Review
Cell Biology
Teruhiko Suzuki, Satoko Takagi, Takahiko Hara
Summary: This article reviews the recent advances in generating conditional knockout clones in mouse embryonic stem cells (ESCs), including two new methods developed in the authors' laboratory and other methods developed by other labs. The advantages, remaining issues, and challenges of each approach are discussed.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Plant Sciences
Hao Chen, Matthew Neubauer, Jack P. Wang
Summary: Gene-editing tools have revolutionized genetic improvement in plants, but the low frequency of homologous recombination (HR) in plant cells poses challenges for achieving efficient plant genome engineering. This review summarizes various strategies, such as targeting DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and considering environmental factors, to increase the frequency of HR in plant cells. By utilizing and refining these strategies, HR-based gene editing may one day become commonplace in plants, as it is in other systems.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Sota Shinkado, Hiroki Saito, Masaya Yamazaki, Shunsuke Kotera, Takayuki Arazoe, Tsutomu Arie, Takashi Kamakura
Summary: Researchers have developed a genome editing technology using the CRISPR/Cas9 system for editing Fusarium species, demonstrating efficient and targeted gene knock-out and editing capabilities. The system can be applied to a broad range of Fusarium species for different research purposes.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Satoshi Kitamura, Shoya Hirata, Katsuya Satoh, Rie Inamura, Issay Narumi, Yutaka Oono
Summary: This study developed a simple system to detect radiation-induced mutations at multiple loci in irradiated Arabidopsis M-1 plants reliably.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Xu Zhao, Yuchen Sun, Xuanzi Sun, Jing Li, Xiaobo Shi, Zhinan Liang, Yuan Ma, Xiaozhi Zhang
Summary: This study demonstrated that AEG-1 depletion enhances radiosensitivity and promotes apoptosis as well as cell cycle arrest in G2 phase of glioma cells. Moreover, RFC5 was identified as the target of AEG-1 and associated with poor prognosis of glioma patients. These findings suggest that AEG-1 may serve as a reliable radiosensitizing target for glioma radiotherapy.
DNA AND CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Felix Wolter, Patrick Schindele, Natalja Beying, Armin Scheben, Holger Puchta
Summary: Research has shown that in plant genomes, single-strand breaks are more common than double-strand breaks, and SSBs induced by CRISPR/Cas9 nickase at a distance are highly mutagenic, leading to genome mutations.
Article
Biochemistry & Molecular Biology
Chunmei Yin, Aiqing Sun, Tongtong Guo, Xuegao Mao, Yuda Fang
Summary: CROWDED NUCLEI proteins associate with γ-H2AX foci and interact with SUPPRESSOR OF NPR1-1 INDUCIBLE 1 and RAD51D to ensure effective DNA damage repair and maintenance of genome stability.
Article
Biotechnology & Applied Microbiology
Garima Jain, Helga Ertesvag
Summary: In this study, the homologous recombination method in Rhodococcus opacus was improved by constructing and evaluating a conjugative, conditional suicide plasmid based on a replicon derived from Corynebacterium glutamicum. The low recombination frequency issue was successfully solved. It was also discovered that mycolic acid is essential for the viability of R. opacus.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Immunology
Sen Wang, Dongfang Li, Fangwei Chen, Weijun Jiang, Wanxin Luo, Guan Zhu, Junlong Zhao, Lan He
Summary: This study successfully developed a genetic modification method for Babesia duncani and validated its feasibility by knocking out a gene. This method will facilitate gene function research and vaccine development of B. duncani.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Editorial Material
Medicine, Research & Experimental
Jonas Schwickert, Franziska M. Zickgraf, Martin R. Sprick
Summary: Ovarian cancer, especially high-grade serous ovarian cancer (HGSOC), has the worst prognosis among all gynecological cancers. RAD51 expression is proposed as a biomarker of platinum resistance in HGSOC patients, which can help in selecting effective therapies for therapy-resistant patients.
