Article
Plant Sciences
Pol Vendrell-Mir, Pierre-Francois Perroud, Fabian B. Haas, Rabea Meyberg, Florence Charlot, Stefan A. Rensing, Fabien Nogue, Josep M. Casacuberta
Summary: Next-generation sequencing techniques have been used to identify new plant viruses, increasing our knowledge beyond economically important crops. A study identified a virus named PHPAV1 infecting Physcomitrium patens, which can be vertically transmitted throughout the plant cell cycle.
Review
Plant Sciences
Wenye Lin, Ying Wang, Yoan Coudert, Daniel Kierzkowski
Summary: Specialized photosynthetic organs have evolved independently multiple times in land plants, with bryophytes like mosses displaying leaf-like organs called phyllids that differ greatly from vascular tissues in flowering plants. Despite the differences, there are morphological similarities between the leaf structures of mosses and flowering plants. By studying leaf morphogenesis in the moss Physcomitrium patens, researchers can uncover cellular patterns and molecular regulatory mechanisms, and potentially identify parallels with leaf development in flowering plants. This research direction may help answer fundamental questions in plant development by using moss leaves as a model system.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Franko Merida-Quesada, Fernando Vergara-Valladares, Maria Eugenia Rubio-Melendez, Naomi Hernandez-Rojas, Angelica Gonzalez-Gonzalez, Erwan Michard, Carlos Navarro-Retamal, Ingo Dreyer
Summary: Through analyzing the genome of Physcomitrium patens, it was found that TPC1b channels have variations in critical amino acids, leading to a lower calcium ion coordination capacity compared to common TPC1 channels.
Article
Plant Sciences
Paul Rosas-Santiago, Karla Zechinelli Perez, Maria Fernanda Gomez Mendez, Francisco Vera Lopez Portillo, Jorge Luis Ruiz Salas, Elizabeth Cordoba Martinez, Alexis Acosta Maspon, Omar Pantoja
Summary: Physcomitrella patens, a moss, provides genetic information on early Embryophytes' adaptation to land life with two COPT proteins playing different roles in copper homeostasis. PpaCOPT1 and PpaCOPT2 restored growth in yeast at micromolar Cu concentrations, with PpaCOPT1 expressed in different locations compared to PpaCOPT2.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Plant Sciences
Md Arif Sakil, Kyosuke Mukae, Junyu Bao, Abhishek Sadhu, Md. Shyduzzaman Roni, Yuko Inoue-Aono, Yuji Moriyasu
Summary: Autophagy promotes cell death induced by H2O2 in the autophagy-defective mutants of Physcomitrium patens, and autophagy inhibitors can lower the levels of H2O2 and the cell death rate.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Hanno Christoph Resemann, Kirstin Feussner, Ellen Hornung, Ivo Feussner
Summary: Plant oxylipins are lipid-derived signaling molecules involved in regulating stress responses. OPDA and its metabolite JA are common oxylipins, but the occurrence of JA in plants is still debated. We studied the metabolism of oxylipins in the non-vascular plant P. patens and identified several compounds, including isobaric molecules to JA, after wounding. These findings will contribute to further understanding of the oxylipin-receptor interactions in P. patens.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Zhuo Yang, Liu Duan, Hongyu Li, Ting Tang, Liuzhu Chen, Keming Hu, Hong Yang, Li Liu
Summary: This study reveals the important roles of PpRNH1A in the development and heat stress response in bryophytes. PpRNH1A may participate in these processes by affecting the numbers and mobilization of lipid droplets and regulating the expression of heat-related genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Anouchka Guyon-Debast, Alessandro Alboresi, Zoe Terret, Florence Charlot, Floriane Berthier, Pol Vendrell-Mir, Josep M. Casacuberta, Florian Veillet, Tomas Morosinotto, Jean-Luc Gallois, Fabien Nogue
Summary: CRISPR-Cas9 base editors can achieve efficient and precise single-base mutations in Physcomitrium patens, facilitating gene functional analysis and enabling the production of randomly mutagenized variants of a specific gene through multiple sgRNA base editing. The development of a co-editing selection system further enhances the efficiency of site-specific base editing in P. patens.
