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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).
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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
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Glöckner N, zur Oven-Krockhaus S, Rohr L, Wackenhut F, Burmeister M, Wanke F, Holzwart E, Meixner AJ, Wolf S, Harter K. Three-Fluorophore FRET Enables the Analysis of Ternary Protein Association in Living Plant Cells. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192630. [PMID: 36235497 PMCID: PMC9571070 DOI: 10.3390/plants11192630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/19/2022] [Accepted: 09/24/2022] [Indexed: 05/13/2023]
Abstract
Protein-protein interaction studies provide valuable insights into cellular signaling. Brassinosteroid (BR) signaling is initiated by the hormone-binding receptor Brassinosteroid Insensitive 1 (BRI1) and its co-receptor BRI1 Associated Kinase 1 (BAK1). BRI1 and BAK1 were shown to interact independently with the Receptor-Like Protein 44 (RLP44), which is implicated in BRI1/BAK1-dependent cell wall integrity perception. To demonstrate the proposed complex formation of BRI1, BAK1 and RLP44, we established three-fluorophore intensity-based spectral Förster resonance energy transfer (FRET) and FRET-fluorescence lifetime imaging microscopy (FLIM) for living plant cells. Our evidence indicates that RLP44, BRI1 and BAK1 form a ternary complex in a distinct plasma membrane nanodomain. In contrast, although the immune receptor Flagellin Sensing 2 (FLS2) also forms a heteromer with BAK1, the FLS2/BAK1 complexes are localized to other nanodomains. In conclusion, both three-fluorophore FRET approaches provide a feasible basis for studying the in vivo interaction and sub-compartmentalization of proteins in great detail.
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Affiliation(s)
- Nina Glöckner
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Sven zur Oven-Krockhaus
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
- Institute for Physical & Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Leander Rohr
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Frank Wackenhut
- Institute for Physical & Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Moritz Burmeister
- Institute for Physical & Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Friederike Wanke
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Eleonore Holzwart
- Centre for Organismal Studies (COS), University of Heidelberg, 69117 Heidelberg, Germany
| | - Alfred J. Meixner
- Institute for Physical & Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Sebastian Wolf
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, 69117 Heidelberg, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-(0)-7071-2972605
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Großeholz R, Wanke F, Rohr L, Glöckner N, Rausch L, Scholl S, Scacchi E, Spazierer AJ, Shabala L, Shabala S, Schumacher K, Kummer U, Harter K. Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to 5elongation growth of the Arabidopsis root. eLife 2022; 11:73031. [PMID: 36069528 PMCID: PMC9525061 DOI: 10.7554/elife.73031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/03/2022] [Indexed: 11/13/2022] Open
Abstract
Brassinosteroids (BR) are key hormonal regulators of plant development. However, whereas the individual components of BR perception and signaling are well characterized experimentally, the question of how they can act and whether they are sufficient to carry out the critical function of cellular elongation remains open. Here, we combined computational modeling with quantitative cell physiology to understand the dynamics of the plasma membrane (PM)-localized BR response pathway during the initiation of cellular responses in the epidermis of the Arabidopsis root tip that are be linked to cell elongation. The model, consisting of ordinary differential equations, comprises the BR-induced hyperpolarization of the PM, the acidification of the apoplast and subsequent cell wall swelling. We demonstrate that the competence of the root epidermal cells for the BR response predominantly depends on the amount and activity of H+-ATPases in the PM. The model further predicts that an influx of cations is required to compensate for the shift of positive charges caused by the apoplastic acidification. A potassium channel was subsequently identified and experimentally characterized, fulfilling this function. Thus, we established the landscape of components and parameters for physiological processes potentially linked to cell elongation, a central process in plant development.
