Article
Plant Sciences
Dexing Jiang, Huihui Wu, Hui Cai, Guoxiang Chen
Summary: This study investigated the role of silicon in alleviating aluminum-induced damage in the root-apex transition zone (TZ) and root-growth inhibition of rice. It was found that silicon can directly alleviate aluminum toxicity, reduce root-growth inhibition and aluminum accumulation, and modify the cell wall to promote extensibility, thus reducing the sensitivity of rice roots to aluminum toxicity.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Microbiology
Tingting Dai, Yue Xu, Xiao Yang, Binbin Jiao, Min Qiu, Junxin Xue, Felipe Arredondo, Brett M. Tyler
Summary: Phytophthora cinnamomi is a destructive pathogen causing root rot and dieback diseases. An improved transformation system using PEG/CaCl2 successfully generated transformants displaying green fluorescence, with one of them showing similar virulence to wild-type isolate. This system could be useful for functional genomics studies of P. cinnamomi.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Horticulture
Pornprapa Kongtragoul, Koichiro Ishikawa, Hideo Ishii
Summary: Research has shown the presence of metalaxyl-resistant strains in populations of Phytophthora palmivora in Thailand, posing challenges for disease management.
Review
Plant Sciences
L. M. Quesada-Ocampo, C. H. Parada-Rojas, Z. Hansen, G. Vogel, C. Smart, M. K. Hausbeck, R. M. Carmo, E. Huitema, R. P. Naegele, C. S. Kousik, P. Tandy, K. Lamour
Summary: Phytophthora capsici is a destructive pathogen that affects vegetables, ornamental plants, and tropical crops. Its high genetic diversity and adaptability make it difficult to control and manage. This article provides an overview of the research progress on P. capsici in the past 100 years, including its biology, genetic diversity, and disease management.
ANNUAL REVIEW OF PHYTOPATHOLOGY
(2023)
Review
Plant Sciences
Delia A. Narvaez-Barragan, Omar E. Tovar-Herrera, Arturo Guevara-Garcia, Mario Serrano, Claudia Martinez-Anaya
Summary: Cell wall integrity is crucial for plant defense against biotic and abiotic stresses. Expansins, which modify cell walls, can enhance or weaken plant resistance to pathogens. Changes in cell wall mechanical properties can directly influence the outcome of pathogen infection, while expansins also play a role in triggering defense responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Elena Marone Fassolo, Beatrice Lecchi, Demetrio Marciano, Giuliana Maddalena, Silvia Laura Toffolatti
Summary: Durable resistance is a key objective in grapevine genetic improvement for disease resistance. This study found that two resistant cultivars were able to effectively control the disease. However, suitable practices must be adopted in the field to prevent the spread of adapted pathogen strains and protect the resistance genes from erosion.
Article
Biochemistry & Molecular Biology
Stephanie Tan, Kelvin Cho, Justin R. Nodwell
Summary: WalKR is a essential two-component system in Gram-positive bacteria that regulates autolysins in cell wall homeostasis. Investigation of this system is crucial for addressing antibiotic resistance. A mutation in walR, namely T101M, leads to reduced autolysis, thicker cell wall, and decreased susceptibility to certain antibiotics, resembling the clinical resistance in vancomycin intermediate-resistant Staphylococcus aureus (VISA). Additionally, this mutation sensitizes the bacteria to tunicamycin. The underlying mechanism is the partial collapse of a pathway involving several enzymes, resulting in substrate shortage and hypersensitivity to tunicamycin inhibition. These findings provide a new molecular model for antibiotic sensitivity in S. aureus and offer a promising avenue for antibiotic discovery.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Plant Sciences
Mengmeng Wang, Shu Zhou, Junyang Lu, Anqi Xu, Yuan Huang, Zhilong Bie, Fei Cheng
Summary: The CmRCC1 gene plays a crucial role in regulating root architecture and increasing cold tolerance in tobacco plants, as evidenced by its differential expression under cold stress and interaction with CmLAZY1, ultimately affecting root diameter and volume in the plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Lovepreet Singh, Arunima Sinha, Megha Gupta, Shunyuan Xiao, Rosemarie Hammond, Nidhi Rawat
Summary: The wheat PFT protein provides broad-spectrum quantitative resistance to fungal pathogens, but not to bacterial or oomycete pathogens. It specifically binds to chitin in fungal cell walls, which may explain its specificity for fungal pathogens.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2023)
Review
Biochemistry & Molecular Biology
Tianyuan Qin, Ali Kazim, Yihao Wang, Dormatey Richard, Panfeng Yao, Zhenzhen Bi, Yuhui Liu, Chao Sun, Jiangping Bai
Summary: Crop growth and development are often affected by various stresses, with the root system playing a crucial role in drought response. Understanding the genes that control root development can lead to the incorporation of stress-tolerant genes in breeding and the development of drought-tolerant cultivars.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jinlong Yin, Liqun Wang, Tongtong Jin, Yang Nie, Hui Liu, Yanglin Qiu, Yunhua Yang, Bowen Li, Jiaojiao Zhang, Dagang Wang, Kai Li, Kai Xu, Haijian Zhi
Summary: In this study, a unique NLR that recognizes plant virus in the apoplast was identified, providing a simple and effective method for identifying resistant genes against SMV infection.
