Article
Environmental Sciences
R. J. Strickman, S. Larson, H. Huang, E. Kakouros, M. Marvin-DiPasquale, C. P. J. Mitchell, R. B. Neumann
Summary: The presence or absence of rice plants was found to have different effects on the concentration of MeHg in rice paddy soil, with methylation being the dominant control in non-vegetated soil and demethylation being the dominant control in vegetated soil. The presence of rice plants reduced MeHg production capacity and resulted in lower variance of MeHg concentrations in the soil.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Biotechnology & Applied Microbiology
Yu Wang, Fengcheng Li, Fan Zhang, Lian Wu, Na Xu, Qi Sun, Hao Chen, Zhiwen Yu, Jiahao Lu, Kai Jiang, Xiaoche Wang, Siyu Wen, Yao Zhou, Hui Zhao, Qian Jiang, Jiahong Wang, Ruizong Jia, Jian Sun, Liang Tang, Hai Xu, Wei Hu, Zhengjin Xu, Wenfu Chen, Anping Guo, Quan Xu
Summary: This study compared 58 long-read assemblies of cultivated and wild rice species, revealing numerous genomic structural variations (SVs) and their effects on agronomic traits. Integrating these variations into the analysis allowed for the precise identification of breeding signatures resulting from complex breeding histories.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biology
Abhinandan M. Tripathi, Yael Admoni, Arie Fridrich, Magda Lewandowska, Joachim M. Surm, Reuven Aharoni, Yehu Moran
Summary: The biogenesis of miRNAs in animals and plants depends on RNase III Dicer, but their partner proteins are considered distinct. However, a homolog of the plant-specific Dicer partner HYL1 has been discovered in the cnidarian phylum, challenging the idea that miRNAs evolved convergently in animals and plants. This study shows that the HYL1 homolog Hyl1La is crucial for development and miRNA biogenesis in the cnidarian model Nematostella vectensis, suggesting an early emergence of the miRNA system.
Article
Multidisciplinary Sciences
Lining Lu, Xiaoguo Zhai, Xiaolong Li, Shuansuo Wang, Lijun Zhang, Luyang Wang, Xi Jin, Lujun Liang, Zhiheng Deng, Zichen Li, Yanfeng Wang, Xiangdong Fu, Honggang Hu, Jiawei Wang, Ziqing Mei, Zhengguo He, Feng Wang
Summary: This study identifies rice OTUB1 as a deubiquitinase targeting Met1-linked ubiquitin chains, characterized the structural determinants of this activity, and shows that these features are conserved in green plants.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Raquel Rodriguez-Perez, Juergen Bajorath
Summary: This study introduces a new approach that uses compound activity predictions to uncover relationships between target proteins, showing feature importance correlation analysis and functional relationships between proteins. The approach does not rely on specific representations, algorithms, or metrics and has potential practical applications in drug discovery.
SCIENTIFIC REPORTS
(2021)
Review
Plant Sciences
M. Regina Scarpin, Carl H. Simmons, Jacob O. Brunkard
Summary: mRNA translation is a crucial step in genome expression, and the target of rapamycin (TOR) plays a central regulatory role in eukaryotes. Recent studies have revealed that TOR regulates mRNA translation in plants through conserved signaling mechanisms and plant-specific pathways.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Review
Biochemistry & Molecular Biology
Yu Gao, Baohua Feng, Caixia Gao, Huiquan Zhang, Fengting Wen, Longxing Tao, Guanfu Fu, Jie Xiong
Summary: This review investigates the evolutionary pathway and regulatory mechanisms of miR408 in plants and summarizes its functions in regulating plant growth, development, and responses to various stresses. The study reveals that miR408 is an ancient and highly conserved microRNA that is widely distributed in different plants. miR408 regulates plant growth and development by down-regulating its target genes encoding blue copper proteins and by enhancing cellular antioxidants to improve stress tolerance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Agronomy
Jonne Rodenburg, Dennis E. Tippe, Amadou Toure, Runyambo Irakiza, Juma Kayeke, Lammert Bastiaans
Summary: Competition from weeds is the most important yield reducing factor in African rice production systems. Effective and affordable weed management strategies are highly needed in the face of challenges such as lack of water management infrastructure, access to herbicides, and knowledge and equipment for safe and effective application. The literature review suggests the importance of developing integrated weed management strategies that reduce weed recruitment, seed bank sizes, and improve crop competitiveness.
FIELD CROPS RESEARCH
(2022)
Editorial Material
Plant Sciences
Jaime Santos, Salvador Ventura
Summary: A recent study identified a functional amyloid in plants that plays a crucial role in seed longevity, indicating the universal utilization of amyloids in organisms' adaptation.