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Affiliation(s)
| | - Friederike Wanke
- Center for Molecular Biology of Plants, University of Tübingen, Tübingen, Germany
| | - Leander Rohr
- Center for Molecular Biology of Plants, University of Tübingen, Tübingen, Germany
| | - Nina Glöckner
- Center for Molecular Biology of Plants, University of Tübingen, Tübingen, Germany
| | - Luiselotte Rausch
- Center for Molecular Biology of Plants, University of Tübingen, Tübingen, Germany
| | - Stefan Scholl
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Emanuele Scacchi
- Center for Molecular Biology of Plants, University of Tübingen, Tübingen, Germany
| | | | - Lana Shabala
- Tasmanian Institute for Agriculture, University of Tasmania, Hobard, Australia
| | - Sergey Shabala
- Tasmanian Institute for Agriculture, University of Tasmania, Hobart, Australia
| | - Karin Schumacher
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Ursula Kummer
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Klaus Harter
- Center for Molecular Biology of Plants, University of Tübingen, Tübingen, Germany
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24-Epibrassinolide protects against ethanol-induced behavioural teratogenesis in zebrafish embryo. Chem Biol Interact 2020; 328:109193. [PMID: 32668205 DOI: 10.1016/j.cbi.2020.109193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/18/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Embryonic studies have demonstrated the neurotoxic, teratogenic, and neurobehavioral toxicity of ethanol (EtOH). Although multiple mechanisms may contribute to these effects, oxidative stress has been described as the major damage pathway. In this regard, natural antioxidants have the potential to counteract oxidative stress-induced cellular damage. Therefore, the present study aimed to investigate the potential protective role of 24-epibrassinolide (24-EPI), a natural brassinosteroid with proved antioxidant properties, in EtOH-induced teratogenic effects during early zebrafish development. Embryos (~2 h post-fertilization - hpf) were exposed to 1 % EtOH, co-exposed to 24-EPI (0.01, 0.1 and 1 μM) and to 24-EPI alone (1 μM) for 24 h. Following exposure, biochemical evaluations were made at 26 hpf, developmental analysis was made throughout the embryo-larval period, and behavioural responses were evaluated at 120 hpf. Exposure to 1 % EtOH caused an increase in the number of malformations, which were diminished by 24-EPI. In addition, EtOH induced an accumulation of GSSG and consequent reduction of GSH:GSSG ratio, indicating the involvement of oxidative mechanisms in the EtOH-induced effects. These were reverted by 24-EPI as proved by the GSSG levels and GSH:GSSG ratio that returned to control values. Furthermore, exposure to EtOH resulted in behavioural deficits at 120 hpf as observed by the disrupted response to an aversive stimulus, suggesting the involvement of neurotoxic mechanisms. 24-EPI restored the behavioural deficits observed in a dose-dependent manner. The absence of effects in the embryos exposed solely to 24-EPI showed its safety during the exposure period. In conclusion, EtOH caused developmental teratogenicity and behavioural toxicity by inducing glutathione changes, which were prevented by 24-EPI.
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Großeholz R, Feldman-Salit A, Wanke F, Schulze S, Glöckner N, Kemmerling B, Harter K, Kummer U. Specifying the role of BAK1-interacting receptor-like kinase 3 in brassinosteroid signaling. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:456-469. [PMID: 30912278 DOI: 10.1111/jipb.12803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/27/2019] [Indexed: 05/26/2023]
Abstract
Brassinosteroids (BR) are involved in the control of several developmental processes ranging from root elongation to senescence and adaptation to environmental cues. Thus, BR perception and signaling have to be precisely regulated. One regulator is BRI1-associated kinase 1 (BAK1)-interacting receptor-like kinase 3 (BIR3). In the absence of BR, BIR3 forms complexes with BR insensitive 1 (BRI1) and BAK1. However, the biophysical and energetic requirements for complex formation in the absence of the ligand have yet to be determined. Using computational modeling, we simulated the potential complexes between the cytoplasmic domains of BAK1, BRI1 and BIR3. Our calculations and experimental data confirm the interaction of BIR3 with BAK1 and BRI1, with the BAK1 BIR3 interaction clearly favored. Furthermore, we demonstrate that BIR3 and BRI1 share the same interaction site with BAK1. This suggests a competition between BIR3 and BRI1 for binding to BAK1, which results in preferential binding of BIR3 to BAK1 in the absence of the ligand thereby preventing the active participation of BAK1 in BR signaling. Our model also suggests that BAK1 and BRI1 can interact even while BAK1 is in complex with BIR3 at an additional binding site of BAK1 that does not allow active BR signaling.
