Article
Biochemistry & Molecular Biology
Julia Legen, Sara Duehnen, Anton Gauert, Michael Goetz, Christian Schmitz-Linneweber
Summary: Human papillomavirus (HPV) infection is the main cause of cervical cancer, and vaccination has been successful in controlling it. However, vaccination coverage, especially in developing countries, is not universal. Expressing the HPV L1 protein in plants could provide a cost-effective solution. Efforts have been made to produce the L1 protein in plants, but manipulating chloroplast gene expression has proven challenging.
Article
Plant Sciences
Hao Wang, Ning Li, Hang Li, Songjie Zhang, Xiaoquan Zhang, Xiaoxiao Yan, Zhaojun Wang, Yongxia Yang, Songtao Zhang
Summary: In this study, researchers found that overexpression of the NtGCN2 gene improves the drought tolerance of tobacco plants. Transcriptome analysis revealed that NtGCN2 may regulate plant drought resistance by modulating proline accumulation, reactive oxygen species scavenging, and stomatal closure. These findings suggest the potential application of the NtGCN2 gene in genetic modification for crop drought tolerance.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Galina N. Raldugina, Lilia R. Bogoutdinova, Olga V. Shelepova, Vera V. Kondrateva, Ekaterina V. Platonova, Tatiana L. Nechaeva, Varvara V. Kazantseva, Pyotr V. Lapshin, Helen I. Rostovtseva, Tatiana S. Aniskina, Pyotr N. Kharchenko, Natalia V. Zagoskina, Alexander A. Gulevich, Ekaterina N. Baranova
Summary: Transgenic tobacco plants overexpressing the choline oxidase gene showed increased resistance to salinity. However, under normal conditions, these transgenic plants exhibited characteristics of juvenilization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Liqun Ma, Ke Cheng, Jinyan Li, Zhiqi Deng, Chunjiao Zhang, Hongliang Zhu
Summary: In recent years, significant progress has been made in understanding the functional roles of plant glycine-rich RNA-binding proteins (GR-RBPs) in development and stress responses. However, many aspects of their function, RNA targeting, interaction with proteins, and consequences of RNA processes are still not well understood. Recent findings have shed light on new roles and actions of GR-RBPs in target RNA metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Rui Shi, Sheri P. Kernodle, Tyler M. Steede, Ramsey S. Lewis
Summary: Nitrogen physiology plays an important role in tobacco growth and yield, and the mutant genes Yb-1 and Yb-2 may have negative effects on nitrogen utilization and alkaloid levels. Overexpression of the Yb-1 gene can benefit mutant genotypes but not wild-type genotypes. Transcriptome analysis reveals that altered expression of Yb-1 can affect metabolic pathways related to carbon and nitrogen metabolism.
Article
Plant Sciences
Galina N. Raldugina, Sergey V. Evsukov, Liliya R. Bogoutdinova, Alexander A. Gulevich, Ekaterina N. Baranova
Summary: In this study, transgenic tobacco lines overexpressing the bacterial enzyme choline oxidase gene were evaluated for their response to NaCl stress. The results showed that these transgenic plants had better regeneration and survival ability under high salt stress.
Article
Plant Sciences
Sheri P. Kernodle, Sydney Webb, Tyler M. Steede, Ramsey S. Lewis
Summary: Reducing the expression of two gene families in tobacco can result in ultra-low nicotine accumulation. Current commercial tobacco cultivars do not meet the proposed standard of nicotine levels below 0.4 mg g(-1). However, this study successfully lowered nicotine levels below the standard by using RNAi technology and induced mutations.
PLANT CELL REPORTS
(2022)
Article
Plant Sciences
Kumiko Takagi, Kosuke Tasaki, Hirotomo Komori, Shinpei Katou
Summary: Salicylic acid (SA) plays a key role in plant resistance to pathogens, and the transcription factors CBP60g and SARD1 are involved in its synthesis. The mechanisms underlying SA synthesis in tobacco remain unknown, but the genes NtCBP60g and NtSARD1 are associated with SA accumulation induced by wounding. Furthermore, NtCBP60g and NtSARD1 regulate the expression of hypersensitivity-related genes and are required for elicitor-induced SA synthesis.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Genetics & Heredity
Xiaodong Xie, Jingjing Jin, Chen Wang, Peng Lu, Zefeng Li, Jiemeng Tao, Peijian Cao, Yalong Xu
Summary: In this study, researchers identified a large number of lncRNAs in tobacco, which play important roles in the nicotine biosynthesis pathway. These lncRNAs showed distinct features compared to protein-coding genes in terms of exon number, sequence length, A/U content, and tissue-specific expression pattern. The study also predicted the potential regulatory effects of lncRNAs on protein-coding genes and discovered their involvement in the nicotine pathway.