EMBO MOLECULAR MEDICINE
(2021)
Article
Biochemical Research Methods
Guangqing Liu, Huiying Wang, Baisong Tong, Yali Cui, Sibylle C. Vonesch, Huina Dong, Dawei Zhang
Summary: Researchers have developed a CRISPR/Cas12e-based genome engineering toolkit that allows precise and traceless genetic engineering in the bacterium Sinorhizobium meliloti 320 (SM320). By optimizing the promoter and using a low copy plasmid, the expression level of CRISPR/Cas12e was adjusted to the low homologous recombination efficiency of SM320, resulting in improved transformation and precision editing efficiencies. Additionally, the accuracy of CRISPR/Cas12eGET was enhanced by deleting the ku gene involved in NHEJ repair in SM320. This advancement will benefit metabolic engineering and basic research on SM320, and provide a platform for developing the CRISPR/Cas system in strains with low homologous recombination efficiency.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Teng-Kuei Huang, Brittney Armstrong, Patrick Schindele, Holger Puchta
Summary: Nicotiana tabacum, a non-food herb, shows potential as a bio-factory for producing medicines, vaccines, or valuable metabolites, but improving genetic tools for targeted genome modifications is crucial. By replacing SpCas9 with other CRISPR/Cas-based nucleases like SaCas9 and ttLbCas12a, targeting the tobacco SuRB gene showed improved efficiencies, suggesting ttLbCas12a as a superior alternative for gene editing in tobacco and other crops.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Thomas Bachelot, Thomas Filleron, Ivan Bieche, Monica Arnedos, Mario Campone, Florence Dalenc, Florence Coussy, Marie-Paule Sablin, Marc Debled, Claudia Lefeuvre-Plesse, Anthony Goncalves, Marie-Ange Mouret Reynier, William Jacot, Benoit You, Philippe Barthelemy, Benjamin Verret, Nicolas Isambert, Xavier Tchiknavorian, Christelle Levy, Jean-Christophe Thery, Tifenn L'Haridon, Jean-Marc Ferrero, Alice Mege, Francesco Del Piano, Etienne Rouleau, Alicia Tran-Dien, Julien Adam, Amelie Lusque, Marta Jimenez, Alexandra Jacquet, Ingrid Garberis, Fabrice Andre
Summary: The study found that single-agent antibodies against PD-L1 as maintenance therapy did not significantly benefit the overall population with metastatic breast cancer, but showed improved overall survival in patients with triple-negative breast cancer. Durvalumab may have better sensitivity in patients with CD274 amplification. Analysis of lymphocyte infiltration and homologous recombination deficiency did not predict sensitivity to durvalumab, warranting further research. Maintenance chemotherapy was more effective than durvalumab in patients with hormone receptor-positive and Her2-negative disease.
Article
Biochemistry & Molecular Biology
Keziah M. Omenge, Florian Ruempler, Subha Suvetha Kathalingam, Alexandra C. U. Furch, Guenter Theissen
Summary: Research has shown that different phytoplasma effector proteins have varying effects on host plants depending on the timing and manner of induction, all interfering with flower development and shoot branching. This suggests functional redundancy among these effector proteins, but also subtle differences that have important implications for plant branching patterns.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Swarnalatha Manickavinayaham, Briana K. Dennehey, David G. Johnson
Summary: RB and E2F proteins collaborate to regulate the cell cycle in eukaryotes and also have important functions in DNA repair. In some organisms, other proteins have taken over the cell cycle regulation function of RB and E2F. Apart from cell cycle regulation, E2F and RB homologs in various organisms also possess non-canonical functions.
Article
Plant Sciences
Nobuko Sumiya
Summary: The study revealed that even in unicellular algae with multiple chloroplasts, there are two mechanisms similar to those in unicellular algae with a single chloroplast to coordinate cell and chloroplast division.
Article
Plant Sciences
Nachiketa Bairagi, Satoru Watanabe, Kaori Nimura-Matsune, Kenya Tanaka, Tatsuhiro Tsurumaki, Shuji Nakanishi, Kan Tanaka
Summary: This study investigates the mechanism of the Hik2-Rre1 two-component system in cyanobacteria, revealing the positive regulation of signaling and phosphorylation by Hik34, while the redox status of PQ does not directly influence Rre1 phosphorylation. A model for Hik2-dependent Rre1 phosphorylation was proposed based on the findings.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biology
Yu Kanesaki, Mitsuo Ogura
Summary: The addition of glucose enhanced the expression of extra-cytoplasmic function sigma factors in Bacillus subtilis, and regulatory factors including YqfO, CshA, and YlxR were identified. Further analysis revealed YqfO functions as a global regulator in B. subtilis.
BMC RESEARCH NOTES
(2021)
Article
Microbiology
Naoya Kataoka, Minenosuke Matsutani, Nami Matsumoto, Misuzu Oda, Yuki Mizumachi, Kohei Ito, Shuhei Tanaka, Yu Kanesaki, Toshiharu Yakushi, Kazunobu Matsushita
Summary: Acetic acid bacterium Komagataeibacter medellinensis NBRC 3288 was adapted to higher growth temperatures through experimental evolution, resulting in improved growth and fermentation ability. The adapted strains exhibited changes in cell morphology.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Baifeng Zhou, Hiroki Shima, Kazuhiko Igarashi, Kan Tanaka, Sousuke Imamura
Summary: In this study, researchers identified a negative domain of CmMYB1, a transcription factor involved in nitrogen assimilation in plants. They found that this negative domain, along with a protein called CmNDB1, regulates the function of CmMYB1 under nitrogen-repleted conditions. These findings provide important insights into the regulatory mechanisms of nitrogen assimilation in C. merolae.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Sornsiri Pattanakittivorakul, Tatsuya Tsuzuno, Tomoyuki Kosaka, Masayuki Murata, Yu Kanesaki, Hirofumi Yoshikawa, Savitree Limtong, Mamoru Yamada
Summary: This study aims to develop multi-stress tolerant strains of Kluyveromyces marxianus through a novel evolutionary adaptation procedure called RLCGT, and to increase ethanol production at high temperatures. Four adapted strains showed increased tolerance to ethanol and other stress factors, as well as higher ethanol production at high temperatures. Possible mechanisms of stress tolerance in adapted strains were discussed based on genome and transcriptome analyses.