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Affiliation(s)
- Ruth Großeholz
- Centre for Organismal Studies/ BioQuant, Heidelberg University, 69120, Heidelberg, Germany
| | - Anna Feldman-Salit
- Centre for Organismal Studies/ BioQuant, Heidelberg University, 69120, Heidelberg, Germany
| | - Friederike Wanke
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Sarina Schulze
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Nina Glöckner
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Birgit Kemmerling
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Ursula Kummer
- Centre for Organismal Studies/ BioQuant, Heidelberg University, 69120, Heidelberg, Germany
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Local and Systemic Effects of Brassinosteroid Perception in Developing Phloem. Curr Biol 2020; 30:1626-1638.e3. [PMID: 32220322 DOI: 10.1016/j.cub.2020.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/28/2020] [Accepted: 02/12/2020] [Indexed: 12/23/2022]
Abstract
The plant vasculature is an essential adaptation to terrestrial growth. Its phloem component permits efficient transfer of photosynthates between source and sink organs but also transports signals that systemically coordinate physiology and development. Here, we provide evidence that developing phloem orchestrates cellular behavior of adjacent tissues in the growth apices of plants, the meristems. Arabidopsis thaliana plants that lack the three receptor kinases BRASSINOSTEROID INSENSITIVE 1 (BRI1), BRI1-LIKE 1 (BRL1), and BRL3 ("bri3" mutants) can no longer sense brassinosteroid phytohormones and display severe dwarfism as well as patterning and differentiation defects, including disturbed phloem development. We found that, despite the ubiquitous expression of brassinosteroid receptors in growing plant tissues, exclusive expression of the BRI1 receptor in developing phloem is sufficient to systemically correct cellular growth and patterning defects that underlie the bri3 phenotype. Although this effect is brassinosteroid-dependent, it cannot be reproduced with dominant versions of known downstream effectors of BRI1 signaling and therefore possibly involves a non-canonical signaling output. Interestingly, the rescue of bri3 by phloem-specific BRI1 expression is associated with antagonism toward phloem-specific CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 45 (CLE45) peptide signaling in roots. Hyperactive CLE45 signaling causes phloem sieve element differentiation defects, and consistently, knockout of CLE45 perception in bri3 background restores proper phloem development. However, bri3 dwarfism is retained in such lines. Our results thus reveal local and systemic effects of brassinosteroid perception in the phloem: whereas it locally antagonizes CLE45 signaling to permit phloem differentiation, it systemically instructs plant organ formation via a phloem-derived, non-cell-autonomous signal.
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Minami A, Takahashi K, Inoue SI, Tada Y, Kinoshita T. Brassinosteroid Induces Phosphorylation of the Plasma Membrane H+-ATPase during Hypocotyl Elongation in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:935-944. [PMID: 30649552 DOI: 10.1093/pcp/pcz005] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/07/2019] [Indexed: 05/19/2023]
Abstract
Brassinosteroids (BRs) are steroid phytohormones that regulate plant growth and development, and promote cell elongation at least in part via the acid-growth process. BRs have been suggested to induce cell elongation by the activating plasma membrane (PM) H+-ATPase. However, the mechanism by which BRs activate PM H+-ATPase has not been clarified. In this study, we investigated the effects of BR on hypocotyl elongation and the phosphorylation status of a penultimate residue, threonine, of PM H+-ATPase, which affects the activation, in the etiolated seedlings of Arabidopsis thaliana. Brassinolide (BL), an active endogenous BR, induced hypocotyl elongation, phosphorylation of the penultimate, threonine residue of PM H+-ATPase, and binding of the 14-3-3 protein to PM H+-ATPase in the endogenous BR-depleted seedlings. Changes in both BL-induced elongation and phosphorylation of PM H+-ATPase showed similar concentration dependency. BL did not induce phosphorylation of PM H+-ATPase in the BR receptor mutant bri1-6. In contrast, bikinin, a specific inhibitor of BIN2 that acts as a negative regulator of BR signaling, induced its phosphorylation. Furthermore, BL accumulated the transcripts of SMALL AUXIN UP RNA 9 (SAUR9) and SAUR19, which suppress dephosphorylation of the PM H+-ATPase penultimate residue by inhibiting D-clade type 2C protein phosphatase in the hypocotyls of etiolated seedlings. From these results, we conclude that BL-induced phosphorylation of PM H+-ATPase penultimate residue is mediated via the BRI1-BIN2 signaling pathway, together with the accumulation of SAURs during hypocotyl elongation.
