Review
Plant Sciences
Sanjay Joshi, Priyanka Paul, Jeanne M. Hartman, Sharyn E. Perry
Summary: Plants have remarkable regenerative properties through somatic embryogenesis, which can lead to fully developed plants. Investigating the mechanisms of somatic embryo induction and development is crucial for seed development models and engineered crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Angelina Schindele, Fabienne Gehrke, Carla Schmidt, Sarah Roehrig, Annika Dorn, Holger Puchta
Summary: CRISPR/Cas is mainly used for mutagenesis, but this study shows that induction of cell death can be achieved using the SaCas9 nuclease, referred to as CRISPR-Kill, for tissue engineering. By replacing the promoter, organogenesis can be blocked and specific traits can be targeted, such as eliminating petals and reducing lateral root numbers and length. CRISPR-Kill may have implications not only for controlling development but also altering biochemical properties of plants.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Louise Noren Lindback, Yan Ji, Luis Cervela-Cardona, Xu Jin, Ullas V. Pedmale, Asa Strand
Summary: Researchers have identified three bZIP transcription factors (bZIP16, bZIP68, and GBF1) that play important roles in regulating chloroplast establishment. The activity of these factors is dependent on the redox status of a conserved cysteine residue, allowing for fine-tuning of light-responsive gene expression. In addition, they have been identified as novel interaction partners of the blue-light cryptochrome photoreceptors (CRY).
Article
Plant Sciences
Nan Wang, Zhidan Wang, Sofia Tzourtzou, Xu Wang, Xiuli Bi, Julia Leimeister, Linhao Xu, Takuya Sakamoto, Sachihiro Matsunaga, Andreas Schaller, Hua Jiang, Chang Liu
Summary: The nuclear lamina is a complex network of proteins that scaffolds the nucleus and maintains its structural integrity. In Arabidopsis, nuclear matrix constituent proteins (NMCPs) are essential for the nuclear lamina and play a role in organizing chromatin positioning. The nuclear lamina disassembles under various stresses, impacting genome organization and gene transcription.
Article
Biochemistry & Molecular Biology
Hyuk Sung Yoon, Kaien Fujino, Shenkui Liu, Tetsuo Takano, Daisuke Tsugama
Summary: The study shows that Arabidopsis PP2A B''-family subunits interact with PP2A A (scaffold) subunits and can mediate VIP1 dephosphorylation. This provides important insights into the molecular mechanism of VIP1 dephosphorylation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biology
Juan S. Ramirez-Prado, David Latrasse, Moussa Benhamed
Summary: Characterizing the molecular mechanisms regulating gene expression is crucial for understanding physiological responses in eukaryotes. ChIP-seq has become a key method for determining histone modification profiles, and the described protocol in this study offers a cost-effective approach for performing ChIP-seq of histone modifications in Arabidopsis thaliana plantlets.
Article
Chemistry, Multidisciplinary
Luca Pagano, Marta Marmiroli, Marco Villani, Jacopo Magnani, Riccardo Rossi, Andrea Zappettini, Jason C. White, Nelson Marmiroli
Summary: This study found that nanoparticles can affect the functionality and genome of chloroplasts and mitochondria in A. thaliana, and different nanoparticles have different effects, which are related to the toxicity and dissolution rate of the metal salts. These findings suggest that changes in stoichiometry are an adaptive response to nanoparticle exposure.
Article
Plant Sciences
Daniel Matsusaka, Javier F. Botto, Diego H. Sanchez
Summary: This study reveals the central regulatory role of specific noncoding tandem repeats in the intersection between epigenetic silencing and gene expression, and their importance in plant stress responses.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Plant Sciences
Shuang Yang, Tianqi Zhang, Ze Wang, Xiaofei Zhao, Rui Li, Jing Li
Summary: In this study, it was found that NIT1/2/3 positively regulate flowering by repressing MAF4 through manipulating H3K4me3 modification. This finding provides new insights into the regulatory mechanisms of plant adaptation and growth development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Hongcheng Zhao, Nan Sun, Lin Huang, Ruyi Qian, Xianyong Lin, Chengliang Sun, Yongguan Zhu
Summary: The molecular mechanism of root development mediated by the beneficial bacterium Azospirillum brasilense is not fully understood. A. brasilense induces extensive transcriptional changes but inhibits primary root elongation in Arabidopsis. Through analysis of root cell type-specific markers, it was found that A. brasilense does not alter the overall organization or cell division of the primary root meristem. The inhibition of root elongation is primarily due to the reduction of cell elongation, which is caused by bacterially activated peroxidase leading to cell wall cross-linking. The activation of peroxidase, in combination with the downregulation of cell wall loosening enzymes, results in an increase in cell wall thickness.
