Review
Biochemistry & Molecular Biology
Elizabeth A. Komives
Summary: The kinetic control of NF-kappa B transcription activation system relies on the folding and unfolding of intrinsically disordered regions, which determines the rates of various cellular processes.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Medicine, Research & Experimental
Chunhua Chen, Shiheng Li, Junli Xue, Manlong Qi, Xin Liu, Yan Huang, Jinghua Hu, Haidong Dong, Kun Ling
Summary: The study reveals that PD-L1 promotes EMT in TNBC by inhibiting the destruction of Snail. PD-L1 antibodies restrict TNBC progression by targeting the PD-L1/Snail pathway. Targeting both intratumoral and extratumoral functions of PD-L1 shows a strong synergistic tumor suppression effect in a TNBC mouse model.
Review
Biochemistry & Molecular Biology
Manon Julien, Rania Ghouil, Ambre Petitalot, Sandrine M. Caputo, Aura Carreira, Sophie Zinn-Justin
Summary: BRCA2 protein plays essential roles in DNA repair, replication protection, and cell division. Pathogenic variants in BRCA2 can lead to genome instability and are associated with breast and/or ovarian cancers. The disordered regions in BRCA2 are predicted to mediate important interactions during DNA repair, mitosis, and meiosis.
Article
Chemistry, Physical
Shahar Zuri, Arthur Shapiro, Leeor Kronik, Efrat Lifshitz
Summary: In this work, the anharmonic ground state of the (PEA)(2)PbI4 compound was thoroughly investigated using low-temperature X-ray diffraction and photoluminescence spectroscopy, supported by density functional theory calculations. It was found that the ground state has two coexisting chiral sublattices and uneven anharmonicity, where the state population can be tuned by surface effects. These findings uncover a disordered ground state that may induce intrinsic grain boundaries, which are important in practical applications.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Tuan Minh Tran, Choon-Peng Chng, Xiaoming Pu, Zhiming Ma, Xiao Han, Xiaolin Liu, Liang Yang, Changjin Huang, Yansong Miao
Summary: This study demonstrates that interactions between OMVs and the Arabidopsis thaliana plasma membrane can modulate various host processes, including endocytosis, immune responses, and suppression of pathogenesis. OMVs have a highly ordered lipid phase and directly insert into the plant PM, enhancing lipid order and strengthening plant defenses; this process is dependent on host nanodomains and remorin. Computational simulations show that OMV integration into the plant PM depends on membrane lipid order and the saturation level of OMV lipids can fine-tune the enhancement of host lipid order.
Editorial Material
Oncology
Aaron M. Hosios, Brendan D. Manning
Summary: Research has deepened the understanding of oncogenic control of metabolism, particularly glycolysis. Current focus is on understanding the benefits and risks associated with glycolytic metabolism, and finding inhibitors that could be clinically beneficial for targeting glycolytic cancer cells.
Article
Ophthalmology
David J. Taylor Gonzalez, Mak Djulbegovic, Michael Antonietti, Matthew Cordova, Guy W. Dayhoff II, Robby Mattes, Anat Galor, Vladimir N. Uversky, Carol L. Karp
Summary: The purpose of this study was to characterize the proteome of human tears and investigate the presence of intrinsically disordered proteins (IDPs). The findings revealed an abundance of IDPs in tears, indicating their significant role in protein function and interaction networks. These findings have promising implications for disease biomarker identification and drug target development.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2023)
Editorial Material
Plant Sciences
Pooja Singh, Vipul Mishra, Durgesh Kumar Tripathi, Francisco J. Corpas, Vijay Pratap Singh
Summary: Reactive oxygen species (ROS) play a crucial role in plant development and stress response. Recent research by Li et al. showed that ROS production is regulated by receptor-like cytoplasmic kinase (RLCK)-mediated phosphorylation of respiratory burst oxidase homolog D (RBOHD), which in turn modulates plant immunity and enhances biotic stress tolerance.