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Affiliation(s)
- Anzu Minami
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Koji Takahashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Shin-Ichiro Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
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Jakubowska D, Janicka M. The role of brassinosteroids in the regulation of the plasma membrane H +-ATPase and NADPH oxidase under cadmium stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 264:37-47. [PMID: 28969801 DOI: 10.1016/j.plantsci.2017.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 05/10/2023]
Abstract
The present research aim was to define the role of brassinosteroids (BRs) in plant adaptation to cadmium stress. We observed a stimulating effect of exogenous BR on the activity of two plasma membrane enzymes which play a key role in plants adaptation to cadmium stress, H+-ATPase (EC 3.6.3.14) and NADPH oxidase (EC 1.6.3.1). Using anti-phosphothreonine antibody we showed that modification of PM H+-ATPase activity under BR action could result from phosphorylation of the enzyme protein. Also the relative expression of genes encoding both PM H+-ATPase and NADPH oxidase was affected by BR. To confirm the role of BR in the cadmium stimulating effect on activity of both studied plasma membrane enzymes, an assay in the presence of a BR biosynthesis inhibitor (propiconazole) was performed. Moreover, as a tool in our work we used commercially available plant mutants unable to BR biosynthesis or with dysfunctional BR signaling pathway, to further confirm participation of BR in plant adaptation to heavy metal stress. Presented results demonstrate some elements of the brassinosteroid-induced pathway activated under cadmium stress, wherein H+-ATPase and NADPH oxidase are key factors.
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Affiliation(s)
- Dagmara Jakubowska
- Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wrocław, Kanonia Street 6/8, 50-328 Wrocław, Poland.
| | - Małgorzata Janicka
- Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wrocław, Kanonia Street 6/8, 50-328 Wrocław, Poland.
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Falhof J, Pedersen JT, Fuglsang AT, Palmgren M. Plasma Membrane H(+)-ATPase Regulation in the Center of Plant Physiology. MOLECULAR PLANT 2016; 9:323-337. [PMID: 26584714 DOI: 10.1016/j.molp.2015.11.002] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/30/2015] [Accepted: 11/01/2015] [Indexed: 05/21/2023]
Abstract
The plasma membrane (PM) H(+)-ATPase is an important ion pump in the plant cell membrane. By extruding protons from the cell and generating a membrane potential, this pump energizes the PM, which is a prerequisite for growth. Modification of the autoinhibitory terminal domains activates PM H(+)-ATPase activity, and on this basis it has been hypothesized that these regulatory termini are targets for physiological factors that activate or inhibit proton pumping. In this review, we focus on the posttranslational regulation of the PM H(+)-ATPase and place regulation of the pump in an evolutionary and physiological context. The emerging picture is that multiple signals regulating plant growth interfere with the posttranslational regulation of the PM H(+)-ATPase.
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Affiliation(s)
- Janus Falhof
- Department of Plant and Environmental Science, Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Jesper Torbøl Pedersen
- Department of Plant and Environmental Science, Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Anja Thoe Fuglsang
- Department of Plant and Environmental Science, Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Science, Center for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, University of Copenhagen, 1871 Frederiksberg, Denmark.
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Lin LL, Hsu CL, Hu CW, Ko SY, Hsieh HL, Huang HC, Juan HF. Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis. BMC Genomics 2015; 16:533. [PMID: 26187819 PMCID: PMC4506601 DOI: 10.1186/s12864-015-1753-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 07/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains to be delineated in plants. In this study, we performed a mass spectrometry (MS)-based phosphoproteomics to conduct a global and dynamic phosphoproteome profiling across five time points of BR treatment in the period between 5 min and 12 h. MS coupling with phosphopeptide enrichment techniques has become the powerful tool for profiling protein phosphorylation. However, MS-based methods tend to have data consistency and coverage issues. To address these issues, bioinformatics approaches were used to complement the non-detected proteins and recover the dynamics of phosphorylation events. RESULTS A total of 1104 unique phosphorylated peptides from 739 unique phosphoproteins were identified. The time-dependent gene ontology (GO) analysis shows the transition of biological processes from signaling transduction to morphogenesis and stress response. The protein-protein interaction analysis found that most of identified phosphoproteins have strongly connections with known BR signaling components. The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families. To uncover the dynamic activities of kinases, the enriched motifs were combined with phosphorylation profiles and revealed that the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively. The time-dependent kinase-substrate interaction networks were constructed and showed many substrates are the downstream of other signals, such as auxin and ABA signaling. While comparing BR responsive phosphoproteome and gene expression data, we found most of phosphorylation changes were not led by gene expression changes. Our results suggested many downstream proteins of BR signaling are induced by phosphorylation via various kinases, not through transcriptional regulation. CONCLUSIONS Through a large-scale dynamic profile of phosphoproteome coupled with bioinformatics, a complicated kinase-centered network related to BR-regulated growth was deciphered. The phosphoproteins and phosphosites identified in our study provide a useful dataset for revealing signaling networks of BR regulation, and also expanded our knowledge of protein phosphorylation modification in plants as well as further deal to solve the plant growth problems.
