1
|
Rohr L, Ehinger A, Rausch L, Glöckner Burmeister N, Meixner AJ, Gronnier J, Harter K, Kemmerling B, zur Oven-Krockhaus S. OneFlowTraX: a user-friendly software for super-resolution analysis of single-molecule dynamics and nanoscale organization. FRONTIERS IN PLANT SCIENCE 2024; 15:1358935. [PMID: 38708397 PMCID: PMC11066300 DOI: 10.3389/fpls.2024.1358935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024]
Abstract
Super-resolution microscopy (SRM) approaches revolutionize cell biology by providing insights into the nanoscale organization and dynamics of macromolecular assemblies and single molecules in living cells. A major hurdle limiting SRM democratization is post-acquisition data analysis which is often complex and time-consuming. Here, we present OneFlowTraX, a user-friendly and open-source software dedicated to the analysis of single-molecule localization microscopy (SMLM) approaches such as single-particle tracking photoactivated localization microscopy (sptPALM). Through an intuitive graphical user interface, OneFlowTraX provides an automated all-in-one solution for single-molecule localization, tracking, as well as mobility and clustering analyses. OneFlowTraX allows the extraction of diffusion and clustering parameters of millions of molecules in a few minutes. Finally, OneFlowTraX greatly simplifies data management following the FAIR (Findable, Accessible, Interoperable, Reusable) principles. We provide a detailed step-by-step manual and guidelines to assess the quality of single-molecule analyses. Applying different fluorophores including mEos3.2, PA-GFP, and PATagRFP, we exemplarily used OneFlowTraX to analyze the dynamics of plant plasma membrane-localized proteins including an aquaporin, the brassinosteroid receptor Brassinosteroid Insensitive 1 (BRI1) and the Receptor-Like Protein 44 (RLP44).
Collapse
Affiliation(s)
- Leander Rohr
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Alexandra Ehinger
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Luiselotte Rausch
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | | | - Alfred J. Meixner
- Institute for Physical and Theoretical Chemistry, University of Tübingen, Tübingen, Germany
| | - Julien Gronnier
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Birgit Kemmerling
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Sven zur Oven-Krockhaus
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Institute for Physical and Theoretical Chemistry, University of Tübingen, Tübingen, Germany
| |
Collapse
|
2
|
Delesalle C, Vert G, Fujita S. The cell surface is the place to be for brassinosteroid perception and responses. NATURE PLANTS 2024; 10:206-218. [PMID: 38388723 DOI: 10.1038/s41477-024-01621-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/05/2024] [Indexed: 02/24/2024]
Abstract
Adjusting the microenvironment around the cell surface is critical to responding to external cues or endogenous signals and to maintaining cell activities. In plant cells, the plasma membrane is covered by the cell wall and scaffolded with cytoskeletal networks, which altogether compose the cell surface. It has long been known that these structures mutually interact, but the mechanisms that integrate the whole system are still obscure. Here we spotlight the brassinosteroid (BR) plant hormone receptor BRASSINOSTEROID INSENSITIVE1 (BRI1) since it represents an outstanding model for understanding cell surface signalling and regulation. We summarize how BRI1 activity and dynamics are controlled by plasma membrane components and their associated factors to fine-tune signalling. The downstream signals, in turn, manipulate cell surface structures by transcriptional and post-translational mechanisms. Moreover, the changes in these architectures impact BR signalling, resulting in a feedback loop formation. This Review discusses how BRI1 and BR signalling function as central hubs to integrate cell surface regulation.