TRENDS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Joshua Ames, Tejabhiram Yadavalli, Rahul Suryawanshi, James Hopkins, Alexander Agelidis, Chandrashekhar Patil, Brian Fredericks, Henry Tseng, Tibor Valyi-Nagy, Deepak Shukla
Summary: The study demonstrates that the autophagy receptor OPTN plays a crucial neuroprotective role during HSV-1 infection by degrading viral proteins, preventing virus spread and neuronal necroptosis. Lack of OPTN leads to cognitive decline and susceptibility to lethal CNS infection in mice, indicating its importance in survival from potentially deadly viral infections.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Michael J. P. Crowley, Bhavneet Bhinder, Geoffrey J. Markowitz, Mitchell Martin, Akanksha Verma, Tito A. Sandoval, Chang-Suk Chae, Shira Yomtoubian, Yang Hu, Sahil Chopra, Diamile A. Tavarez, Paolo Giovanelli, Dingcheng Gao, Timothy E. McGraw, Nasser K. Altorki, Olivier Elemento, Juan R. Cubillos-Ruiz, Vivek Mittal
Summary: IRE1 alpha-XBP1 signaling is crucial for malignant progression and immunosuppression in different cancers. XBP1s mRNA isoform expression predicts poor survival in NSCLC patients. Inhibition of IRE1 alpha delays tumor progression, prolongs survival, and induces adaptive anti-cancer immunity in mouse models of NSCLC. IRE1 alpha activation in cancer cells regulates mPGES-1 expression, leading to the production of immunosuppressive prostaglandin E-2. Targeting the IRE1 alpha pathway may enhance anti-tumor immunity in NSCLC.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Guy W. W. Dayhoff, Vladimir N. N. Uversky
Summary: This article presents RIDAO, a high-efficiency web-based disorder predictor for protein intrinsic disorder analysis. RIDAO integrates six disorder predictors into a unified platform, offering high accuracy and processing efficiency.
Article
Multidisciplinary Sciences
Christopher A. Waudby, Saul Alvarez-Teijeiro, E. Josue Ruiz, Simon Suppinger, Nikos Pinotsis, Paul R. Brown, Axel Behrens, John Christodoulou, Anastasia Mylona
Summary: Protein phosphorylation regulates cellular signaling, and the phosphorylation of c-JUN at multiple sites controls various functional states in signal response.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Jennifer M. Kunselman, Achla Gupta, Ivone Gomes, Lakshmi A. Devi, Manojkumar A. Puthenveedu
Summary: The study shows that while multiple physiological agonists can activate the same receptor, it may not necessarily be true redundancy, but rather a way to regulate downstream signaling specificity by controlling the spatiotemporal profile of signaling molecules.
Article
Plant Sciences
Hui Li, Xiao Wang, Yue Zhuo, Shuisen Chen, Jingwei Lin, Hui Ma, Ming Zhong
Summary: In this study, 17 SlREM genes were identified in the tomato genome and classified into 6 groups based on phylogenetic analysis. These genes were unevenly distributed on the eight chromosomes of tomato and showed similarities in gene structure and motif composition. The promoter sequences of SlREM genes contained tissue-specific, hormone, and stress-related cis-regulatory elements. Expression analysis showed that these genes were differentially expressed in different tissues and responded to various treatments. These results provide valuable information for further research on the biological functions of SlREM genes.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Goran Vinterhalter, Jovana J. Kovacevic, Vladimir N. Uversky, Gordana M. Pavlovic-Lazetic
Summary: The research investigates the correlation between protein structure and function using different datasets and functional annotations. Results show consistent findings in protein disorder prediction between Gene Ontology (GO terms) and Swiss-Prot keywords. Additionally, a new method for deriving missing mappings between GO terms and Swiss-Prot keywords is proposed based on protein function similarity measurement.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Pengbo Liang, Clara Schmitz, Beatrice Lace, Franck Anicet Ditengou, Chao Su, Eija Schulze, Julian Knerr, Robert Grosse, Jean Keller, Cyril Libourel, Pierre-Marc Delaux, Thomas Ott
Summary: Legumes have the ability to associate with rhizobia for nitrogen-fixing root nodule symbiosis. In Medicago truncatula, root hair colonization by Sinorhizobium meliloti begins from young root hairs, which physically entwine around the symbiont to form rhizobial traps. This unique process involves alterations in membrane organization, cytosolic calcium gradient, actin rearrangements, and symbiotic responses in legumes.
Article
Plant Sciences
Moira Giovannoni, Lucia Marti, Simone Ferrari, Natsuki Tanaka-Takada, Masayoshi Maeshima, Thomas Ott, Giulia De Lorenzo, Benedetta Mattei
Summary: This study demonstrates the essential role of the protein PCaP1 in mediating late responses to oligogalacturonides and flagellin. PCaP1 is not involved in early responses but may be important for maintaining its stability on the plasma membrane through endocytic turnover. The findings suggest a mechanism of PCaP1 endocytosis induced by oligogalacturonides.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Melanie K. Rich, Nicolas Vigneron, Cyril Libourel, Jean Keller, Li Xue, Mohsen Hajheidari, Guru Radhakrishnan, Aurelie Le Ru, Seydina Issa Diop, Giacomo Potente, Elena Conti, Danny Duijsings, Aurelie Batut, Pauline Le Faouder, Kyoichi Kodama, Junko Kyozuka, Erika Sallet, Guillaume Becard, Marta Rodriguez-Franco, Thomas Ott, Justine Bertrand-Michel, Giles E. D. Oldroyd, Peter Szovenyi, Marcel Bucher, Pierre-Marc Delaux
Summary: Symbiosis with arbuscular mycorrhizal fungi benefits plant nutrition and elicits a conserved transcriptomic response among land plants, including activation of lipid metabolism. Transfer of lipids from liverwort to AMF is regulated by the transcription factor WRINKLED, and the formation of arbuscules is essential for mutualism. The symbiotic transfer of lipids is orthologous across land plants, indicating the presence of mutualism with AMF in the most recent ancestor of land plants 450 million years ago.