FRONTIERS IN GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Wenbo Xu, Shengchun Li, Ralph Bock, Jiang Zhang
Summary: Inducible expression systems can help balance high-level transgene expression and its effects on plant growth. This study presents a temperature-inducible expression system for plastids, which can efficiently induce the expression of green fluorescent protein (GFP) in plastids under elevated temperatures in a light-dependent process. Introducing a T7 RNA polymerase-based expression system further enhances the temperature-dependent accumulation of GFP.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Yufeng Liang, Sydney Willey, Yu-Chieh Chung, Yi-Meng Lo, Shiqin Miao, Sarah Rundell, Li-Chun Tu, Dennis Bong
Summary: FLURIL tagging method utilizes fluorogenic bPNA probes to label nucleic acids in fixed and live cells, while maintaining a light molecular footprint and compatibility with existing methods.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Mengmeng Duan, Mei Zong, Ning Guo, Shuo Han, Guixiang Wang, Liming Miao, Fan Liu
Summary: This study identified 19 BoiRBG genes in broccoli through genome-wide analysis and revealed their evolution and expression patterns. The expansion of the BoiRBG gene family was primarily driven by genome duplication and tandem duplication events, and these genes were up-regulated under different abiotic stress conditions, playing different roles.
Article
Biotechnology & Applied Microbiology
Yinchao Zhang, Xiaoling Qu, Xiuchun Li, Min Ren, Ying Tong, Xiuming Wu, Yangyang Sun, Fengyan Wu, Aiguo Yang, Shuai Chen
Summary: This study explored the potential functions of anthocyanins and anthocyanin-related regulatory factors in resistance to low-temperature by conducting transcriptome analysis and classification analysis. The results showed that key enzymes in the late stage of anthocyanin metabolism were significantly up-regulated in the mutant. Several genes related to transcription factors, phytohormones, and osmoregulators were also differentially expressed. WGCNA analysis identified hub genes in the flavonoid pathway for low-temperature stress resistance.
Article
Multidisciplinary Sciences
Jianyu An, Yihan Liu, Jiajun Han, Can He, Min Chen, Xiaobo Zhu, Weimin Hu, Wenjian Song, Jin Hu, Yajing Guan
Summary: This study revealed the transcriptional mechanism of seed deterioration in tobacco and identified key genes involved. The application of key genes in rice confirmed the feasibility of the multiomics method, providing guidance for precisely delaying seed deterioration in other species of seed research.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Biology
Juan Carlos Rengifo-Gonzalez, Krystel El Hage, Marie-Jeanne Clement, Emilie Steiner, Vandana Joshi, Pierrick Craveur, Dominique Durand, David Pastre, Ahmed Bouhss
Summary: The study reveals that the tandem RNA recognition motifs of TDP-43 cooperatively bind to long GU-repeats, maintaining its solubility. The cooperative binding of TDP-43 to mRNA is crucial for preserving its solubility in the nucleus and miscibility in cytoplasmic stress granules.
Article
Biochemical Research Methods
Clara L. van Emmerik, Ivana Gachulincova, Vincenzo R. Lobbia, Mark A. Daniels, Hans A. Heus, Abdenour Soufi, Frank H. T. Nelissen, Hugo van Ingen
ANALYTICAL BIOCHEMISTRY
(2020)
Article
Microbiology
Wouter Elings, Anamika Gaur, Anneloes J. Blok, Monika Timmer, Hugo van Ingen, Marcellus Ubbink
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2020)
Correction
Medicine, Research & Experimental
Kaian Teles, Vinicius Fernandes, Isabel Silva, Manuela Leite, Cesar Grisolia, Vincenzo R. Lobbia, Hugo van Ingen, Rodrigo Honorato, Paulo Lopes-de-Oliveira, Werner Treptow, Guilherme Santos
BIOMEDICINE & PHARMACOTHERAPY
(2020)
Article
Medicine, Research & Experimental
Kaian Teles, Vinicius Fernandes, Isabel Silva, Manuela Leite, Cesar Grisolia, Vincenzo R. Lobbia, Hugo van Ingen, Rodrigo Honorato, Paulo Lopes-de-Oliveira, Werner Treptow, Guilherme Santos
BIOMEDICINE & PHARMACOTHERAPY
(2020)
Article
Chemistry, Multidisciplinary
Shahul Dharjath Hameed, Gabrielle B. A. van Tilburg, Remco Merkx, Dennis Flierman, Hans Wienk, Farid El Oualid, Kay Hofmann, Rolf Boelens, Huib Ovaa
FRONTIERS IN CHEMISTRY
(2020)
Review
Chemistry, Multidisciplinary
Siddarth Narasimhan, Gert E. Folkers, Marc Baldus
Article
Chemistry, Multidisciplinary