Review
Plant Sciences
Nobutoshi Yamaguchi
Summary: Certain eukaryotic transcription factors have the ability to reprogram one cell type into another, with pioneer factors being able to engage target sites in closed chromatin. In plants, the TF LEAFY acts as a pioneer factor specifying floral fate and interacts with other factors to regulate floral development.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Hongyu Chen, Yang Lv, Xinxin Yin, Xi Chen, Qinjie Chu, Qian-Hao Zhu, Longjiang Fan, Longbiao Guo
Summary: The study evaluated the impact of sample size on single-cell transcriptome analysis outcomes, finding that the most significant principal components can be achieved with 20,000-30,000 cells sampled, and relatively high reliability of cell clustering can be achieved with 20,000 cells.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Haiyue Ai, Julia Bellstaedt, Kai Steffen Bartusch, Lennart Eschen-Lippold, Steve Babben, Gerd Ulrich Balcke, Alain Tissier, Bettina Hause, Tonni Grube Andersen, Carolin Delker, Marcel Quint
Summary: Roots are able to sense and respond to elevated temperature independently of shoot-derived signals. This response is mediated by an unknown root thermosensor that uses auxin as a messenger to relay temperature signals to the cell cycle. Growth promotion is primarily achieved by increasing cell division rates in the root apical meristem, dependent on de novo local auxin biosynthesis and temperature-sensitive organization of the polar auxin transport system.
Article
Biochemistry & Molecular Biology
Attila Meszaros, Kevin Muwonge, Steven Janvier, Junaid Ahmed, Peter Tompa
Summary: Intrinsically disordered proteins (IDPs) lack well-defined 3D structures and can interact promiscuously due to their high flexibility. This unique property allows them to play diverse regulatory roles in cellular processes. However, their exposed structural state makes them more susceptible to proteolytic degradation compared to globular proteins.
Article
Chemistry, Multidisciplinary
Dong Hyeun Ka, Ryza Aditya Priatama, Joo Young Park, Soon Ju Park, Seong Bong Kim, In Ah Lee, Young Koung Lee
Summary: Low-temperature atmospheric pressure plasma technology has been used for direct and indirect treatment of bio-samples in agriculture and plant science. This study explored the effects of plasma-activated water (PAW) generated from a surface dielectric barrier discharge device on the early developmental stage of Arabidopsis thaliana L. Results showed that PAW treatment affected root development by modulating root hair cell density and was associated with the expression of root developmental-related genes.
APPLIED SCIENCES-BASEL
(2021)
Review
Agronomy
Alain Gojon, Laurent Nussaume, Doan T. Luu, Erik H. Murchie, Alexandra Baekelandt, Vandasue Lily Rodrigues Saltenis, Jean-Pierre Cohan, Thierry Desnos, Dirk Inze, John N. Ferguson, Emmanuel Guiderdonni, Anne Krapp, Rene Klein Lankhorst, Christophe Maurel, Hatem Rouached, Martin A. J. Parry, Mathias Pribil, Lars B. Scharff, Philippe Nacry
Summary: Plant scientists and farmers are facing challenges in providing food security while preserving natural resources and adapting to climate change. Breeding resilient crops and improving nutrient use efficiency are crucial for sustainable agriculture. Understanding the physiological and molecular bases of plant environmental responses is essential, as well as exploring genetic resources and utilizing technological advancements.