Article
Biochemistry & Molecular Biology
Casandra Hernandez-Reyes, Elisabeth Lichtenberg, Jean Keller, Pierre-Marc Delaux, Thomas Ott, Sebastian T. Schenk
Summary: This study investigated the response of the non-legume plant Arabidopsis to changes in root system architecture induced by rhizobia under different nitrate conditions. The study found that rhizobium-induced lateral root growth, increased root hair length, and density are regulated by a nitrate-related signaling pathway. AtNLP4 and AtNLP5 were identified as key players in this process. At the cellular level, AtNLP4 and AtNLP5 control a rhizobium-induced decrease in cell elongation rates.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Plant Sciences
Duncan B. Crosbie, Maryam Mahmoudi, Viviane Radl, Andreas Brachmann, Michael Schloter, Eric Kemen, Macarena Marin
Summary: Nodule microbiota, primarily consisting of symbiotic nitrogen-fixing rhizobia, are influenced by other non-rhizobial bacteria, which may impact root-nodule symbiosis in a plant host-specific manner.
Article
Biochemistry & Molecular Biology
Mohammad Zarrabian, Jesus Montiel, Niels Sandal, Shaun Ferguson, Haojie Jin, Yen-Yu Lin, Verena Klingl, Macarena Marin, Euan K. James, Martin Parniske, Jens Stougaard, Stig U. Andersen
Summary: The research reveals that Lotus burttii has a higher promiscuity in interactions with rhizobia compared to Lotus japonicus, allowing it to form nodules with rhizobia from five different genera. The mapping of the Gifu/burttii promiscuity quantitative trait locus (QTL) to the same genetic locus regardless of the rhizobial genus suggests a common genetic mechanism for symbiont-range expansion.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Chao Su, Guofeng Zhang, Marta Rodriguez-Franco, Rosula Hinnenberg, Jenny Wietschorke, Pengbo Liang, Wei Yang, Leonard Uhler, Xia Li, Thomas Ott
Summary: The root nodule symbiosis is a process in which legume roots are colonized by rhizobia, leading to a global impact on nitrogen fertilization of soils. In this process, rhizobia progress through root cortical and nodular cell layers via an infection thread, repeatedly passing host plasma membranes and cell walls. This study reveals the coordinated action of a symbiosis-specific pectin methyl esterase (SyPME1) and a nodulation pectate lyase (NPL) in mediating pectin alterations at the cell-cell interface, allowing bacteria to be temporarily released into and taken up from the subjacent cell, facilitating the successful intracellular progression of infection threads through the entire root cortical tissue.
Article
Multidisciplinary Sciences
Rafael E. Venado, Lucas E. Wange, Defeng Shen, Fabienne Pinnau, Tonni Grube Andersen, Wolfgang Enard, Macarena Marin
Summary: This study provides genetic evidence for the formation of the nodule oxygen diffusion barrier in legumes, which is crucial for nitrogen fixation in root nodules.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Emilia Neuwirt, Giovanni Magnani, Tamara Cikovic, Svenja Woehrle, Larissa Fischer, Anna Kostina, Stephan Flemming, Nora J. Fischenich, Benedikt S. Saller, Oliver Gorka, Steffen Renner, Claudia Agarinis, Christian N. Parker, Andreas Boettcher, Christopher J. Farady, Rebecca Kesselring, Christopher Berlin, Rolf Backofen, Marta Rodriguez-Franco, Clemens Kreutz, Marco Prinz, Martina Tholen, Thomas Reinheckel, Thomas Ott, Christina J. Gross, Philipp J. Jost, Olaf Gross
Summary: The activation mechanisms of NOD-like receptor (NLR) protein-mediated inflammasomes were investigated. It was discovered that tyrosine kinase inhibitors (TKIs), including clinically approved drugs like imatinib and crizotinib, activated the NLRP3 inflammasome. These TKIs caused lysosomal swelling and damage, resulting in cell lysis and activation of NLRP3. This finding suggests a potential off-target effect of TKIs that may contribute to their clinical efficacy or adverse effects.