Article
Microbiology
Adriana Otero-Blanca, Yordanis Perez-Llano, Guillermo Reboledo-Blanco, Veronica Lira-Ruan, Daniel Padilla-Chacon, Jorge Luis Folch-Mallol, Maria del Rayo Sanchez-Carbente, Ines Ponce De Leon, Ramon Alberto Batista-Garcia
Summary: Anthracnose caused by Colletotrichum gloeosporioides is a devastating plant disease affecting plant productivity. The defense response of the model moss Physcomitrium patens to C. gloeosporioides involves appressoria formation at 24 hours post-inoculation, massive tissue colonization and cell death at 48 hours, and upregulation of genes related to pathogen recognition, secondary metabolism, and cell wall reinforcement. This study highlights the transcriptional changes in P. patens during interaction with C. gloeosporioides, shifting from primary metabolism to defense mechanisms.
Article
Plant Sciences
Melanie Kreiss, Fabian B. Haas, Maike Hansen, Stefan A. Rensing, Ute Hoecker
Summary: The PpCOP1 and PpSPA proteins in Physcomitrium work together to regulate growth and development, but unlike their counterparts in Arabidopsis, they only partially suppress light signaling in darkness. Additional repressors may exist that contribute to the repression of a light response in dark-exposed Physcomitrium.
Article
Plant Sciences
Katsuaki Takechi, Hiroaki Nagase, Tomoyuki Furuya, Koro Hattori, Yoshikatsu Sato, Kensuke Miyajima, Tomofumi Higuchi, Ryuya Matsuda, Susumu Takio, Hirokazu Tsukaya, Hiroyoshi Takano
Summary: This study found that the PpAN2 genes play a crucial role in cell elongation regulation in moss plants, showing partial redundancy with the PpAN1 genes. Additionally, transgenic experiments revealed that the activity of AN is dependent on the N-terminal regions.
Review
Plant Sciences
Mamoru Sugita
Summary: Pentatricopeptide repeat (PPR) proteins, a type of helical repeat protein, are widely found in eukaryotes, especially flowering plants. They play crucial roles in RNA metabolism during gene expression in the plastids and mitochondria. Physcomitrium patens, an early land plant, has numerous PPR genes, but their functions are largely unknown. Through reverse-genetics, the functions of 22 PPR proteins have been identified in mRNA processing, stabilization, splicing, and editing. This review discusses the PPR gene family in P. patens and its functions, highlighting similarities, and diversity in comparison to flowering plants and their roles in post-transcriptional regulation of organellar gene expression.
Article
Biochemistry & Molecular Biology
Pierre-Francois Perroud, Viktor Demko, Ako Eugene Ako, Rajendra Khanal, Boris Bokor, Andrej Pavlovic, Jan Jasik, Wenche Johansen
Summary: In Physcomitrium patens, GUCT-domain-containing DEAD-BOX RNA helicases PpRH1 and PpRH2 are localized in the nucleus and are involved in cell and tissue development throughout the moss life cycle. These enzymes are important for various RNA metabolic processes and potentially play roles in plant development and stress responses. Specifically, the nuclear GUCT-containing RNA helicases in P. patens are primarily linked to developmental processes related to photosynthesis activity.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Plant Sciences
Claudia Beraldo, Anouchka Guyon-Debast, Alessandro Alboresi, Fabien Nogue, Tomas Morosinotto
Summary: Plants use non-photochemical quenching (NPQ) as a reversible mechanism to dissipate excess absorbed energy as heat, protecting them from photodamage. The presence of the membrane protein PsbS is essential for NPQ in plants, as it interacts with antenna proteins to induce dissipative conformation. This study utilized base editing in the moss Physcomitrium patens to investigate the role of specific amino acid changes in PsbS and identified residues and hydrophobic amino acid clusters that impact PsbS activity, providing new insights into its molecular mechanism.
Article
Plant Sciences
Stacy D. Singer, Neil W. Ashton
Summary: This study provides a preliminary characterization of transgene silencing in Physcomitrella targeted gene knockout lines. The research reveals that cytosine methylation of transgenes is correlated with their silencing in Physcomitrella, and this silencing occurs through metastable epigenetic inheritance via repetitive mitosis and variable stability through meiosis.