Article
Biochemistry & Molecular Biology
Mojtaba Mohammadi, Eric A. Smith, Michael E. Stanghellini, Rakesh Kaundal
Summary: Pythium brassicum P1 is a recently characterized root pathogen specific to Brassicaceae plants, showing distinct differences in virulence mechanisms, protein secretion, and enzyme genes compared to other oomycetes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Demetrio Marciano, Valentina Ricciardi, Giuliana Maddalena, Annamaria Massafra, Elena Marone Fassolo, Simona Masiero, Piero Attilio Bianco, Osvaldo Failla, Gabriella De Lorenzis, Silvia Laura Toffolatti
Summary: Downy mildew, caused by Plasmopara viticola, is a major threat to viticulture. Nitrogen fertilization affects disease severity but not the expression of susceptibility/resistance genes. Exploiting these genes could lead to new environmentally friendly disease management tools.
Editorial Material
Microbiology
Hajar Yaakoub, Jean-Paul Latge, Nicolas Papon
Summary: The human opportunistic pathogen Aspergillus fumigatus is known for its adaptable cell wall, which allows it to remodel its components to resist antifungal drugs. Previous studies have shown that sugar metabolism plays a specific role in regulating the synthesis of cell wall polymers. In-depth research into central sugar metabolism may uncover unexpected fundamental aspects of cell wall construction, as demonstrated by the study on the phosphoglucose isomerase of A. fumigatus conducted by Zhou et al. (mBio 13:e01426-22, 2022).
Review
Plant Sciences
Bastien G. Dauphin, Philippe Ranocha, Christophe Dunand, Vincent Burlat
Summary: Plant cell walls show cellular and subcellular specificities, and wall microdomains play a crucial role in macroscopic developmental processes. This study focuses on the contribution of two categories of wall-remodeling molecular actors in wall microdomains.
TRENDS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Mahtab Moghaddam, Atsushi Ohta, Motoki Shimizu, Ryohei Terauchi, Shahrokh Kazempour-Osaloo
Summary: The complete plastome of O. gaubae was sequenced and compared with other legume species. The study identified hypervariable regions that can be used as molecular markers for phylogenetic analysis and species identification. The results reveal the dynamic nature of plastomes in the IRLC and provide new insights into plastome evolution.