Collapse
Affiliation(s)
- Charlotte Delesalle
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/Université Toulouse 3, Auzeville-Tolosane, France
| | - Grégory Vert
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/Université Toulouse 3, Auzeville-Tolosane, France
| | - Satoshi Fujita
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/Université Toulouse 3, Auzeville-Tolosane, France.
| |
Collapse
|
3
|
Samalova M, Melnikava A, Elsayad K, Peaucelle A, Gahurova E, Gumulec J, Spyroglou I, Zemlyanskaya EV, Ubogoeva EV, Balkova D, Demko M, Blavet N, Alexiou P, Benes V, Mouille G, Hejatko J. Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth. PLANT PHYSIOLOGY 2023; 194:209-228. [PMID: 37073485 PMCID: PMC10762514 DOI: 10.1093/plphys/kiad228] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Expansins facilitate cell expansion by mediating pH-dependent cell wall (CW) loosening. However, the role of expansins in controlling CW biomechanical properties in specific tissues and organs remains elusive. We monitored hormonal responsiveness and spatial specificity of expression and localization of expansins predicted to be the direct targets of cytokinin signaling in Arabidopsis (Arabidopsis thaliana). We found EXPANSIN1 (EXPA1) homogenously distributed throughout the CW of columella/lateral root cap, while EXPA10 and EXPA14 localized predominantly at 3-cell boundaries in the epidermis/cortex in various root zones. EXPA15 revealed cell-type-specific combination of homogenous vs. 3-cell boundaries localization. By comparing Brillouin frequency shift and AFM-measured Young's modulus, we demonstrated Brillouin light scattering (BLS) as a tool suitable for non-invasive in vivo quantitative assessment of CW viscoelasticity. Using both BLS and AFM, we showed that EXPA1 overexpression upregulated CW stiffness in the root transition zone (TZ). The dexamethasone-controlled EXPA1 overexpression induced fast changes in the transcription of numerous CW-associated genes, including several EXPAs and XYLOGLUCAN:XYLOGLUCOSYL TRANSFERASEs (XTHs), and associated with rapid pectin methylesterification determined by in situ Fourier-transform infrared spectroscopy in the root TZ. The EXPA1-induced CW remodeling is associated with the shortening of the root apical meristem, leading to root growth arrest. Based on our results, we propose that expansins control root growth by a delicate orchestration of CW biomechanical properties, possibly regulating both CW loosening and CW remodeling.
Collapse
Affiliation(s)
- Marketa Samalova
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Alesia Melnikava
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Kareem Elsayad
- Division of Anatomy, Centre for Anatomy & Cell Biology, Medical University of Vienna, Vienna 1090, Austria
| | | | - Evelina Gahurova
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Jaromir Gumulec
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - Ioannis Spyroglou
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Elena V Zemlyanskaya
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630073, Russia
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Ubogoeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Darina Balkova
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Martin Demko
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Nicolas Blavet
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Panagiotis Alexiou
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | | | - Jan Hejatko
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| |
Collapse
|
4
|
Serre NBC, Wernerová D, Vittal P, Dubey SM, Medvecká E, Jelínková A, Petrášek J, Grossmann G, Fendrych M. The AUX1-AFB1-CNGC14 module establishes a longitudinal root surface pH profile. eLife 2023; 12:e85193. [PMID: 37449525 PMCID: PMC10414970 DOI: 10.7554/elife.85193] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 07/10/2023] [Indexed: 07/18/2023] Open
Abstract
Plant roots navigate in the soil environment following the gravity vector. Cell divisions in the meristem and rapid cell growth in the elongation zone propel the root tips through the soil. Actively elongating cells acidify their apoplast to enable cell wall extension by the activity of plasma membrane AHA H+-ATPases. The phytohormone auxin, central regulator of gravitropic response and root development, inhibits root cell growth, likely by rising the pH of the apoplast. However, the role of auxin in the regulation of the apoplastic pH gradient along the root tip is unclear. Here, we show, by using an improved method for visualization and quantification of root surface pH, that the Arabidopsis thaliana root surface pH shows distinct acidic and alkaline zones, which are not primarily determined by the activity of AHA H+-ATPases. Instead, the distinct domain of alkaline pH in the root transition zone is controlled by a rapid auxin response module, consisting of the AUX1 auxin influx carrier, the AFB1 auxin co-receptor, and the CNCG14 calcium channel. We demonstrate that the rapid auxin response pathway is required for an efficient navigation of the root tip.