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Affiliation(s)
- Li-Ling Lin
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Chia-Lang Hsu
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Chia-Wei Hu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Shiao-Yun Ko
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan.
| | - Hsueh-Fen Juan
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. .,Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. .,Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
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Rodrigues RB, Sabat G, Minkoff BB, Burch HL, Nguyen TT, Sussman MR. Expression of a translationally fused TAP-tagged plasma membrane proton pump in Arabidopsis thaliana. Biochemistry 2014; 53:566-78. [PMID: 24397334 PMCID: PMC3985734 DOI: 10.1021/bi401096m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The Arabidopsis thaliana plasma
membrane proton ATPase genes, AHA1 and AHA2, are the two most highly expressed isoforms of an 11 gene family
and are collectively essential for embryo development. We report the
translational fusion of a tandem affinity-purification tag to the
5′ end of the AHA1 open reading frame in a genomic clone. Stable
expression of TAP-tagged AHA1 in Arabidopsis rescues the embryonic lethal phenotype of endogenous double aha1/aha2 knockdowns. Western blots of SDS-PAGE and Blue
Native gels show enrichment of AHA1 in plasma membrane fractions and
indicate a hexameric quaternary structure. TAP-tagged AHA1 rescue
lines exhibited reduced vertical root growth. Analysis of the plasma
membrane and soluble proteomes identified several plasma membrane-localized
proteins with alterred abundance in TAP-tagged AHA1 rescue lines compared
to wild type. Using affinity-purification mass spectrometry, we uniquely
identified two additional AHA isoforms, AHA9 and AHA11, which copurified
with TAP-tagged AHA1. In conclusion, we have generated transgenic Arabidopsis lines in which a TAP-tagged AHA1 transgene
has complemented all essential endogenous AHA1 and AHA2 functions
and have shown that these plants can be used to purify AHA1 protein
and to identify in planta interacting proteins by
mass spectrometry.
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Affiliation(s)
- Rachel B Rodrigues
- Department of Biochemistry, Biotechnology Center, University of Wisconsin , 425 Henry Mall, Madison, Wisconsin 53706, United States
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Jiang J, Zhang C, Wang X. Ligand perception, activation, and early signaling of plant steroid receptor brassinosteroid insensitive 1. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:1198-211. [PMID: 23718739 DOI: 10.1111/jipb.12081] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/23/2013] [Indexed: 05/23/2023]
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) belong to a large group of cell surface proteins involved in many aspects of plant development and environmental responses in both monocots and dicots. Brassinosteroid insensitive 1 (BRI1), a member of the LRR X subfamily, was first identified through several forward genetic screenings for mutants insensitive to brassinosteroids (BRs), which are a class of plant-specific steroid hormones. Since its identification, BRI1 and its homologs had been proved as receptors perceiving BRs and initiating BR signaling. The co-receptor BRI1-associated kinase 1 and its homologs, and other BRI1 interacting proteins such as its inhibitor BRI1 kinase inhibitor 1 (BKI1) were identified by genetic and biochemical approaches. The detailed mechanisms of BR perception by BRI1 and the activation of BRI1 receptor complex have also been elucidated. Moreover, several mechanisms for termination of the activated BRI1 signaling were also discovered. In this review, we will focus on the recent advances on the mechanism of BRI1 phosphorylation and activation, the regulation of its receptor complex, the structure basis of BRI1 ectodomain and BR recognition, its direct substrates, and the termination of the activated BRI1 receptor complex. [Figure: see text] Xuelu Wang (Corresponding author).