FOOD AND ENERGY SECURITY
(2023)
Article
Biochemistry & Molecular Biology
Christian Damian Lorenzo, Kevin Debray, Denia Herwegh, Ward Develtere, Lennert Impens, Dries Schaumont, Wout Vandeputte, Stijn Aesaert, Griet Coussens, Yara De Boe, Kirin Demuynck, Tom Van Hautegem, Laurens Pauwels, Thomas B. Jacobs, Tom Ruttink, Hilde Nelissen, Dirk Inze
Summary: Ensuring food security while adapting to climate change is the main challenge for agriculture in the 21st century. Recent advances in CRISPR/Cas9 gene engineering have provided a way to accelerate plant breeding to meet the increasing demand. The gene discovery pipeline BREEDIT combines multiplex genome editing with crossing schemes to improve complex traits such as yield and drought tolerance.
Review
Plant Sciences
Thomas Depuydt, Bert De Rybel, Klaas Vandepoele
Summary: Despite the availability of high-quality plant genome sequences, our understanding of the functions of genes is still limited. New multi-omics approaches and advanced annotation strategies, such as machine learning and network biology, are being used to uncover the functions of all plant genes. Additionally, emerging single-cell methods and algorithms have the potential to provide more detailed insights into plant biology.
TRENDS IN PLANT SCIENCE
(2023)
Article
Agronomy
Alexandra Baekelandt, Vandasue L. R. Saltenis, Mathias Pribil, Philippe Nacry, Jeremy Harbinson, Norbert Rolland, Ralf Wilhelm, Jessica Davies, Dirk Inze, Martin A. J. Parry, Rene Klein Lankhorst
Summary: To meet the increasing demand for food and feed and mitigate climate change, the world needs to double its agricultural productivity by 2050. Developing and integrating new crops adapted to the future climate can help achieve this goal. The H2020 CropBooster-P project aims to identify and prioritize breeding options for sustainable crop yield increases, taking into account socio-economic and environmental factors.
FOOD AND ENERGY SECURITY
(2023)
Article
Plant Sciences
Amit Shtern, Alexandra Keren-Keiserman, Jean-Philippe Mauxion, Chihiro Furumizu, John Paul Alvarez, Ziva Amsellem, Naama Gil, Etel Motenko, Sharon Alkalai-Tuvia, Elazar Fallik, Nathalie Gonzalez, Alexander Goldshmidt
Summary: TKN-II genes regulate tomato fruit shape through gibberellin and fruit size through a gibberellin-independent pathway.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Alex Willems, Yuanke Liang, Jefri Heyman, Thomas Depuydt, Thomas Eekhout, Balkan Canher, Hilde van den Daele, Ilse Vercauteren, Klaas Vandepoele, Lieven De Veylder
Summary: PKN1 is a novel, plant-specific protein that plays a crucial role in cell division and is likely regulated by the CCS52A2-activated APC/C protease.
Article
Multidisciplinary Sciences
Lore Gryffroy, Evi Ceulemans, Nicolas Manosalva Perez, Jhon Venegas-Molina, Ana Cristina Jaramillo-Madrid, Savio D. Rodrigues, Liesbeth De Milde, Veronique Jonckheere, Marc Van Montagu, Barbara De Coninck, Klaas Vandepoele, Petra Van Damme, Alain Goossens
Summary: Rhizogenic Agrobacterium strains are biotrophic pathogens that infect hydroponically grown Solanaceae and Cucurbitaceae crops, causing hairy root disease (HRD). They are also widely used for hairy root cultures to produce specialized plant metabolites. The development of hairy roots is regulated by genes encoded on the T-DNA of the root-inducing (Ri) plasmid, including the important rolB gene. In this study, through proximity labeling in tomato hairy roots, the repressor proteins TOPLESS (TPL) and Novel Interactor of JAZ (NINJA) were identified as direct interactors of RolB. The interactions between RolB, TPL, and NINJA were found to play a role in the transcriptional regulation and reprogramming of phytohormone signaling, immunity, growth, and developmental processes in the host plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Ellen Broucke, Thi Tuong Vi Dang, Yi Li, Sander Hulsmans, Jelle Van Leene, Geert De Jaeger, Ildoo Hwang, Van den Ende Wim, Filip Rolland
Summary: Plants have developed a specialized secondary metabolism, such as the production of flavonoid anthocyanins, to protect against stress and promote plant growth. The biosynthesis of anthocyanins is regulated by various factors, including environmental cues and sugar levels. The SnRK1 protein kinase plays a role in repressing anthocyanin biosynthesis by inhibiting the activity of the MBW transcriptional complex. This repression occurs through transcriptional repression, complex dissociation, protein degradation, and phosphorylation of MBW complex proteins.