Collapse
Affiliation(s)
- Nelson BC Serre
- Department of Experimental Plant Biology, Faculty of Science, Charles UniversityPragueCzech Republic
| | - Daša Wernerová
- Department of Experimental Plant Biology, Faculty of Science, Charles UniversityPragueCzech Republic
- Institute of Cell and Interaction Biology, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Pruthvi Vittal
- Department of Experimental Plant Biology, Faculty of Science, Charles UniversityPragueCzech Republic
| | - Shiv Mani Dubey
- Department of Experimental Plant Biology, Faculty of Science, Charles UniversityPragueCzech Republic
| | - Eva Medvecká
- Department of Experimental Plant Biology, Faculty of Science, Charles UniversityPragueCzech Republic
| | - Adriana Jelínková
- Institute of Experimental Botany, Czech Academy of SciencesPragueCzech Republic
| | - Jan Petrášek
- Department of Experimental Plant Biology, Faculty of Science, Charles UniversityPragueCzech Republic
- Institute of Experimental Botany, Czech Academy of SciencesPragueCzech Republic
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Faculty of Science, Charles UniversityPragueCzech Republic
| |
Collapse
|
5
|
Sree KS, Appenroth KJ, Oelmüller R. Sustainable Stress Management: Aquatic Plants vs. Terrestrial Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112208. [PMID: 37299187 DOI: 10.3390/plants12112208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/27/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The Indo-German Science and Technology Centre (IGSTC) funded an Indo-German Workshop on Sustainable Stress Management: Aquatic plants vs. Terrestrial plants (IGW-SSMAT) which was jointly organized at the Friedrich Schiller University of Jena, Germany from 25 to 27 July 2022 by Prof. Dr. Ralf Oelmüller, Friedrich Schiller University of Jena, Germany as the German coordinator and Dr. K. Sowjanya Sree, Central University of Kerala, India as the Indian Coordinator. The workshop constituted researchers working in this field from both India and Germany and brought together these experts in the field of sustainable stress management for scientific discussions, brainstorming and networking.
Collapse
Affiliation(s)
- K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
| | - Klaus J Appenroth
- Matthias Schleiden Institute-Plant Physiology, Friedrich Schiller University of Jena, 07743 Jena, Germany
| | - Ralf Oelmüller
- Matthias Schleiden Institute-Plant Physiology, Friedrich Schiller University of Jena, 07743 Jena, Germany
| |
Collapse
|
6
|
Samalova M, Gahurova E, Hejatko J. Expansin-mediated developmental and adaptive responses: A matter of cell wall biomechanics? QUANTITATIVE PLANT BIOLOGY 2022; 3:e11. [PMID: 37077967 PMCID: PMC10095946 DOI: 10.1017/qpb.2022.6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 05/03/2023]
Abstract
Biomechanical properties of the cell wall (CW) are important for many developmental and adaptive responses in plants. Expansins were shown to mediate pH-dependent CW enlargement via a process called CW loosening. Here, we provide a brief overview of expansin occurrence in plant and non-plant species, their structure and mode of action including the role of hormone-regulated CW acidification in the control of expansin activity. We depict the historical as well as recent CW models, discuss the role of expansins in the CW biomechanics and address the developmental importance of expansin-regulated CW loosening in cell elongation and new primordia formation. We summarise the data published so far on the role of expansins in the abiotic stress response as well as the rather scarce evidence and hypotheses on the possible mechanisms underlying expansin-mediated abiotic stress resistance. Finally, we wrap it up by highlighting possible future directions in expansin research.
Collapse
Affiliation(s)
- Marketa Samalova
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Evelina Gahurova
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biotechnological Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jan Hejatko
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biotechnological Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Author for correspondence: J. Hejatko, E-mail:
| |
Collapse
|