Article
Agriculture, Multidisciplinary
David Camilo Corrales, Celine Schoving, Helene Raynal, Philippe Debaeke, Etienne-Pascal Journet, Julie Constantin
Summary: In this study, a surrogate model was developed to improve soybean yield prediction by using feature selection techniques and regression learners. By using the STICS simulator and different models, the researchers found that the combination of feature selection techniques with SVR and LR models provided the best results.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2022)
Review
Biochemistry & Molecular Biology
Justine M. Toulotte, Chrysoula K. Pantazopoulou, Maria Angelica Sanclemente, Laurentius A. C. J. Voesenek, Rashmi Sasidharan
Summary: Cereal crops are crucial for global diets, but their production is severely impacted by climate change. Exploring the genetic diversity of crop wild relatives can help improve stress resistance and yields in these crops.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Napaporn Sriden, Varodom Charoensawan
Summary: Comparative transcriptomic analysis provides a comprehensive understanding of transcriptional responses to temperature changes in different plant tissues, as well as the unique regulatory functions of temperature-mediating transcription factors. The goal of this study is to develop resilient cultivars to mitigate the threats of climate change on plant diversity and food security. By analyzing publicly available datasets, the researchers identified sets of temperature-responsive genes that were common or tissue-specific. Interestingly, some known temperature-responsive genes were found to be involved in cold response as well. Furthermore, the study elucidated the distinct DNA-binding patterns of key temperature transcription factors to their target genes with different transcriptional responses.
PLANT MOLECULAR BIOLOGY
(2022)
Article
Plant Sciences
Michie Kobayashi, Hiroe Utsushi, Koki Fujisaki, Takumi Takeda, Tetsuro Yamashita, Ryohei Terauchi
Summary: This article investigates a protein called JRL in the plant extracellular space, which has virulence effects and can suppress plant immune responses. The study found that JRL proteins secreted by the pathogen Sg can enhance the pathogenicity of the pathogen in Poaceae crops. Furthermore, it was discovered that JRL proteins localize to the apoplastic space in N. benthamiana leaves.
MOLECULAR PLANT PATHOLOGY
(2022)
Article
Multidisciplinary Sciences
H. Kato, K. Nemoto, M. Shimizu, A. Abe, S. Asai, N. Ishihama, S. Matsuoka, T. Daimon, M. Ojika, K. Kawakita, K. Onai, K. Shirasu, M. Yoshida, M. Ishiura, D. Takemoto, Y. Takano, R. Terauchi
Summary: In plants, invading microbial pathogens are recognized by cell-surface receptors, triggering defense responses. The pathogen-derived lipid molecules from the oomycete P. infestans can induce defense responses in Arabidopsis by interacting with specific enzymes and receptors.
Article
Multidisciplinary Sciences
Yu Sugihara, Lester Young, Hiroki Yaegashi, Satoshi Natsume, Daniel J. Shea, Hiroki Takagi, Helen Booker, Hideki Innan, Ryohei Terauchi, Akira Abe
Summary: Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method for identifying loci contributing to important phenotypic traits. The new pipelines described here are faster and easier to use than the previous ones, and can be easily installed through bioconda.
Article
Multidisciplinary Sciences
Jantarika Kumar Arora, Anunya Opasawatchai, Tiraput Poonpanichakul, Natnicha Jiravejchakul, Waradon Sungnak, Oranart Matangkasombut, Sarah A. Teichmann, Ponpan Matangkasombut, Varodom Charoensawan
Summary: This study analyzed the single-cell transcriptomic profiles of two DENV patients and found that different immune cell types exhibit dynamic responses during the infection. Several genes in the adaptive immunological pathways were highly expressed on the day before defervescence, and unique effector T cell clusters were identified. These findings could improve the management of DENV infection in patients.
Article
Multidisciplinary Sciences
Motoki Shimizu, Akiko Hirabuchi, Yu Sugihara, Akira Abe, Takumi Takeda, Michie Kobayashi, Yukie Hiraka, Eiko Kanzaki, Kaori Oikawa, Hiromasa Saitoh, Thorsten Langner, Mark J. Banfield, Sophien Kamoun, Ryohei Terauchi
Summary: Throughout their evolution, plant nucleotide-binding leucine-rich-repeat receptors (NLRs) have acquired widely divergent unconventional integrated domains that enhance their ability to detect pathogen effectors. However, the functional dynamics that drive the evolution of NLRs with integrated domains (NLR-IDs) remain poorly understood. Here, we reconstructed the evolutionary history of an NLR locus prone to unconventional domain integration and experimentally tested hypotheses about the evolution of NLR-IDs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Basavaraj Kovi, Toshiyuki Sakai, Akira Abe, Eiko Kanzaki, Ryohei Terauchi, Motoki Shimizu
Summary: Blast disease caused by the fungus Pyricularia oryzae is a major rice disease. The Shoni cultivar showed resistance against multiple P. oryzae isolates. Genetic analysis revealed that the resistance was controlled by a single gene called Pi-Shoni.