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Affiliation(s)
- Jianjun Jiang
- State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
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Vriet C, Russinova E, Reuzeau C. From squalene to brassinolide: the steroid metabolic and signaling pathways across the plant kingdom. MOLECULAR PLANT 2013; 6:1738-57. [PMID: 23761349 DOI: 10.1093/mp/sst096] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The plant steroid hormones, brassinosteroids (BRs), and their precursors, phytosterols, play major roles in plant growth, development, and stress tolerance. Here, we review the impressive progress made during recent years in elucidating the components of the sterol and BR metabolic and signaling pathways, and in understanding their mechanism of action in both model plants and crops, such as Arabidopsis and rice. We also discuss emerging insights into the regulations of these pathways, their interactions with other hormonal pathways and multiple environmental signals, and the putative nature of sterols as signaling molecules.
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Affiliation(s)
- Cécile Vriet
- CropDesign NV, a BASF Plant Science Company, 9052 Gent, Belgium
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van Esse GW, Harter K, de Vries SC. Computational modelling of the BRI1 receptor system. PLANT, CELL & ENVIRONMENT 2013; 36:1728-1737. [PMID: 23421559 DOI: 10.1111/pce.12077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/29/2013] [Accepted: 01/30/2013] [Indexed: 06/01/2023]
Abstract
Computational models are useful tools to help understand signalling pathways in plant cells. A systems biology approach where models and experimental data are combined can provide experimentally verifiable predictions and novel insights. The brassinosteroid insensitive 1 (BRI1) receptor is one of the best-understood receptor systems in Arabidopsis with clearly described ligands, mutants and associated phenotypes. Therefore, BRI1-mediated signalling is attractive for mathematical modelling approaches to understand and interpret the spatial and temporal dynamics of signal transduction cascades in planta. To establish such a model, quantitative data sets incorporating local protein concentration, binding affinity and phosphorylation state of the different pathway components are essential. Computational modelling is increasingly employed in studies of plant growth and development. In this section, we have focused on the use of quantitative imaging of fluorescently labelled proteins as an entry point in modelling studies.
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Affiliation(s)
- G Wilma van Esse
- Department of Biochemistry, Wageningen University, Wageningen, The Netherlands.
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Fàbregas N, Li N, Boeren S, Nash TE, Goshe MB, Clouse SD, de Vries S, Caño-Delgado AI. The brassinosteroid insensitive1-like3 signalosome complex regulates Arabidopsis root development. THE PLANT CELL 2013; 25:3377-88. [PMID: 24064770 PMCID: PMC3809538 DOI: 10.1105/tpc.113.114462] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Brassinosteroid (BR) hormones are primarily perceived at the cell surface by the leucine-rich repeat receptor-like kinase brassinosteroid insensitive1 (BRI1). In Arabidopsis thaliana, BRI1 has two close homologs, BRI1-LIKE1 (BRL1) and BRL3, respectively, which are expressed in the vascular tissues and regulate shoot vascular development. Here, we identify novel components of the BRL3 receptor complex in planta by immunoprecipitation and mass spectrometry analysis. Whereas BRI1 associated kinase1 (BAK1) and several other known BRI1 interactors coimmunoprecipitated with BRL3, no evidence was found of a direct interaction between BRI1 and BRL3. In addition, we confirmed that BAK1 interacts with the BRL1 receptor by coimmunoprecipitation and fluorescence microscopy analysis. Importantly, genetic analysis of brl1 brl3 bak1-3 triple mutants revealed that BAK1, BRL1, and BRL3 signaling modulate root growth and development by contributing to the cellular activities of provascular and quiescent center cells. This provides functional relevance to the observed protein-protein interactions of the BRL3 signalosome. Overall, our study demonstrates that cell-specific BR receptor complexes can be assembled to perform different cellular activities during plant root growth, while highlighting that immunoprecipitation of leucine-rich repeat receptor kinases in plants is a powerful approach for unveiling signaling mechanisms with cellular resolution in plant development.