TRENDS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Jin-Yu Li, Chuang Yang, Jiming Xu, Hai-Ping Lu, Jian-Xiang Liu
Summary: Global climate change has a significant impact on plant growth and reduces crop productivity worldwide. Rice, as a vital food crop, is vulnerable to high-temperature stress from its early growth to reproductive stages. This review summarizes recent advancements in understanding the molecular mechanisms of heat stress responses in rice, including heat sensing and signaling, transcriptional regulation, transcript processing, protein translation, and post-translational regulation. The irreversible effects of high temperature on rice reproduction and grain quality are also highlighted. Challenges and opportunities for future research in this area are discussed.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Developmental Biology
Tushar Garg, Zeenu Singh, Kunchapu Chennakesavulu, Khrang Khrang Khunggur Mushahary, Anuj Kumar Dwivedi, Vijina Varapparambathu, Harshita Singh, Raj Suryan Singh, Debabrata Sircar, Divya Chandran, Kalika Prasad, Mukesh Jain, Shri Ram Yadav
Summary: In this study, the researchers investigated the molecular mechanisms controlling the development of shoot-borne adventitious/crown roots in rice. They identified transcription factors from the WUSCHEL-RELATED HOMEOBOX and PLETHORA gene families that play non-redundant and species-specific roles in determining root architecture. The study also revealed the involvement of PLT genes in promoting crown root development through the activation of local auxin biosynthesis genes. Interestingly, the PLT genes from rice were able to rescue lateral root primordia outgrowth defects in Arabidopsis mutants, indicating their conserved role in root primordia outgrowth regardless of their developmental origin. This research provides a molecular framework for understanding the tissue transdifferentiation during root primordia establishment and the evolution of transcription regulation in acquiring species-specific function.
Article
Biochemistry & Molecular Biology
Miao Ye, Zhengcan Zhang, Guanjun Huang, Yong Li
Summary: This study investigated the effects of leaf anatomical traits and environmental stimuli on the photosynthesis of rice plants. It found that the response of mesophyll conductance to temperature was stronger at the mid-tillering stage and with high nitrogen treatment, which could be attributed to a higher activation energy of the membrane.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Hao Zhang, Chaoyue Gai, Min Shao, Linzhi Fang, Xinyu Li, Yuanyuan Song, Rensen Zeng, Daoqian Chen, Fajun Chen
Summary: Polyamines play an important role in the interaction between rice and striped stem borer (SSB). SSB larval infestation leads to an accumulation of polyamines in rice plants, which benefits the growth of SSB. The defense responses in rice are regulated by the addition of polyamines or the inhibition of polyamine biosynthesis.
Review
Biochemistry & Molecular Biology
Halina Pietrykowska, Alisha Alisha, Bharti Aggarwal, Yuichiro Watanabe, Misato Ohtani, Artur Jarmolowski, Izabela Sierocka, Zofia Szweykowska-Kulinska
Summary: Functional regulatory non-coding RNAs (ncRNAs) play a vital role in plant growth and development. The liverwort Marchantia polymorpha serves as an excellent model species for studying the evolution of regulatory ncRNAs and proteins involved in ncRNA biogenesis. Recent studies on Marchantia have revealed the similarities and differences in the production and function of ncRNAs between bryophytes and other land plants. Understanding the molecular mechanisms controlling ncRNA-directed developmental processes requires further functional studies.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Plant Sciences
Xinyi Zhou, Wei Xie, Hao Jing, Junru Fu, Maomao Li, Jianmin Bian, Jie Xu, Yicong Cai, Haohua He, Dahu Zhou
Summary: This study used a functional rice variety, Zibaoxiangnuo 1 (ZBXN 1), rich in total flavonoids and anthocyanins, as the experimental material, and crossed it with Minghui63 (MH63), a variety without anthocyanins, to construct Recombination Inbred Lines (RILs). The contents of anthocyanins and total flavonoids in RILs and two parents were determined for three consecutive generations. The results showed that ZBXN 1 had abundant and stable anthocyanins, making it a potential breeding material for high-quality rice varieties with high anthocyanin content.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Philipp M. Grande, Dennis Weidener, Dietrich Sabine, Murali Dama, Martin Bellof, Ruth Maas, Markus Pauly, Walter Leitner, Klose Holger, Pablo Dominguez de Maria
Article
Multidisciplinary Sciences
Sang-Jin Kim, Balakumaran Chandrasekar, Anne C. Rea, Linda Danhof, Starla Zemelis-Durfee, Nicholas Thrower, Zachary S. Shepard, Markus Pauly, Federica Brandizzi, Kenneth Keegstra
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biotechnology & Applied Microbiology
Dennis Weidener, Murali Dama, Sabine K. Dietrich, Benedict Ohrem, Markus Pauly, Walter Leitner, Pablo Dominguez de Maria, Philipp M. Grande, Holger Klose
BIOTECHNOLOGY FOR BIOFUELS
(2020)
Article
Biochemistry & Molecular Biology
Yves Verhertbruggen, Axelle Bouder, Jacqueline Vigouroux, Camille Alvarado, Audrey Geairon, Fabienne Guillon, Mark D. Wilkinson, Fabian Stritt, Markus Pauly, Mi Yeon Lee, Jenny C. Mortimer, Henrik Scheller, Rowan A. C. Mitchell, Catalin Voiniciuc, Luc Saulnier, Anne-Laure Chateigner-Boutin
Summary: Mannan is a type of cell wall polysaccharide widely found in the plant kingdom, with structure and properties varying across species and organs. This study aimed to investigate the biosynthesis and function of wheat grain mannan, identifying the TaCslA12 gene as a potential candidate responsible for synthesizing wheat endosperm mannan.