Fredj Ben Bdira, Christopher A. Waudby, Alexander N. Volkov, Sybrin P. Schroder, A. B. Eiso, Jeroen D. C. Codee, Hermen S. Overkleeft, Johannes M. F. G. Aerts, Hugo van Ingen, Marcellus Ubbink
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Biochemistry & Molecular Biology
Velten Horn, Seino A. K. Jongkees, Hugo van Ingen
Article
Chemistry, Multidisciplinary
Ilektra-Chara Giassa, Andrea Vavrinska, Jiri Zelinka, Jakub Sebera, Vladimir Sychrovsky, Rolf Boelens, Radovan Fiala, Lukas Trantirek
Review
Biochemistry & Molecular Biology
Vincenzo R. Lobbia, Maria Cristina Trueba Sanchez, Hugo van Ingen
Summary: The regulation of chromatin biology relies heavily on manipulating the smallest subunit, the nucleosome, and molecular interactions must be tuned to navigate the complexity of the dense nuclear environment. This review analyzes the interplay between nucleosome-protein interactions and higher-order chromatin structure, shedding light on how these factors operate in a complex environment. Additionally, characteristics of nucleosome-protein interactions that can lead to phase separation of chromatin are reviewed, highlighting the challenges in characterizing interactions beyond the nucleosome.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemical Research Methods
Siddarth Narasimhan, Cecilia Pinto, Alessandra Lucini Paioni, Johan van der Zwan, Gert E. Folkers, Marc Baldus
Summary: Solid-state nuclear magnetic resonance (ssNMR) has been widely used to study complex biomolecular systems. This protocol outlines a biochemical preparation scheme for obtaining cellular samples of soluble and insoluble or membrane-associated proteins, suitable for studying a protein of interest in both whole cells and in cell envelope or isolated membrane preparations.
Article
Biochemistry & Molecular Biology
Bram Henneman, Thomas B. Brouwer, Amanda M. Erkelens, Gert-Jan Kuijntjes, Clara van Emmerik, Ramon A. van der Valk, Monika Timmer, Nancy C. S. Kirolos, Hugo van Ingen, John van Noort, Remus T. Dame
Summary: Archaea express histones which play a key role in organizing the genome and gene regulation, forming hypernucleosomes that depend on stacking interactions, torque, and force for stability. The assembly of hypernucleosomes on long DNA substrates is facilitated by cooperative binding of histones to DNA. In response to environmental changes, modulation of the archaeal hypernucleosome structure may be important for transcription regulation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Hessel Poelman, Hans Ippel, Berke Gurkan, Rolf Boelens, Gert Vriend, Cornelis van 't Veer, Esther Lutgens, Gerry A. F. Nicolaes
Summary: Researchers elucidated the structure of IRAK-M death domain using NMR and performed docking studies to reveal its position in the Myddosome and the molecular basis for its selectivity towards IRAK1 over IRAK2 binding. They identified structural issues in the original model and built a more accurate homology model based on high-resolution crystal structures, which better matched known information about the death domain structure.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Multidisciplinary Sciences
Ivan Corbeski, Xiaohu Guo, Bruna Eckhardt, Domenico Fasci, Wouter Wiegant, Melissa A. Graewert, Kees Vreeken, Hans Wienk, Dmitri Svergun, Albert J. R. Heck, Haico van Attikum, Rolf Boelens, Titia K. Sixma, Francesca Mattiroli, Hugo van Ingen
Summary: Nucleosome assembly requires specific histone chaperones, but this study found that the acidic domain of DNA repair factor APLF can directly assemble the histone octamer and deposit it on DNA to form nucleosomes, which may be a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.
Article
Biochemistry & Molecular Biology
Francesca Cantini, Paola Gianni, Sara Bobone, Cassandra Troiano, Hugo van Ingen, Renato Massoud, Nicoletta Perini, Luciana Migliore, Philippe Savarin, Charles Sanders, Lorenzo Stella, Marco Sette
Summary: Antimicrobial resistance is a pressing public health issue, and the development of new antimicrobial agents is actively pursued. In this study, an improved version of the crabrolin peptide was designed and characterized for its functional and structural properties using various techniques. The newly designed crabrolin21 exhibited enhanced antimicrobial activity and specific selectivity towards bacterial cells. These findings suggest that further investigations on crabrolin21 are warranted.