wu
Summary: This study identified the high nitrogen use efficiency (NUE) black sesame variety 17-156 and analyzed its underlying physiological and molecular mechanisms. The results showed that 17-156 possesses a sophisticated nitrogen metabolizing machinery to uptake and assimilate higher quantities of inorganic nitrogen, simultaneously improving carbon metabolism and growth. Many important genes were up-regulated in 17-156 under high nitrogen condition. Additionally, 38 potential candidate genes were identified for future studies to improve sesame's NUE. These findings provide valuable resources for understanding the regulatory network of nitrogen metabolism and developing sesame cultivars with improved NUE.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2024)
Article
Plant Sciences
He Dong, Chongmei Xu, Chengtao Zhang, Li Zhang, Yaqin Yao, Suiqi Zhang
Summary: The study found that short cells in maize leaves not only improve leaf mechanical support and photosynthetic performance, enhance drought resistance, but also participate in stomatal regulation.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2024)
Article
Plant Sciences
Na Liu, Wenyan Shang, Mengxin Guan, Jibin Xiao, Guangxiang Tian, Baozhan Ma, Wenjing Shang, Xu Li, Shijia Zhao, Chuang Li, Kun Cheng, Wenming Zheng
Summary: This study cloned the full-length cDNA sequence of TaSPX3 gene in wheat and found that TaSPX3 responds to low phosphorus stress in multiple wheat genotypes. Overexpressing TaSPX3 can alleviate phosphorus deficiency symptoms and promote plant growth in Arabidopsis. The study also revealed the interaction of TaSPX3 with other genes related to the phosphorus starvation signaling pathway.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2024)
Article
Plant Sciences
Kongyuan Wu, Lizhen Wang, Zihan Wu, Ziqing Liu, Zengfei Li, Jun Shen, Shengjie Shi, Hong Liu, Christopher Rensing, Renwei Feng
Summary: Selenium (Se) can reduce uptake and translocation of cadmium (Cd) in plants by regulating root morphology. This study investigated the effects of Se(IV) on root exudates, root morphology, root endogenous hormones, and Cd uptake efficiency in rice under Cd stress. The results showed that Se(IV) significantly reduced Cd concentrations in shoots and roots, and decreased Cd uptake efficiency via root hairs. Se(IV) also affected root morphology, root exudates, and the synthesis of hormones like IAA and JA. However, transcriptome analysis revealed no upregulated differentially expressed genes (DEGs) in IAA synthesis.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2024)
Article
Plant Sciences
Di Wang, Huaifang Zhang, Xuefei Hu, Haizhen Zhang, Shuang Feng, Aimin Zhou
Summary: This study identified a cell number regulator gene called SlCNR8 in willow, which enhances resistance to trace metals in transgenic poplar seedlings. SlCNR8 reduces Cd uptake and accumulation, and can be used as a candidate gene for genetic improvement of phytostabilisation of trace metals.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2024)