Article
Plant Sciences
Aniko Meijer, Mohammad Reza Atighi, Kristof Demeestere, Tim De Meyer, Klaas Vandepoele, Tina Kyndt
Summary: In this study, it is demonstrated that offspring of rice plants attacked by underground parasitic nematodes can acquire intergenerational resistance. Transcriptome analysis revealed the downregulation of defense-related genes in the progeny plants under uninfected conditions, but a stronger induction upon nematode infection. This phenomenon, termed "spring loading," depends on the initial downregulation by the dicer-like 3a (dcl3a) gene involved in the RNA-directed DNA methylation pathway.
Article
Plant Sciences
Li Liu, Michel Heidecker, Thomas Depuydt, Nicolas Manosalva Perez, Martin Crespi, Thomas Blein, Klaas Vandepoele
Summary: A study identified 6599 high-confidence lincRNA loci in Arabidopsis and constructed a TF-lincRNA regulatory network containing 2659 lincRNAs and 15686 interactions. Experimental validation confirmed the role of three transcription factors in controlling root-specific lincRNA expression.
Article
Plant Sciences
Jirina Zackova Suchanova, Gust Bilcke, Beata Romanowska, Ali Fatlawi, Martin Pippel, Alastair Skeffington, Michael Schroeder, Wim Vyverman, Klaas Vandepoele, Nils Kroeger, Nicole Poulsen
Summary: This study used various methods to investigate the evolutionary history and function of diatom adhesive proteins, and discovered a new protein family called Trailins, which contains a unique amino acid sequence acquired from bacteria. The findings provide new insights into the molecular basis for diatom biofilm formation.
Article
Biochemistry & Molecular Biology
Alaeddine Safi, Wouter Smagghe, Amanda Goncalves, Qing Wang, Ke Xu, Ana Ibis Fernandez, Benjamin Cappe, Franck B. Riquet, Evelien Mylle, Dominique Eeckhout, Nancy De Winne, Eveline Van De Slijke, Freya Persyn, Geert Persiau, Daniel Van Damme, Danny Geelen, Geert De Jaeger, Tom Beeckman, Jelle Van Leene, Steffen Vanneste
Summary: In this study, a SYMPL-vector set was used to detect protein-protein interactions (PPIs) and kinase activities in plants based on phase separation. The technology allowed easy detection of inducible, binary, and ternary PPIs among cytoplasmic and nuclear proteins in plant cells. Furthermore, a reporter for SNF1-related kinase 1 activity was developed, enabling visualization of tissue-specific, dynamic SnRK1 activity in transgenic Arabidopsis plants.
Article
Plant Sciences
Dajo Smet, Helder Opdebeeck, Klaas Vandepoele
Summary: Plants have developed mechanisms to adapt to environmental stresses, such as gene expression regulation controlled by specific regulators. Recent studies have demonstrated the use of machine learning algorithms to predict gene expression in response to specific stresses, providing insights into the regulatory code. This study trained ML models to predict gene expression in rice under heat or drought stress, evaluating the importance of promoter and gene body sequence features. By comparing genomic feature importance scores, stress-specific and general features contributing to model performance and temporal variation were identified, enabling novel insights into abiotic stress responses.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Trang Hieu Nguyen, Louis Thiers, Alex Van Moerkercke, Yuechen Bai, Patricia Fernandez-Calvo, Max Minne, Thomas Depuydt, Maite Colinas, Kevin Verstaen, Gert Van Isterdael, Hans-Wilhelm Nutzmann, Anne Osbourn, Yvan Saeys, Bert De Rybel, Klaas Vandepoele, Andres Ritter, Alain Goossens
Summary: This research describes a transcriptional regulatory network that controls cell-specific and jasmonate-inducible triterpene biosynthesis in Arabidopsis root tips. Plant specialized metabolites are important for development and ecological functions, but the mechanism behind their cell-specific expression is still unknown.
Review
Plant Sciences
Michele Schneider, Michiel Van Bel, Dirk Inze, Alexandra Baekelandt
Summary: This article focuses on the genetic networks governing leaf cell proliferation and discusses the evolutionary conservation among species. It also explores the interconnectedness between these genetic pathways.