Review
Plant Sciences
Noe Fernandez-Pozo, Fabian B. Haas, Sven B. Gould, Stefan A. Rensing
Summary: Bryophytes are valuable models for various studies in plant evolution, development, stress responses, and gametogenesis. Advances in genomics research have provided a wealth of resources, including annotations, databases, and bioinformatics tools, for better understanding bryophytes. The use of bioinformatics, phylogenetics, and comparative genomics has significantly contributed to our knowledge of bryophytes and their evolution.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemical Research Methods
Noe Fernandez-Pozo, Aureliano Bombarely
Summary: EasyGDB is an easy-to-implement and low-maintenance tool for genomic data management, specifically designed for the development of genomics portals in non-model species. It provides a range of bioinformatics tools and a modern web style, allowing users to efficiently manage and analyze genomic data.
Article
Plant Sciences
Melanie Kreiss, Fabian B. Haas, Maike Hansen, Stefan A. Rensing, Ute Hoecker
Summary: The PpCOP1 and PpSPA proteins in Physcomitrium work together to regulate growth and development, but unlike their counterparts in Arabidopsis, they only partially suppress light signaling in darkness. Additional repressors may exist that contribute to the repression of a light response in dark-exposed Physcomitrium.
Article
Multidisciplinary Sciences
Corentin Conart, Dikki Pedenla Bomzan, Xing-Qi Huang, Jean-Etienne Bassard, Saretta N. Paramita, Denis Saint-Marcoux, Aurelie Rius-Bony, Gal Hivert, Anthony Anchisi, Hubert Schaller, Latifa Hamama, Jean-Louis Magnard, Agata Lipko, Ewa Swiezewska, Patrick Jame, Genevieve Riveill, Laurence Hibrand-Saint Oyant, Michel Rohmer, Efraim Lewinsohn, Natalia Dudareva, Sylvie Baudino, Jean-Claude Caissard, Benoit Boachon
Summary: The cytosolic geranyl diphosphate (GPP) in rose flowers is synthesized by a bifunctional geranyl/farnesyl diphosphate synthase, RcG/FPPS1, through the cytosolic mevalonate (MVA) pathway. RcG/FPPS1 is involved not only in the production of geraniol and germacrene D, but also in the synthesis of dihydro-β-ionol. This study reveals the origin of cytosolic GPP in rose flowers and the key role of RcG/FPPS1 in the biosynthesis of volatile terpenoid compounds.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Thomas E. Hughes, Olga Sedelnikova, Mimi Thomas, Jane A. Langdale
Summary: This study reveals the role of the SCARECROW gene in C-4 plants, showing that SCR and NAKED-ENDOSPERM together regulate the differentiation of internal leaf tissues. The authors found that SCR is involved in the patterning of internal leaf tissues in C-4 plants, with NKD enhancing its function. This study sheds light on the evolutionary process of cell patterning in grass leaves.
Article
Plant Sciences
Amanda Bullones, Antonio Jesus Castro, Elena Lima-Cabello, Juan de Dios Alche, Francisco Luque, Manuel Gonzalo Claros, Noe Fernandez-Pozo
Summary: OliveAtlas is an interactive gene expression atlas for olive, providing multiple bioinformatics tools and visualization methods. It contains 70 RNA-seq experiments and allows for multiple gene comparison, replicate inspection, gene set enrichment, and data downloading.
Article
Plant Sciences
Aynhoa Gomez-Olle, Amanda Bullones, Jose I. Hormaza, Lukas A. Mueller, Noe Fernandez-Pozo
Summary: MangoBase is a web portal dedicated to mango genomics, providing various interactive bioinformatics tools, sequences, and annotations to analyze, visualize, and download omics data related to mango. It also includes a gene expression atlas with multiple datasets and experiments that study mango fruit ripening, postharvest treatment, infection, and organ tissues.
Article
Biodiversity Conservation
Alicia Talavera, Noe Fernandez-Pozo, Antonio J. Matas, Jose I. Hormaza, Aureliano Bombarely
Summary: This study provides important genomic resources to fill the knowledge gap and enhance the crop's resilience under different climate change scenarios, thereby increasing food security in regions with subtropical climates.