Article
Multidisciplinary Sciences
Jiahuan Chen, Zhijuan Wang, Lixiang Wang, Yangyang Hu, Qiqi Yan, Jingjing Lu, Ziyin Ren, Yujie Hong, Hongtao Ji, Hui Wang, Xinying Wu, Yanru Lin, Chao Su, Thomas Ott, Xia Li
Summary: The success of legumes relies on the formation and maintenance of optimal symbiotic nodules, which require a balance between symbiosis and plant growth. Cytokinin plays a key role in the regulation of nodulation, but its mechanism is not fully understood. In this study, the authors identified a response regulator called GmRR11d that mediates the systemic inhibition of nodulation. GmRR11d is induced by rhizobia and low levels of cytokinin, and it can suppress the transcriptional activity of GmNSP1 on GmNIN1a, leading to the inhibition of soybean nodulation. GmRR11d positively regulates cytokinin response and its binding on the GmNIN1a promoter is enhanced by cytokinin. Furthermore, the induction of GmRR11d by rhizobia and its function are dependent on GmNARK, a CLV1-like receptor kinase that inhibits nodule formation in shoots. Overall, GmRR11d controls a transcriptional program associated with nodulation attenuation and cytokinin response activation, which is essential for systemic regulation of nodulation.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Chao Su, Marta Rodriguez-Franco, Beatrice Lace, Nils Nebel, Casandra Hernandez-Reyes, Pengbo Liang, Eija Schulze, Evgeny V. Mymrikov, Nikolas M. Gross, Julian Knerr, Hong Wang, Lina Siukstaite, Jean Keller, Cyril Libourel, Alexandra A. M. Fischer, Katharina E. Gabor, Eric Mark, Claudia Popp, Carola Hunte, Wilfried Weber, Petra Wendler, Thomas Stanislas, Pierre-Marc Delaux, Oliver Einsle, Robert Grosse, Winfried Roemer, Thomas Ott
Summary: The organization of membranes in plants is mainly controlled by the cell wall and cytoskeleton, with some proteins, such as remorins, playing a role in protein and lipid organization. Symbiosis-specific SYMREM1 gene mutations disrupt membrane organization in root nodules. AlphaFold modeling and biochemical analyses reveal that SYMREM1 forms oligomers and may contribute to higher-order membrane scaffolding.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Bushra Saeed, Florian Deligne, Carla Brillada, Kai Duenser, Franck Aniset Ditengou, Ilona Turek, Alaa Allahham, Nenad Grujic, Yasin Dagdas, Thomas Ott, Juergen Kleine-Vehn, Gregory Vert, Marco Trujillo
Summary: Unlike other eukaryotic model organisms, the main sources of K63-linked Ub chains in Arabidopsis are UBC35 and UBC36. Previous research has associated K63-linked chains with vesicle trafficking regulation but lacked definitive evidence for their role in endocytosis. This study demonstrates that K63-Ub chains are essential for endocytic trafficking in plants and are also involved in selective autophagy through the interaction with NBR1. These findings highlight the importance of K63-Ub chains in maintaining proteostasis in plants.
Editorial Material
Plant Sciences
Jinhong Yuan, Thomas Ott, Andreas Hiltbrunner
TRENDS IN PLANT SCIENCE
(2023)
Article
Biology
Beatrice Lace, Chao Su, Daniel Invernot Perez, Marta Rodriguez-Franco, Tatiana Vernie, Morgane Batzenschlager, Sabrina Egli, Cheng-Wu Liu, Thomas Ott
Summary: Host-controlled intracellular accommodation of nitrogen-fixing bacteria is essential for the establishment of a functional Root Nodule Symbiosis (RNS). Comparative phylogenomic studies have identified RPG as a critical genetic determinant for bacterial infection. This study provides evidence that RPG is part of a protein complex involved in membrane polarization, cytoskeleton-mediated connectivity, and polar secretion during bacterial infection.
Article
Plant Sciences
Jesus Montiel, Dugald Reid, Thomas H. Gronbaek, Caroline M. Benfeldt, Euan K. James, Thomas Ott, Franck A. Ditengou, Marcin Nadzieja, Simon Kelly, Jens Stougaard
Summary: This study reports intercellular infection of the model legume Lotus japonicus by the IRBG74 strain and reveals the genetic requirements and differences in the pathways governing this process compared to intracellular infection. The results indicate a differential requirement for cytokinin signaling during intercellular rhizobial entry, highlighting distinct modalities of inter- and intracellular infection mechanisms in L. japonicus.