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Affiliation(s)
- Norma Fàbregas
- Department of Molecular Genetics, Centre de Recerca en Agrigenòmica, 08193 Barcelona, Spain
| | - Na Li
- Department of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands
| | - Sjef Boeren
- Department of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands
| | - Tara E. Nash
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Michael B. Goshe
- Department of Molecular and Structural Biochemistry, Raleigh, North Carolina 27695
| | - Steven D. Clouse
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Sacco de Vries
- Department of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands
| | - Ana I. Caño-Delgado
- Department of Molecular Genetics, Centre de Recerca en Agrigenòmica, 08193 Barcelona, Spain
- Address correspondence to
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Harter K, Meixner AJ, Schleifenbaum F. Spectro-microscopy of living plant cells. MOLECULAR PLANT 2012; 5:14-26. [PMID: 21914652 DOI: 10.1093/mp/ssr075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Spectro-microscopy, a combination of fluorescence microscopy with spatially resolved spectroscopic techniques, provides new and exciting tools for functional cell biology in living organisms. This review focuses on recent developments in spectro-microscopic applications for the investigation of living plant cells in their native tissue context. The application of spectro-microscopic methods led to the recent discovery of a fast signal response pathway for the brassinosteroide receptor BRI1 in the plasma membrane of living plant cells. Moreover, the competence of different plant cell types to respond to environmental or endogenous stimuli was determined in vivo by correlation analysis of different optical and spectroscopic readouts such as fluorescence lifetime (FLT). Furthermore, a new spectro-microscopic technique, fluorescence intensity decay shape analysis microscopy (FIDSAM), has been developed. FIDSAM is capable of imaging low-expressed fluorophore-tagged proteins at high spatial resolution and precludes the misinterpretation of autofluorescence artifacts. In addition, FIDSAM provides a very effective and sensitive tool on the basis of Förster resonance energy transfer (FRET) for the qualitative and quantitative determination of protein-protein interaction. Finally, we report on the quantitative analysis of the photosystem I and II (PSI/PSII) ratio in the chloroplasts of living Arabidopsis plants at room temperature, using high-resolution, spatially resolved fluorescence spectroscopy. With this technique, it was not only possible to measure PSI/PSII ratios, but also to demonstrate the differential competence of wild-type and carbohydrate-deficient plants to adapt the PSI/PSII ratio to different light conditions. In summary, the information content of standard microscopic images is extended by several dimensions by the use of spectro-microscopic approaches. Therefore, novel cell physiological and molecular topics can be addressed and valuable insights into molecular and subcellular processes can be obtained in living plants.
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Affiliation(s)
- Klaus Harter
- Center for Plant Molecular Biology, Plant Physiology and Biophysical Chemistry, University of Tübingen, Auf der Morgenstelle 1, 72076 Tuebingen, Germany
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Witthöft J, Harter K. Latest news on Arabidopsis brassinosteroid perception and signaling. FRONTIERS IN PLANT SCIENCE 2011; 2:58. [PMID: 22639599 PMCID: PMC3355717 DOI: 10.3389/fpls.2011.00058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 09/10/2011] [Indexed: 05/05/2023]
Abstract
Brassinosteroids (BRs) are plant hormones regulating growth and development. In interaction with other hormones, they are involved in environmental cue responses. The present model of the BR response pathway in Arabidopsis includes the perception of the hormone by the plasma membrane (PM) receptor brassinosteroid insensitive 1 (BRI1) and its hetero-oligomerization with the co-receptor BRI1-associated receptor kinase 1 (BAK1), followed by the activation of a signaling-cascade finally resulting in the expression of BR-responsive genes. New findings have shed light on the receptor density in the PM and on the molecular mechanism of BR perception, which includes the hormone-induced formation of a platform in the BRI1 extracellular domain for interaction with BAK1. Furthermore, new knowledge on early, BRI1-initiated signaling events at the PM-cytoplasm interface has recently been gained. In addition, a fast BR response pathway that modifies the membrane potential and the expansion of the cell wall - both crucial processes preceding cell elongation growth - have been identified. In this review, these latest findings are summarized and discussed against the background of the present model of BRI1 signaling.
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Affiliation(s)
- Janika Witthöft
- Zentrum für Molekularbiologie der Pflanzen, Universität TübingenTübingen, Germany
| | - Klaus Harter
- Zentrum für Molekularbiologie der Pflanzen, Universität TübingenTübingen, Germany
- *Correspondence: Klaus Harter, Zentrum für Molekularbiologie der Pflanzen, Pflanzenphysiologie, Universität Tübingen, Auf der Morgenstelle 1, 72076 Tübingen, Germany. e-mail:
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