GENES & GENETIC SYSTEMS
(2023)
Article
Biochemistry & Molecular Biology
Juthamard Chantaraamporn, Pongpannee Phumikhet, Sarintip Nguantad, Todsapol Techo, Varodom Charoensawan
Summary: Predicting phenotypes and complex traits from genomic variations has always been a challenge in molecular biology. With advances in machine learning (ML) and omic data, it is now possible to uncover the molecular mechanisms that control gene expression and phenotypes. This article provides a summary of ML concepts and examples in molecular biology, focusing on transcriptomics.
Article
Biochemistry & Molecular Biology
Yu Sugihara, Yoshiko Abe, Hiroki Takagi, Akira Abe, Motoki Shimizu, Kazue Ito, Eiko Kanzaki, Kaori Oikawa, Jiorgos Kourelis, Thorsten Langner, Joe Win, Aleksandra Bialas, Daniel Ludke, Mauricio P. Contreras, Izumi Chuma, Hiromasa Saitoh, Michie Kobayashi, Shuan Zheng, Yukio Tosa, Mark J. Banfield, Sophien Kamoun, Ryohei Terauchi, Koki Fujisaki
Summary: Studies integrating genetic analyses of rice and rice blast fungus have discovered a new pathogen recognition specificity in the immune receptor Pik, which mediates resistance to the fungus. The resistance is triggered by the recognition of a previously unidentified effector protein encoded by the avirulence gene AVR-Mgk1. This discovery highlights the complexity of host-pathogen gene-for-gene interactions and the coevolution between the immune receptor and effector proteins.
Article
Genetics & Heredity
Toshiyuki Sakai, Tomoaki Fujioka, Toyokazu Uemura, Shinichi Saito, Ryohei Terauchi, Akira Abe
Summary: Elucidating genotype-by-environment interactions is fundamental for understanding the interplay between genetic and environmental factors that shape complex traits in crops. We describe a method for genotype-by-environment detection using linear mixed models, which successfully detected genotype-by-environment interactions in rice recombinant inbred lines grown at three locations. We identified a quantitative trait locus (QTL) associated with heading date, grain number, and leaf length, whose effect on plant growth-related traits varied with environmental conditions, indicating the presence of genotype-by-environment interactions. Therefore, our method enables a powerful genotype-by-environment detection pipeline that should facilitate the production of high-yielding crops in a given environment.
G3-GENES GENOMES GENETICS
(2023)
Article
Biology
Josephine H. R. Maidment, Motoki Shimizu, Adam R. Bentham, Sham Vera, Marina Franceschetti, Apinya Longya, Clare E. M. Stevenson, Juan Carlos De la Concepcion, Aleksandra Bialas, Sophien Kamoun, Ryohei Terauchi, Mark J. Banfield, Jian-Min Zhou
Summary: A subset of plant intracellular NLR immune receptors can detect effector proteins secreted by phytopathogens through unconventional integrated domains resembling the effectors' host targets, activating plant defenses. This study engineered novel Pik-1 variants using knowledge of the biochemical interactions between the effector AVR-Pik and its host target, resulting in disease resistance in transgenic rice against blast fungus isolates carrying AVR-PikC/F. This demonstrates that effector target-guided engineering of NLR receptors can provide new-to-nature disease resistance in crops.
Article
Biochemical Research Methods
Jantarika Kumar Arora, Anunya Opasawatchai, Sarah A. Teichmann, Ponpan Matangkasombut, Varodom Charoensawan
Summary: We propose a computational approach to study highly variable genes (HVGs) associated with specific biological pathways in single-cell RNA-sequencing data across different time points and cell types. Using publicly available datasets for dengue virus and COVID-19, we demonstrate how to use this framework to analyze the dynamic expression levels of HVGs related to common and cell-type-specific biological pathways in immune cells. For more detailed instructions on the usage of this protocol, please refer to Arora et al.1