Article
Biotechnology & Applied Microbiology
Madalen Robert, Julian Waldhauer, Fabian Stritt, Bo Yang, Markus Pauly, Catalin Voiniciuc
Summary: This study demonstrated the successful assembly of cellulose synthase-like A (CSLA) enzymes in yeast to produce tunable heteromannan (HM) polysaccharides. Engineering chimeric CSLA proteins led to increased production of beta-1,4-linked mannan with reduced burden on yeast growth. The results offer novel routes for engineering polysaccharide-based biomaterials, potentially benefiting the sustainable bioeconomy.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Biochemical Research Methods
Jan W. Huebbers, Kim Buttgen, Franz Leissing, Melissa Mantz, Markus Pauly, Pitter F. Huesgen, Ralph Panstruga
Summary: A revised method for isolating Arabidopsis thaliana leaf trichomes has been developed, which significantly increases yield and purity. The method allows for comprehensive proteomic analysis of trichomes and can be applied to different plant species, providing valuable insights into trichome biology.
Article
Plant Sciences
Nicolai D. Jablonowski, Markus Pauly, Murali Dama
Summary: This study investigated the potential of Szarvasi biomass as a biorefinery feedstock and found that alkali pretreatment significantly enhanced its saccharification efficiency, while acid pretreatment directly converted cellulose into glucose. Furthermore, a lignin chemical model structure present in Szarvasi biomass was successfully established.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Thomas Perrot, Markus Pauly, Vicente Ramirez
Summary: Plant beta-glucanases play crucial roles in the synthesis, remodelling and turnover of cell wall components. They cleave different types of glycoside bonds to remodel and disassemble the cell wall, and are involved in regulating symbiotic and hostile plant-microbe interactions.
Article
Multidisciplinary Sciences
Miguel Perez-Anton, Ilsa Schneider, Patrizia Kroll, Hugo Hofhuis, Sabine Metzger, Markus Pauly, Angela Hay
Summary: Exploding seed pods in Cardamine hirsuta evolved through morphomechanical innovations, including asymmetric lignin deposition within endocarpb cell walls. The genetic control of this lignin pattern involves three laccases and the transcription factor gene SPL7. Additionally, the SPL7 pathway links mineral nutrition and efficient seed dispersal.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Bilal Oekmen, Elaine Jaeger, Lena Schilling, Natalie Finke, Amy Klemd, Yoon Joo Lee, Raphael Wemhoener, Markus Pauly, Ulla Neumann, Gunther Doehlemann
Summary: The corn smut effector Erc1 has 1,3-beta-glucanase activity and promotes virulence in maize leaves by attenuating beta-glucan-induced defense responses. Smut fungi secrete effector proteins that suppress host plant immunity and modulate cellular functions and development of the host.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Hila Behar, Yaseen Mottiar, Rohan Chandrasekhar, Allegra Corelli Grappadelli, Markus Pauly, A. Lacey Samuels, Shawn D. Mansfield, Harry Brumer
Summary: This study used a hybrid polar plant model, Populus alba x Populus grandidentata (P39), to investigate the expression, subcellular localization, and phenotypes and chemotypes of EG16-downregulated P39 plants. The results showed that Populus EG16 is strongly expressed in young tissues, but RNAi-mediated downregulation did not affect plant growth or the fine structure of hemicellulose xyloglucan, suggesting a restricted or currently unknown role in angiosperm physiology.
Article
Biochemistry & Molecular Biology
Balakumaran Chandrasekar, Alan Wanke, Stephan Wawra, Pia Saake, Lisa Mahdi, Nyasha Charura, Miriam Neidert, Gereon Poschmann, Milena Malisic, Meik Thiele, Kai Stuehler, Murali Dama, Markus Pauly, Alga Zuccaro
Summary: Plant pathogenic and beneficial fungi have evolved strategies to resist plant immune response. The different layers of fungal cell wall and extracellular polysaccharide matrix have different functions. A low molecular weight β-glucan decasaccharide released by plant hydrolase plays an important role in fungal adaption and suppression of plant immunity.
Article
Plant Sciences
Florian J. Kraemer, China Lunde, Moritz Koch, Benjamin M. Kuhn, Clemens Ruehl, Patrick J. Brown, Philipp Hoffmann, Vera Goehre, Sarah Hake, Markus Pauly, Vicente Ramirez
Summary: In this study, a maize mutant named mlgh1 was identified with increased MLG content due to a mutation in the GRMZM2G137535 gene, which encodes a GH17 licheninase capable of degrading MLG. Overexpression of this gene resulted in a significant reduction in MLG content and increased saccharification yields. Moreover, cycling of MLG content during day/night cycles was disrupted in the mlgh1 mutant, suggesting a regulatory role of MLG degradation in gene expression.
Article
Biochemistry & Molecular Biology
S. A. Sinclair, S. Gille, M. Pauly, U. Kraemer
PLANT SIGNALING & BEHAVIOR
(2020)
Article
Plant Sciences
Vicente Ramirez, Markus Pauly