Article
Multidisciplinary Sciences
Sanghun Baek, Sousuke Imamura, Takeshi Higa, Yumi Nakai, Kan Tanaka, Masato Nakai
Summary: This study reveals the involvement of similar translocon complexes in chloroplast protein import in red algae, and identifies a class of GTP-binding proteins that may function as plastid targeting factors in Rhodophyta.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Devi B. Effendi, Toshio Sakamoto, Shuji Ohtani, Koichiro Awai, Yu Kanesaki
Summary: Cyanobacteria strain Nostoc sp. SO-36, isolated from Antarctica, was found to be psychrotolerant and filamentous when grown at 30 degrees Celsius, with the ability to grow diazotrophically. At 10 degrees Celsius, the cells showed reduced growth, smaller size, and increased aggregation with extracellular polymeric substrates (EPSs) to protect from UV damage. The complete genome sequencing revealed the presence of one main chromosome with plasmids and conserved genes for EPS biosynthesis.
JOURNAL OF PLANT RESEARCH
(2022)
Article
Multidisciplinary Sciences
Shunsuke Hirooka, Takeshi Itabashi, Takako M. Ichinose, Ryo Onuma, Takayuki Fujiwara, Shota Yamashita, Lin Wei Jong, Reiko Tomita, Atsuko H. Iwane, Shin-Ya Miyagishima
Summary: This study discovered that Galdieria exhibits a sexual life cycle, alternating between cell-walled diploid and cell wall-less haploid, while also having the ability for asexual reproduction. By studying the genome and transcriptome data of Galdieria, key transcription factors involved in cell transition and development were identified. Additionally, four actin genes were found to have different functions in motility and cytokinesis between the haploid and diploid stages, reflecting ancestral roles of actin. Furthermore, photosynthesis-deficient mutants were generated for potential industrial pigment production. Overall, these findings enhance our understanding of algae and plant evolution, as well as the industrial use of microalgae.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Keisuke Yoshida, Yuichi Yokochi, Kan Tanaka, Toru Hisabori
Summary: To ensure efficient photosynthesis, the regulation of chloroplast proteins under changing light conditions is crucial. This study investigates the biological importance of the ferredoxin/thioredoxin pathway in activating chloroplast proteins. By using gene editing technology, Arabidopsis mutant plants with a completely defective ferredoxin/thioredoxin pathway were created, resulting in severe growth inhibition and loss of ability to reduce several redox-sensitive proteins in chloroplast stroma. The study provides important insights into the operation of the chloroplast redox-regulatory system in vivo.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Takafumi Maruyama, Satoru Sumi, Mitsuru Kobayashi, Teppei Ebuchi, Yu Kanesaki, Hirofumi Yoshikawa, Kenji Ueda, Hideaki Takano
Summary: PmlR2 is shown to be an effector protein of PmSB-LOV. The direct association between PmSB-LOV and PmlR2 inhibits the DNA-binding activity of PmlR2, enabling transcription of light-inducible promoters.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Masatoshi Miyakoshi, Teppei Morita, Asaki Kobayashi, Anna Berger, Hiroki Takahashi, Yasuhiro Gotoh, Tetsuya Hayashi, Kan Tanaka
Summary: Glutamine synthetase (GS) is a crucial enzyme for nitrogen assimilation under nitrogen limiting conditions. This study reveals that an sRNA GlnZ and a transcriptional regulator Nac both play roles in repressing the expression of the sucA component of 2-oxoglutarate dehydrogenase, thereby controlling the metabolic flow in response to nitrogen availability.
Article
Biochemistry & Molecular Biology
Rajalakshmi Balasubramanian, Koichi Hori, Takayuki Shimizu, Shingo Kasamatsu, Kae Okamura, Kan Tanaka, Hideshi Ihara, Shinji Masuda
Summary: The compositions and activities of bacterial flora in the gastrointestinal tract play a significant role in the metabolism, health, and disease of host humans and animals. The switching mechanism between aerobic and anaerobic growth of enteric bacteria is important for preventing reactive oxygen species production and antibiotic tolerance. YgaV, a sulfide-responsive transcription factor, controls anaerobic respiratory gene expression and H2O2 scavenging in Escherichia coli, maintaining redox homeostasis, ROS scavenging, and antibiotic tolerance.
Article
Plant Sciences
Akito Machida, Kumiko Kondo, Ken-ichi Wakabayashi, Kan Tanaka, Toru Hisabori
Summary: In this study, the importance of the amino acid at position 252 across cyanobacteria was elucidated by introducing amino acid substitutions in Synechocystis sp. PCC 6803. The results showed that the specific volume of this amino acid is crucial for maintaining cell growth and is related to enzyme complex formation.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Hazuki Hasegawa, Ikki Kobayashi, Nachiketa Bairagi, Satoru Watanabe, Kan Tanaka
Summary: This study investigated the mechanism of the Hik2-Rre1 system in high-temperature shift and redox stress and found that overexpression of dnaK2 can alleviate these responses. The results suggest a negative feedback mechanism mediated by DnaK2 to maintain cellular homeostasis.
PLANT AND CELL PHYSIOLOGY
(2023)