PLANTS PEOPLE PLANET
(2023)
Article
Biochemistry & Molecular Biology
Avinash Sreedasyam, Christopher Plott, Md Shakhawat Hossain, John T. Lovell, Jane Grimwood, Jerry W. Jenkins, Christopher Daum, Kerrie Barry, Joseph Carlson, Shengqiang Shu, Jeremy Phillips, Mojgan Amirebrahimi, Matthew Zane, Mei Wang, David Goodstein, Fabian B. Haas, Manuel Hiss, Pierre-Francois Perroud, Sara S. Jawdy, Yongil Yang, Rongbin Hu, Jenifer Johnson, Janette Kropat, Sean D. Gallaher, Anna Lipzen, Eugene Shakirov, Xiaoyu Weng, Ivone Torres-Jerez, Brock Weers, Daniel Conde, Marilia R. Pappas, Lifeng Liu, Andrew Muchlinski, Hui Jiang, Christine Shyu, Pu Huang, Jose Sebastian, Carol Laiben, Alyssa Medlin, Sankalpi Carey, Alyssa A. Carrell, Jin-Gui Chen, Mariano Perales, Kankshita Swaminathan, Isabel Allona, Dario Grattapaglia, Elizabeth A. Cooper, Dorothea Tholl, John P. Vogel, David J. Weston, Xiaohan Yang, Thomas P. Brutnell, Elizabeth A. Kellogg, Ivan Baxter, Michael Udvardi, Yuhong Tang, Todd C. Mockler, Thomas E. Juenger, John Mullet, Stefan A. Rensing, Gerald A. Tuskan, Sabeeha S. Merchant, Gary Stacey, Jeremy Schmutz
Summary: Gene functional descriptions are important for identifying candidate genes involved in trait variation, and plant responses to environmental cues can provide molecular targets for plant improvement. However, many genes across the plant phylogeny lack functional annotations. The Joint Genome Institute (JGI) Plant Gene Atlas is a valuable resource that integrates transcript abundance data from 18 diverse species to identify expression profiles and discover previously undocumented gene functions. The Gene Atlas is accessible through the JGI Plant Gene Atlas and Phytozome websites, allowing users to access differential gene expression, track orthologs, and visualize gene ontology and pathway enrichments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Julia Lambret-Frotte, Georgia Smith, Jane A. Langdale
Summary: This study found that the role of GLK paralogs in controlling chloroplast biogenesis differs between different species of C-4 grasses. However, GLK1 and GLK2 genes from maize can both restore functional chloroplast development in S. viridis mutants, indicating that both orthologs have the ability to induce chloroplast biogenesis.
Article
Plant Sciences
Amanda Bullones, Antonio Jesus Castro, Elena Lima-Cabello, Noe Fernandez-Pozo, Rocio Bautista, Juan de Dios Alche, Manuel Gonzalo Claros
Summary: This study used RNA-seq technology to investigate the genome-wide events during the in vitro germination of olive pollen. The results revealed a deep transcriptional reprogramming in mature olive pollen and identified several important genes related to heat shock proteins and F-box proteins. Additionally, the study found that olive pollen is equipped with transcripts to cope with adverse environments, but in vitro germination induced multiple stress responses. The research also discovered an overall increased number of pollen-specific gene isoforms in olive trees compared to other plants.
Article
Plant Sciences
Omer Murik, Or Geffen, Yoram Shotland, Noe Fernandez-Pozo, Kristian Karsten Ullrich, Dirk Walther, Stefan Andreas Rensing, Haim Treves
Summary: The study compared the genome of Chlorella ohadii, a fast-growing alga, to that of other green algae and revealed the genomic characteristics that contribute to its fast growth rate and resistance to stressors. The findings provide important insights into photosynthesis and stress response research and offer new opportunities for synthetic biology and biotechnology.
Article
Biology
Nina Rittmeier, Andreas Holzinger
Summary: This study investigated the chromosome visualization methods in the filamentous green alga Zygnema. Existing protocols were modified to allow reliable chromosome counting in this genus. The challenges of interference from cell wall components and random cell divisions were addressed.